Abstract:
The gene expression control properties of many different pairs of connectrons are described in terms of the similarity or disparity of the connectron sources and the symmetry or asymmetry of the resulting pairs of connectrons.

Description:
REFERENCE TO RELATED APPLICATIONS  
       [0001]     The present application includes the subject of Provisional Application Ser. No. 60/455,563 filed Mar. 19, 2003  
         [0002]     The present application is a continuation in part of U.S. patent application Ser. No. 09/866,925 filed May 30, 2001 entitled ALGORITHMIC DETERMINATION OF FLANKING DNA SEQUENCES THAT CONTROL THE EXPRESSION OF SETS OF GENES IN PROKARYOTIC, ARCHEA AND EUKARYOTIC GENOMES. (referred to as “basic methods patent application”)  
         [0003]     This present application is related to PCT application PCT/US01/16471 filed May 31, 2001 and entitled ALGORITHMIC DETERMINATION OF FLANKING DNA SEQUENCES THAT CONTROL THE EXPRESSION OF SETS OF GENES IN PROKARYOTIC, ARCHEA AND EUKARYOTIC GENOMES.  
         [0004]     The present application is also related to U.S. patent application Ser. No. 10/339,666 filed Jan. 10, 2003 entitled SIMULATION OF GENE EXPRESSION CONTROL USING CONNECTRONS, INTERFERENCE RNAS (IRNAS) AND SMALL TEMPORAL RNAS (STRNAS) IN PROKARYOTIC, ARCHEA AND EUKARYOTIC GENOMES  
         [0005]     The present application is also related to U.S. patent application Ser. No. 10/364,516 filed Feb. 12, 2003 entitled DETERMINATION OF FLANKING DNA SEQUENCES THAT CONTROL THE EXPRESSION OF SETS OF GENES IN THE  ESCHERICHIA COLI  K-12 MG1655 COMPLETE GENOME  
         [0006]     The present application is also related to U.S. patent application Ser. No. 10/364,412 filed Feb. 12, 2003 entitled DETERMINATION OF FLANKING DNA SEQUENCES THAT CONTROL THE EXPRESSION OF SETS OF GENES IN THE  SACCHAROMYCES CEREVISIAE  COMPLETE GENOME 
     
    
     INTRODUCTION  
       [0007]     The connectron structure of a genome determines sets of four DNA sequences of minimum length of 15-bases (C1 and C2 which are in the 3′ UTR of a gene or pseudogene, and T1 and T2 which bracket a set of genes or pseudogenes). The connectrons in a genome control the expression of sets of genes. This patent application describes new types of connectrons as well as how pairs of equivalent and non-equivalent RNA sequences can bind to double-stranded DNA to form a variety of connectrons.  
       DEFINITIONS  
       [0008]     Previous definitions of connectron structure are included by reference. 
    Connectrome—All the connectrons in a given genome.     Dominant Direction—The DNA sequence of a chromosome or a genome from the 5′ end to the 3′ end of the positive strand.     Anti-Dominant Direction—The DNA sequence of a chromosome or a genome from the 5′ end to the 3′ end of the negative strand.     C1/C2 Polarity—The direction of the binding of the RNA of a connectron in the major groove of the double-stranded DNA in the dominant direction or the anti-dominant direction.     Uni-Polar C1/C2—The binding of the RNA of a connectron such that either (1) both the C1 sequence and the C2 sequence bind in the dominant direction or (2) both the C1 sequence and the C2 sequence bind in the anti-dominant direction.     Bi-Polar C1/C2—The binding of the RNA of a connectron such that either (1) the C1 sequence binds in the dominant direction and the C2 sequence binds in the anti-dominant direction or (2) the C1 sequence binds in the anti-dominant direction and the C2 sequence binds in the dominant direction.    
 
         [0015]     Reverse Complement—Going away from a given point, the same sequence occurs on opposite strands. In the example below the sequence GCATCC in the dominant direction of the positive strand occurs somewhere else in the genome in the anti-dominant direction of the negative strand  
                               Positive Strand   5′-GCATCCGTGTAAT ATTACACGGATGC-3′                   Negative Strand   3′-CGTAGGCACATTA TAATGTGCCTACG-5′          
 
         [0016]     Equivalent Sequences—Two sequences such that the second sequence is in the reverse complement of the first sequence  
                                               First sequence   5′-GCATCCGTGTAAT-3′   (A)                           Second sequence   5′-ATTACACGGATGC-3′   (A′)          
 
 If the first sequence is called A then the second sequence is called A′
    Symmetric Lower-Upper Pair of Connectrons—The binding of two equivalent uni-polar RNA C1/C2 sequence pairs to double-stranded DNA.     Asymmetric Lower-Upper Pair of Connectrons—The binding of two non-equivalent uni-polar RNA C1/C2 sequence pairs to double-stranded DNA.     Symmetric Left-Right Pair of Connectrons—The binding of two equivalent bi-polar RNA C1/C2 sequence pairs to double-stranded DNA.     Asymmetric Left-Right Pair of Connectrons—The binding of two non-equivalent bi-polar RNA C1/C2 sequence pairs to double-stranded DNA.     Connectron Lifetime—A time that varies directly with the length of the shorter of the two triple-stranded generalized Hoogsteen helices formed by the binding of the C1 and C2 RNA connectron sequences to the major groove of the double-stranded DNA.     Connectron Pair Lifetime—A time that varies directly with the product of the lifetimes of the two connectrons in the pair.     Specificity of a Pair of Connectrons—The number of similar or different C1/C2 sources needed to form the pair of connectrons.     Symmetric Connectron Specificity—The specificity of a pair of connectrons formed with equivalent uni-polar or bi-polar RNA sequences.     Asymmetric Connectron Specificity—The specificity of a pair of connectrons formed with non-equivalent uni-polar or bi-polar RNA sequences.     Competitive Mode of Behavior in the Formation of a Connectron Pair—The situation where two different genes produce the same uni-polar or bi-polar C1/C2 sequences of the same or different lengths that bind to the major groove of the double-stranded DNA to form a connectron pair.     Cooperative Mode of Behavior in the Formation of a Connectron Pair—The situation where two different genes produce different uni-polar or bi-polar C1/C2 sequences of the same or different lengths that bind to the major groove of the double-stranded DNA to form a connectron pair such that the connectron pair could only be formed from the two different C1/C2 sequences.    
 
       PRIOR ART  
       [0028]     Included by reference.  
       BRIEF DESCRIPTION OF THE OBJECTS OF THE INVENTION  
       [0029]     The basic methods patent application provides the methods for determining the structure of the connectrons in a variety of prokaryotic, Archeal and eukaryotic genomes.  
         [0030]     An object of this invention is to provide a method for identifying a one or more new classs of connectrons that bind to the major groove of double-stranded DNA in two directions.  
         [0031]     An object of this invention is to provide a method for designing a new class of connectrons that bind to the major groove of double-stranded DNA in two directions.  
         [0032]     An object of this invention is to provide a method for identifying the relationship between a pair of connectrons in a genome.  
         [0033]     An object of this invention is to provide a method for designing the relationship between a pair of connectrons in a genome.  
         [0034]     An object of this invention is to provide a method for identifying the relationship between an existing pair of connectrons in a genome that act in competitive mode such that with respect to the individual connectrons there is an increased lifetime of connectron control of a set of genes.  
         [0035]     An object of this invention is to provide a method for designing a new synthetic pair of connectrons in a genome that act in competitive mode such that with respect to the individual connectrons there is an increased lifetime of connectron control of a set of genes.  
         [0036]     An object of this invention is to provide a method for identifying the relationship between an existing pair of connectrons in a genome that act in cooperative mode such that with respect to the individual connectrons there is an increased lifetime of connectron control of a set of genes.  
         [0037]     An object of this invention is to provide a method for designing a new synthetic pair of connectrons in a genome that act in cooperative mode such that with respect to the individual connectrons there is an increased lifetime of connectron control of a set of genes.  
     
    
     DESCRIPTION OF THE DRAWINGS AND TABLES  
       [0038]      FIG. 1  Shows how (a) a lower connectron and (b) an upper connectron, form (c) an lower-upper connectron pair  
         [0039]      FIG. 2  Shows how (a) a left connectron and (b) a right connectron, form (c) a left-right connectron pair  
         [0040]      FIG. 3  Shows (a) a symmetric lower-upper connectron pair, (b) an asymmetric lower-upper connectron pair  
         [0041]      FIG. 4  Shows (a) a symmetric left-right connectron pair, (b) an asymmetric left-right connectron pair  
         [0042]      FIG. 5  Shows (a) Concise representation of an asymmetric lower-upper connectron pair and (b) detailed representation of a asymmetric lower-upper connectron pair  
         [0043]      FIG. 6  Shows (a) Concise representation of an asymmetric left-right connectron pair and (b) detailed representation of a asymmetric left-right connectron pair  
         [0044]      FIG. 7  Shows the four variations of symmetric lower-upper connectron pairs—(a) dominant—dominant, (b) anti-dominant—dominant, (c) dominant—anti-dominant, and (d) anti-dominant—dominant  
         [0045]      FIG. 8  Shows the four variations of symmetric left-right connectron pairs—(a) dominant—dominant, (b) anti-dominant—dominant, (c) dominant—anti-dominant, and (d) anti-dominant—dominant  
         [0046]      FIG. 9  Shows the four variations of asymmetric lower-upper connectron pairs—(a) dominant—dominant, (b) anti-dominant—dominant, (c) dominant—anti-dominant, and (d) anti-dominant—dominant  
         [0047]      FIG. 10  Shows the four variations of asymmetric left-right connectron pairs—(a) dominant—dominant, (b) anti-dominant—dominant, (c) dominant—anti-dominant, and (d) anti-dominant—dominant  
         [0048]      FIG. 11  Shows (a) the competitive blocking of symmetric lower-upper long-lived connectrons, (b) the competitive blocking of symmetric left-right long-lived connectrons, and (c) the relative timing windows for competitive blocking of symmetric long-lived connectrons  
         [0049]      FIG. 12  Shows (a) the competitive blocking of asymmetric lower-upper long-lived connectrons, (b) the competitive blocking of asymmetric lower-upper long-lived connectrons, (c) the competitive blocking of asymmetric left-right long-lived connectrons, and (d) the competitive blocking of asymmetric left-right long-lived connectrons  
         [0050]      FIG. 13  Shows (a) the timing windows for competitive blocking of asymmetric long-lived connectrons  
         [0051]      FIG. 14  Shows (a) a fully symmetric connectron tetrad, (b) non-competitive blocking effect by a left short-lived connectrons of a long-lived cooperative connectron pair, (c) non-competitive blocking effect by a right short-lived connectrons of a long-lived cooperative connectron pair, and (d) the timing windows for non-competitive blocking of asymmetric long-lived connectrons 
     
    
     DESCRIPTION OF THE INVENTION  
       [0052]     The basic methods patent application for the determination of connectron structure defines the DNA and RNA sequence components that make up a connectron, as well as presenting examples of different sorts of connectrons from many different types of genomes. The computer algorithm presented in that patent application shows how to find connectrons in a particular genome. The genomic patent applications utilize the power of this computer algorithm to determine all of the connectrons in a particular genome. Although the basic methods patent application identifies permanent, transient and one-shot connectrons, the view presented is that of a single connectron. This patent application presents the relationships among pairs of connectrons. This invention will allow us to organize the connectrons in a genome and show how pairs of connectrons work together to produce new gene expression regulation properties. In particular, this invention will allow us to show how different C1/C2 connectron sequences from different gene expression events can cooperate to form a pair of long-lived connectrons. The ability to form very specific and cooperative conjunctive events makes it possible for biological systems to form arbitrarily complex control procedures that may very well be needed for cellular differentiation and the development of a complete multi-celled organism from a single cell.  
         [0053]     A connectron forms a loop in a piece of double-stranded DNA. As shown in figure la the DNA runs from the 5′ end shown on the lower left in a counter-clockwise direction to the 3′ end shown on the lower right. The RNA generated by the promotion and transcription of some gene or pseudo-gene somewhere in the genome binds to two distinct double-stranded DNA sequences to form two distinct triple-stranded generalized Hoogsteen helices. In figure la the first triple-stranded (generalized Hoogsteen) helix is called A and the second helix is called B. The A helix forms along the major groove of the DNA in the 5′ to 3′ direction. Similarly the B helix in  FIG. 1   a  forms along the major groove of the DNA in the 5′ to 3′ direction. The A-B pair of triple-stranded helices occupy the lower position in the X-shape formed by the loop. Hence in  FIG. 1   a  the connectron is described as a “lower connectron”. In  FIG. 1   b  both the A and B helices form in the 5′ to 3′ direction, but they occupy the upper position in the X-shape formed by the loop. Hence in  FIG. 1   b  the connectron is described as an “upper connectron”. In  FIG. 1   c  the lower and upper connectrons are shown binding simultaneously.  
         [0054]     In  FIG. 2   a  the A helix forms along the major groove of the DNA in the 5′ to 3′ direction but the B helix forms along the major groove of the DNA by binding along the major groove of the double helix in the 3′ to 5′ direction. The importance of this connectron is that the RNA switches strands as it moves from A-helix binding to B-helix binding. This is true in all left and right connectrons. The A-B pair of helices in FIG.  2   a  occupy the left position in the X-shape formed by the loop. Hence in  FIG. 2   a  the connectron is described as a “left connectron”. In  FIG. 2   b  the A triple-strand helix forms along the major groove of the DNA in the 3′ to 5′ direction, so this connectron is given the designation A-B and is described as a “right connectron”. In  FIG. 2   c  the left and right connectrons are shown binding simultaneously.  
         [0055]     In  FIG. 3   a  the pair of lower and upper connectrons have the same sequences (i.e. A and B) hence this pair of connectrons is called a “symmetric lower-upper connectron pair”. In  FIG. 3   b  the lower connectron has the sequence A-B and the upper connectron has the sequence C-D hence this pair of connectrons is called an “asymmetric lower-upper connectron pair”.  
         [0056]     In  FIG. 4   a  the pair of left and right connectrons have the same sequences (i.e. A and B) hence this pair of connectrons is called a “symmetric left-right connectron pair”. In  FIG. 4   b  the left connectron has the sequence A-B and the right connectron has the sequence C-D, where C is not equal to A and/or D is not equal to B hence this pair of connectrons is called an “asymmetric left-right connectron pair”.  
         [0057]      FIG. 5   a —a re-statement of  FIG. 3   b —is a concise representation of an asymmetric lower-upper connectron pair.  
         [0058]      FIG. 5   b  is a detailed representation of the same asymmetric lower-upper connectron pair showing the sequence relationships between the RNA strand and the two DNA strands. The equivalence of the RNA-strand sequence and the 5′ to 3′ DNA-strand sequence means that the RNA-strand sequence will share the hydrogen bonds to the 3′ to 5′ DNA-strand sequence.  
         [0059]      FIG. 6   a —a re-statement of  FIG. 4   b —is a concise representation of an asymmetric left-right connectron pair.  
         [0060]      FIG. 6   b  is a detailed representation of the same asymmetric left-right connectron pair showing the sequence relationships between the RNA strand and the two DNA strands. The equivalence of the RNA-strand sequence and the 5′ to 3′ DNA-strand sequence for the first triple helix of each of these connectrons means that the RNA-strand sequence will share the hydrogen bonds to the 3′ to 5′ DNA-strand sequence. Similarly, the equivalence of the RNA-strand sequence and the 3′ to 5′ DNA-strand sequence for the second triple helix of each of these connectrons means that the RNA-strand sequence will share the hydrogen bonds to the 5′ to 3′ DNA-strand sequence.  
         [0061]      FIG. 7   a  shows the lower and upper connectrons both binding in the dominant direction with the sequence A-B hence this pair of connectrons is called a “dominant—dominant symmetric lower-upper connectron pair”.  FIG. 7   b  shows the lower and upper connectrons both binding in the anti-dominant direction with the sequence B′-A′ hence this pair of connectrons is called an “anti-dominant—anti-dominant symmetric lower-upper connectron pair”. In  FIG. 7   c  the lower connectron binds in the dominant direction with the sequence A-B and the upper connectron binds in the anti-dominant direction with the sequence B′-A′ hence this pair of connectrons is called a “dominant—anti-dominant symmetric lower-upper connectron pair”. In  FIG. 7   d  the lower connectron binds in the anti-dominant direction with the sequence B′ A′ and the upper connectron binds in the dominant direction with the sequence A-B. In  FIG. 7  each of the four sequence pairs is different, hence there are four different types of symmetric lower-upper connectron pairs.  
         [0062]      FIG. 8   a  shows the left and right connectrons both binding in the dominant direction with the sequences A-B hence this pair of connectrons is called a “dominant—dominant symmetric left-right connectron pair”.  FIG. 8   b  shows the lower and upper connectrons both binding in the anti-dominant direction with the sequence B′-A′ hence this pair of connectrons is called an “anti-dominant—anti-dominant symmetric left-right connectron pair”. In  FIG. 8   c  the left connectron binds in the dominant direction with the sequence A-B and the right connectron binds in the anti-dominant direction with the sequence B′-A′ hence this pair of connectrons is called a “dominant—anti-dominant symmetric left-right connectron pair”. In  FIG. 8   d  the left connectron binds in the anti-dominant direction with the sequence B′-A′ and the right connectron binds in the dominant direction with the sequence A-B hence this pair of connectrons is called an “anti-dominant—dominant symmetric left-right connectron pair”. In  FIG. 8  each of the four sequence pairs is different, hence there are four different types of symmetric left-right connectron pairs.  
         [0063]      FIG. 9   a  shows the lower and upper connectrons both binding in the dominant direction but the sequences of the two connectrons are different. The lower connectron has the sequence are A-B and the upper connectron has the sequence C-D hence this pair of connectrons is called a “dominant—dominant asymmetric lower-upper connectron pair”. In  FIG. 9   b  the lower connectron binds in the dominant direction with the sequence B′-A′ and the upper connectron binds in the anti-dominant direction with the sequence D′-C′ hence this pair of connectrons is called an “anti-dominant—anti-dominant asymmetric lower-upper connectron pair”. In  FIG. 9   c  the lower connectron binds in the dominant direction with the sequence A-B and the upper connectron binds in the anti-dominant direction with the sequence D′-C′ hence this pair of connectrons is called a “dominant—anti-dominant asymmetric lower-upper connectron pair”. In  FIG. 9   d  the lower connectron binds in the anti-dominant direction with the sequence B′-A′ and the upper connectron binds in the dominant direction with the sequence C-D hence this pair of connectrons is called an “anti-dominant—dominant asymmetric lower-upper connectron pair”. In  FIG. 9  each of the four sequence pairs is different, hence there are four different types of asymmetric lower-upper connectron pairs.  
         [0064]      FIG. 10   a  shows the left and right connectrons both binding in the dominant direction but the sequences of the two connectrons are different. The left connectron has the sequence A-B and the right connectron has the sequence C-D hence this pair of connectrons is called a “dominant—dominant asymmetric left-right connectron pair”. In  FIG. 10   b  the left connectron binds in the anti-dominant direction with the sequence B′-A′ and the right connectron binds in the anti-dominant direction with the sequence D′-C′ hence this pair of connectrons is called an “anti-dominant—anti-dominant asymmetric left-right connectron pair”. In  FIG. 10   c  the left connectron binds in the dominant direction with the sequence A-B and the right connectron binds in the anti-dominant direction with the sequence D′-C′ hence this pair of connectrons is called a “dominant—anti-dominant asymmetric left-right connectron. In  FIG. 10   d  the left connectron binds in the anti-dominant direction with the sequence B′-A′ and the right connectron binds in the dominant direction with the sequence C-D hence this pair of connectrons is called an “anti-dominant—dominant asymmetric left-right connectron. In  FIG. 10  each of the four sequence pairs is different, hence there are four different types of asymmetric left-right connectron pairs.  
         [0065]     The lifetime of a single connectrons is easy to understand. Consider a single connectron as shown in  FIG. 1   a . For the sake of example let the A triple-strand (generalized Hoogsteen) helix be the minimum length of 15 bases and let the B triple-strand helix be some long length, for example 100 bases. Remember that the RNA-DNA structure of the connectrons is immersed in a bath of water at 37 degrees Celsius. Thermal motion will cause the A triple-strand helix to dissolve into the RNA and DNA components much more rapidly than the much longer B triple-strand helix, so the lifetime of the connectrons varies directly with the length of the shorter of the two triple-strand helices. If the length of the A and B helices are the same then the lifetime of the connectron varies directly with the length of either helix.  
         [0066]     Now think about the lifetime of a pair of connectrons as shown in  FIG. 1   c . For the sake of simplicity, assume that the A and B helices are the same length. In order for the loop to open up, at least one lower helix and one upper helix has to dissolve at the same time. Either or both of the two lower helices can dissolve at the same time but as long as the upper pair of helices is not dissolved, the loop will stay closed. The same is true for the reverse—either of both of the two upper helices can dissolve at the same time but as long as the two lower helices stay intact, the loop stays closed. Physical chemistry is replete with two-part binding events like this. The general description of such events is that the lifetime varies directly with the product of the two binding energies. In the case of a pair of lower-upper connectrons, the lifetime varies directly as the product of the shorter of the lower helices and the shorter of the upper helices. Of course, the same thing is true for the left-right connectron pairs shown in  FIG. 2   c.    
         [0067]     Whatever the binding energy of an RNA strand is with respect to its cognate double-stranded DNA sequence, whenever a sequence pair (for example A-B or B′-A′ ) can form a pair of connectrons, the binding energy of the pair of connectrons is the product of the binding energy of the each connectron. When two different sequence pairs (for example A-B and B′-A′ as shown in  FIG. 7 ) form a pair of connectrons then the pair of connectrons can be formed as one of the four following combinations  
                                                               lower (A-B)   and upper (A-B)               lower (B′-A′)   and upper (B′-A′)               lower (A-B)   and upper (B′-A′)               lower (B′-A′)   and upper (A-B)                      
 
         [0068]     In principle, A-B and B′-A′ could be produced by the expression of two different genes. Because the pair of connectrons can form in four different ways, the two genes causing the production of the two different RNAs are competing for control of the formation of the connectron pair.  
         [0069]     The left-right connectron pairs in  FIG. 8  have the same properties as the lower-upper connectron pairs in  FIG. 7 . In principle, A-B and B′-A′ could be produced by the expression of two different genes. Because the pair of connectrons can form in four different ways, the two genes causing the production of the two different RNAs are competing for control of the formation of the connectron pair.  
         [0070]     When two different sequence pairs (for example A-B and C-D) form a pair of connectrons then the pair of connectrons can be formed in only one way as shown in  FIG. 9   a . A-B and C-D can be produced by the expression of two different genes. Because the pair of connectrons can form in only one way, the two genes causing the production of the two different RNAs are cooperating for control of the formation of the connectron pair. The same cooperative behavior is also true of the sequence combinations in  FIGS. 9   b ,  9   c  and  9   d.    
         [0071]     Like  FIGS. 7 and 8  (that describe symmetric connectron pairs),  FIGS. 9 and 10  (that describe asymmetric connectron pairs) share the same properties. When two different sequence pairs (for example A-B and C-D) form a pair of connectrons then the pair of connectrons can be formed in only one way as shown in  FIG. 10   a . A-B and C-D can be produced by the expression of two different genes. Because the pair of connectrons can form in only one way, the two genes causing the production of the two different RNAs are cooperating for control of the formation of the connectron pair. The same cooperative behavior is also true of the sequence combinations in  FIG. 10   b ,  10   c  and  10   d.    
         [0072]     In  FIGS. 7 and 8  (that describe symmetric connectron pairs) the connectron pair constructs produce competition whereas in  FIGS. 9 and 10  (that describe asymmetric connectron pairs) the connectron pair constructs produce cooperation.  FIGS. 7 and 8  are symmetric constructs whereas  FIGS. 9 and 10  are asymmetric constructs.  
         [0073]     Whereas in  FIG. 7  the sequence along the DNA the X-shape of the crossing (i.e. either the/sequence or the\sequence) is the sequence A-B, in  FIG. 8  the same elements are reverse-complements.  
         [0074]     The algorithm described in the basic methods patent application finds all of the uni-polar the connectrons in a genome. This patent application describes connectrons in terms of their symmetry properties (i.e. uni-polar, bi-polar, lower, upper, left, right, symmetric, asymmetric). The original algorithm has been modified and the connectron structure of the genomes recomputed to find both the uni-polar and bi-polar connectrons. The modification of the basic connectron determination algorithm to identify the left-right connectrons required only a half dozen lines of code change which is at or below the level of resolution of the flow charts presented in the basic methods patent application. The utility of this patent application is that we have shown that pairs of connectrons both compete and cooperate by forming in the same place (i.e. the X-shaped loop interaction region) to produce lifetimes that vary directly with the product of the lifetimes of the individual connectrons.  
         [0075]      FIG. 11   a  shows how one source (A-B) of the C1/C2 RNA that forms a lower-upper connectron pair with a relatively short product lifetime can temporally compete with another source of a much longer C1/C2 RNA which could form a much longer-lived symmetric connectron pair.  FIG. 11   b  shows how one source (A-B) of the C1/C2 RNA that forms a left-right connectron pair with a relatively short product lifetime can temporally compete with another source of a much longer C1/C2 RNA which could form a much longer-lived symmetric connectron pair. As shown in  FIG. 11   c , the shorter A-B connectron pair only has to last throughout the expression window of the longer connectron pair in order to prevent the longer-lived connectron pair from forming. After the short-lived A-B connectron pair expires, the loop is effectively open.  
         [0076]      FIG. 12   a  shows how a short-lived lower connectron can block the formation of a much longer-lived asymmetric connectron pair.  FIG. 12   b  shows how a short-lived upper connectron can block the formation of a much longer-lived asymmetric connectron pair.  FIG. 12   c  shows how a short-lived left connectron can block the formation of a much longer-lived asymmetric connectron pair.  FIG. 12   d  shows how a short-lived right connectron can block the formation of a much longer-lived asymmetric connectron pair.  
         [0077]      FIG. 13   a  shows the timing windows for the competitive blocking of an asymmetric long-lived connectron pairs as shown in  FIGS. 12   a  and  12   c .  FIG. 13   b  shows the timing windows for the competitive blocking of an asymmetric long-lived connectron pair pairs as shown in  FIGS. 12   b  and  12   d.    
         [0078]      FIG. 14   a  shows how, in-principle, four connectrons could form at a given site. Clearly not all four of these connectrons can form at this site at the same time because each connectron occupies two of the four target (T1 or T2) sites. The lower A-B and upper C-D pair can form at the same time or the left A-C′ and right D′-B pair can form at the same time.  FIG. 14   b  shows how a short-lived left connectron A-C′ can block the formation of a much longer-lived cooperative connectron pair A-B and C-D.  FIG. 14   c  shows how a short-lived right connectron D′-B can block the formation of a much longer-lived cooperative connectron pair A-B and C-D.  FIG. 14   d  shows the timing chart for this type of temporal blocking.  FIGS. 11   c ,  13   a  and  14   d  show three distinctly different types of temporal blocking. To someone skilled in the art it would be obvious that it does not matter whether the lower-upper or left-right connectrons are used for either the blocking or blocked connectrons—as long as the relative patterns are maintained.  
         [0079]     The utility of the connectron pairs shown in FIGS.  1  to  14  is that they form the primitives of a language that can build arbitrarily large and complex patterns of structural and temporal connectron control of gene expression. These language primitives can be used to analyze patterns of connectron control of gene expression in all types of genomes (i.e. prokaryotic, Archeal and eukaryotic). These language primitives can also be used to create new patterns of connectron control of gene expression in all types of genomes. These same primitives will help us to understand how cells differentiate from each other in terms of their gene expression and how a single cell develops into a complete organism.  
         [0080]     Although FIGS.  1  to  14  function in the first instance to describe the relationships between the control sequences (i.e. the C1s and C2s) produced by the same or different gene expressions and the target sequences (i.e. the T1s and the T2s) in a pair of connectrons, these same figures can also function as the basis for the design of new synthetic pairs of connectrons. For example, the target sequences (A-B) that form the symmetric connectron pair shown in  FIG. 3   a  could be modified by changing the upper connectron Tl sequence from A to C and the upper connectron T2 sequence from B to D to form the asymmetric connectron pair shown in  FIG. 3   b . The C1/C2 sequences C-D could then be inserted in the 3′ UTR of some gene so the A-B and C-D connectron pair would be formed only when two genes expressed. This modification of the upper connectron sequences is an example of how all the connectron pair properties in FIGS.  1  to  14  could be instantiated either by de-novo sequence placement or by partial modification of existing sequences and relationships. Anyone skilled in the art should be able to convert the descriptions of connectron-pair properties in FIGS.  1  to  14  into design specifications thereby opening up the control of gene expression to a whole range of new possibilities.  
         [0081]     The utility of pairs of connectrons (a) whether existing or designed or (b) whether competitive or cooperative is that the lifetime of a single connectron whether it is short or long is multiplied by the existence of an adjacent connectron of similar or different lifetime properties. While the product of the lifetimes of two 15-base connectrons is a modest 225, the product of the lifetimes of two 100-base connectrons would provide an impressive 10,000. Long-lived connectron pairs provide the possibility of turning off a set of genes for extended periods of time. In the examples that follow, Nature has used sequence matches that vary in this range.  
       EXAMPLES  
       [0082]     FIGS.  1  to  14  provide a large number of ways of describing and designing connectron pairs in a genome. We give examples of the description of symmetric and asymmetric connectron pairs in six classes of genomes (prokaryotic, Archeal, single-celled eukaryotic, multi-celled eukaryotic, mammalian and plant). We also give two examples of the design of an asymmetric connectron pair in a single-celled eukaryote and a mammal. It is clear that many other variations of symmetric and asymmetric connectron pairs could be described or designed by someone skilled in the art.  
         [0000]     Description of a Symmetric Lower-Upper Connectron Pair in  E. Coli    
         [0083]      E. coli  is a prokaryotic organism. A single connectron has been selected from the  E. coli  connectrome to illustrate the properties of a lower-upper connectron pair. Because the connectron is very long it can be split into two connectrons that then bind as a pair. In this and each of the following examples, a header indicates the function of each data field. Because of print-page limitations, the “sequence of match” field has been moved to the left side of each example.  
         [0084]     The connectron 1434 has a C1-T1 binding length of 182 bases and a C2-T2 binding length of 171 bases. The shorter of the two matches of 171 bases is then halved with the first half becoming the A and the second half becoming the B in  FIG. 3   a  producing a producted connectron pair lifetime of 7225.  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           genome                  |      Connection id                  |      |   chromosome                  |      |   |   contig                  |      |   |   |      (.groups) id                  |      |   |   |      |   type             |      |   |   |      |   CP = control element on positive strand         |      |   |   |      |   CN = control element on negative strand         |      |   |   |      |   TP = target element on positive strand         |      |   |   |      |   TN = target element on negative strand              |      |   |   |      |   |          match start                  |      |   |   |      |   |          |          match stop                  |      |   |   |      |   |          |          |     type of Connectron             |      |   |   |      |   |          |          |     l/u = lower/upper             |      |   |   |      |   |          |          |     l/r = left/right                  |      |   |   |      |   |          |          |     |   source of Connection             |      |   |   |      |   |          |          |     |   g = gene             |      |   |   |      |   |          |          |     |   p = pseudogene                  |      |   |   |      |   |          |          |     |   |   length of match                sequence of match   |      |   |          |          |     |   |     |                | |      |   |   |      |   |          |          |     |   |     |                eco   1434   1   1   7435   CP   4505.026   4505.207   l/u   g   182                CTGTAGATTCAATCTGTCAATGCAACACCCCTTTCAATTATCTCTTTCGG           TGTTTTGAACTTCAGTGTCTTTCTCGGTCTGTTGTTTAGCTGAGCAGCAA       CCACATCTAGTTCATGTTGAGTATATTGGGCAAGACATGTCTTTTTAGGA       AAGTACTGCCGAATTAGCCCATTTGTGTTCTC                    eco   1434   1   1   508   TN   279.155   279.336   l/u   g   182                CTGTAGATTCAATCTGTCAATGCAACACCCCTTTCAATTATCTCTTTCGG           TGTTTTGAACTTCAGTGTCTTTCTCGGTCTGTTCTTTAGCTGAGCAGCAA       CCAGATCTAGTTCATGTTGAGTATATTGGGCAAGACATGTCTTTTTAGGA       AAGTACTGCCGAATTAGCCCATTTGTGTTCTC                    eco   1434   1   1   7435   CP   4505.031   4505.201   l/u   g   171                GATTCAATCTGTCAATGCAACACCCCTTTCAATTATCTCTTTCGGTGTTT           TGAACTTCAGTGTCTTTCTCGGTCTGTTGTTTAGCTGAGCAGCAACCAGA       TCTAGTTCATGTTGAGTATATTGGGCAAGACATGTCTTTTTAGGAAAGTA       CTGCCGAATTAGCCCATTTGT                    eco   1434   1   1   472   TN   270.811   270.981   l/u   g   171                GATTCAATCTGTCAATGCAACACCCCTTTCAATTATCTCTTTCGGTGTTT           TGAACTTCAGTGTCTTTCTCCGTCTGTTGTTTAGCTGAGCAGCAACCAGA       TCTAGTTCATGTTGAGTATATTGGGCAACACATGTCTTTTTACGAAAGTA       CTGCCGAATTAGCCCATTTGT               Can form an AB symmetric pair of l/u Connectrons with a       lifetime = 85 × 85 = 7225                        171                GATTCAATCTGTCAATGCAACACCCCTTTCAATTATCTCTTTCGGTGTTT           TGAACTTCAGTGTCTTTCTCGGTCTGTTGTTTAGCTGAGCAGCAACCAGA       TCTAGTTCATCTTGAGTATATTCGGCAAGACATGTCTTTTTAGGAAAGTA       CTGCCGAATTAGCCCATTTGT                        171                GATTCAATCTGTCAATGCAACACCCCTTTCAATTATCTCTTTCGGTGTTT           TGAACTTCAGTGTCTTTCTCGGTCTGTTGTTTAGCTGACCAGCAACCAGA       TCTACTTCATCTTGAGTATATTGGGCAAGACATGTCTTTTTAGGAAAGTA       CTGCCGAATTAGCCCATTTGT                    279.155   279.239   279.252   279.336   ---   270.811   270.895   270.897   270.981                           .-----.                     /       \                /         \        279.155 *          *270.981                \         /                 \\    / /                  \\  / /           279.239  *.* 270.897                    \  /                     X                   /    \           270.895*  .  *279.252                 /  /  \ \                /  /    \ \               /           \       270.811*             *279.336             /               \          
 
 Description of a Symmetric Lower-Upper Connectron Pair in  S. tokodaii  
 
         [0085]      S. tokodaii  is a Archeal organism. In this and the following examples, the header does not show all the cases for a given data field.  
         [0086]     The connectron 4240 has a C1-T1 binding length of 67 bases and a C2-T2 binding length of 85 bases. The effective match of 52 bases is then halved with the first half becoming the A and the second half becoming the B in  FIG. 3   a  producing a producted connectron pair lifetime of 676.  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         genome                  |      Connection id                  |      |   chromosome                  |      |   |   contig                  |      |   |   |      (.groups) id                  |      |   |   |      |   type                  |      |   |   |      |   |          match start                  |      |   |   |      |   |          |          match stop                  |      |   |   |      |   |          |          |     type of Connectron                  |      |   |   |      |   |          |          |     |   source of Connection                  |      |   |   |      |   |          |          |     |   |    length of match                sequence of match   |      |   |          |          |     |   |    |                | |      |   |   |      |   |          |          |     |   |    |           sto   4240   1   1   3986   CN   1178.996   1179.062   l/u   g   67                TGTACCCCCTTCAAGTAAGCCTCATTTAAGGGAGTTTTCTCCCTTGAATA           AACTACCGGGTACATGA                    sto   4240   1   1    447   TP   61.903   61.969   l/u   g   67                TGTACCCCCTTCAAGTAAGCCTCATTTAAGGGAGTTTTCTCCCTTGAATA           AACTACCGGGTACATGA                    sto   4240   1   1   3986   CN   1178.963   1179.047   l/u   g   85                TTGTAATATTATATCAGTTTACTTCTAATATACTGTACCCCCTTCAAGTA           AGCCTCATTTAAGGGAGTTTTCTCCCTTGAATAAA                    sto   4240   1   1   646   TP   123.599   123.683   l/u   g   85                TTGTAATATTATATCAGTTTACTTCTAATATACTGTACCCCCTTCAAGTA           AGCCTCATTTAAGGGAGTTTTCTCCCTTGAATAAA               Can form an AB symmetric pair of l/u Connectrons with a       lifetime = 26 × 26 = 676                        52                TGTACCCCCTTCAAGTAAGCCTCATTTAAGGGAGTTTTCTCCCTTGAATA           AA                        52                TGTACCCCCTTCAAGTAAGCCTCATTTAAGGGAGTTTTCTCCCTTGAATA           AA                    61.903   61.928   61.944   61.969   ---   123.599   123.624   123.658   123.683                           .-----.                     /       \                /         \         61.903 *          *123.683                \         /                 \\    / /                  \\  / /            61.928  *.* 123.6587                    \  /                     X                   /   \           123.624*  .  * 61.944                 /  /  \ \                /  /    \ \               /           \       123.599*             * 61.969             /               \          
 
 Description of a Symmetric Lower-Upper Connectron Pair in  S. cerevisiae  
 
         [0087]     The connectron 385 has a C1-T1 binding length of 117 and a C2-T2 binding length also of 117 bases. Since the two matches are equal, the 117 bases are then halved with the first half becoming the A and the second half becoming the B in  FIG. 3   a  producing a producted connectron pair lifetime of 3364.  
         [0088]      S. cerevisiae  is a single-celled eukaryotic organism.  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         genome                  |      Connection id                  |      |   chromosome                  |      |   |   contig                  |      |   |   |      (.groups) id                  |      |   |   |      |   type                  |      |   |   |      |   |         match start                  |      |   |   |      |   |         |         match stop                  |      |   |   |      |   |         |         |     type of Connectron                  |      |   |   |      |   |         |         |     |   source of Connection                  |      |   |   |      |   |         |         |     |   |    length of match                sequence of match   |      |   |         |         |     |   |     |                | |      |   |   |      |   |         |         |     |   |     |           yst    385   15   15   28455   CP   975.950   976.066   l/u   g   117                TTACTAGTATATTATCATATACGGTGTTAGAAGATGACGCAAATGATGAG           AAATAGTCATCTAAATTAGTGGAAGCTGAAACGCAAGGATTGATAATGTA       ATAGGATCAATGAATAT                    yst    385   1   1   419   TN   165.888   166.004   l/u   g   117                TTACTAGTATATTATCATATACGCTGTTAGAAGATGACGCAAATGATGAG           AAATAGTCATCTAAATTAGTGGAAGCTGAAACGCAAGGATTGATAATGTA       ATAGGATCAATGAATAT                    yst    385   15   15   28455   CP   975.950   976.066   l/u   g   117                TTACTAGTATATTATCATATACGGTGTTAGAAGATGACGCAAATGATGAG           AAATAGTCATCTAAATTAGTGGAAGCTGAAACGCAACGATTGATAATGTA       ATAGGATCAATGAATAT                    yst    385   1   1   355   TN   160.257   160.373   l/u   g   117                TTACTAGTATATTATCATATACGGTGTTAGAAGATGACGCAAATGATGAG           AAATAGTCATCTAAATTAGTGGAAGCTGAAACGCAAGGATTGATAATGTA       ATAGGATCAATGAATAT               Can form an AB symmetric pair of l/u Connectrons with a       lifetime = 58 × 58 = 3364                        117                TTACTAGTATATTATCATATACGGTGTTAGAAGATGACGCAAATGATGAG           AAATAGTCATCTAAATTAGTGGAAGCTGAAACGCAAGGATTGATAATGTA       ATAGGATCAATGAATAT                        117                TTACTAGTATATTATCATATACGGTGTTAGAAGATGACGCAAATGATGAG           AAATAGTCATCTAAATTAGTGGAACCTGAAACGCAAGGATTGATAATGTA       ATAGGATCAATGAATAT                    165.888   165.945   165.947   166.004   ---   160.257   160.314   160.316   160.373                           .-----.                     /       \                /         \        165.888 *          *160.3731                \         /                 \\    / /                  \\  / /           165.945  *.* 160.316                    \  /                     X                   /   \           160.314*  .  *165.947                 /  /  \ \                /  /    \ \               /           \       160.257*             *166.004             /               \            
 Description of a Symmetric Lower-Upper Connectron Pair in  C. elegans    
         [0089]      C. elegans  is a 1,000-celled eukaryotic organism.  
         [0090]     The connectron 55 has a C1-T1 binding length of 68 and a C2-T2 binding length also of 68 bases. The effective match of 43 bases is then halved with the first half becoming the A and the second half becoming the B in  FIG. 3   a  producing a producted connectron pair lifetime of 441.  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         genome                  |      Connection id                  |      |   chromosome                  |      |   |   contig                  |      |   |   |      (.groups) id                  |      |   |   |      |   type                  |      |   |   |      |   |         match start                  |      |   |   |      |   |         |         match stop                  |      |   |   |      |   |         |         |     type of Connectron                  |      |   |   |      |   |         |         |     |   source of Connection                  |      |   |   |      |   |         |         |     |   |    length of match                sequence of match   |      |   |         |         |     |   |    |                | |      |   |   |      |   |         |         |     |   |    |           wrm     55   1   1   380   CN   221.205   221.272   l/u   g   68                GGGAATTGCTTCGTCAAATGATCGACGGAGGGCTTTTGGCCATCTGCAAG           GATAAACTCGCATGTCGA                    wrm     55   1   1   433   TN   250.979   251.046   l/u   g   68                GGGAATTGCTTCGTCAAATGATCGACGGAGGGCTTTTGGCCATCTGCAAG           GATAAACTCGCATGTCGA                    wrm     55   1   1   380   CN   221.180   221.247   l/u   g   68                GAGCTCGCAACACCGGCCGAGCAGCGGGAATTGCTTCGTCAAATGATCGA           CGGAGGGCTTTTGGCCAT                    wrm     55   1   1   354   TN   214.904   214.971   l/u   g   68                GAGCTCGCAACACCGGCCGAGCAGCGGGAATTGCTTCGTCAAATGATCGA           CGGAGGGCTTTTGGCCAT               Can form an AB symmetric pair of l/u Connectrons with a       lifetime = 21 × 21 = 441                        43                GGGAATTGCTTCGTCAAATGATCGACGGAGGGCTTTTGGCCAT                            43                GGGAATTGCTTCGTCAAATGATCGACGGAGGGCTTTTGGCCAT                        250.979   250.999   251.026   251.046   ---   214.904   214.924   214.951   214.971                           .-----.                     /       \                /         \        279.155 *          *270.981                \         /                 \\    / /                  \\  / /           279.239  *.* 270.897                   \  /                      X                   /   \           270.895*  .  *279.252                 /  /  \ \                /  /    \ \               /           \       270.811*             *279.336             /               \          
 
 Description of a Symmetric Lower-Upper Connectron Pair in  H. sapiens  
 
         [0091]      H. sapiens  is a multi-celled eukaryotic organism—a mammal.  
         [0092]     The connectron 1211 has a C1-T1 binding length of 58 bases and a C2-T2 binding length also of 58 bases. Since the two matches are equal, 58 is then halved with the first half becoming the A and the second half becoming the B in  FIG. 3   a  producing a producted connectron pair lifetime of 841.  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         genome                  |      Connection id                  |      |   chromosome                  |      |   |   contig                  |      |   |   |      (.groups) id                  |      |   |   |      |   type                  |      |   |   |      |   |        match start                  |      |   |   |      |   |        |        match stop                  |      |   |   |      |   |        |        |     type of Connectron                  |      |   |   |      |   |        |        |     |   source of Connection                  |      |   |   |      |   |        |        |     |   |    length of match                sequence of match   |      |   |        |        |     |   |    |                | |      |   |   |      |   |        |        |     |   |    |           hsd   1211   4   1   1331   CP   16.381   16.438   l/u   g   58                GGTGAGTACCTTTCTATGAAGGTGATAAGGATCCACTGAGTCTTCCATAT           AAAGATCA                    hsd   1211   4   1   1542   TP   500.217   500.274   l/u   g   58                GGTGAGTACCTTTCTATGAAGGTGATAAGGATCCACTGAGTCTTCCATAT           AAAGATCA                    hsd   1211   4   1   1331   CP   16.381   16.438   l/u   g   58                GGTGAGTACCTTTCTATGAAGGTGATAAGGATCCACTGAGTCTTCCATAT           AAAGATCA                    hsd   1211   4   1   1559   TP   504.937   504.994   l/u   g   58                GGTGAGTACCTTTCTATGAAGGTGATAAGGATCCACTGAGTCTTCCATAT           AAAGATCA               Can form an AB symmetric pair of l/u Connectrons with a       lifetime = 29 × 29 = 841                        58                GGTGAGTACCTTTCTATGAAGGTGATAAGGATCCACTGAGTCTTCCATAT           AAAGATCA                        58                GGTGAGTACCTTTCTATGAAGGTGATAAGGATCCACTGAGTCTTCCATAT           AAAGATCA                    500.217   500.245   500.246   500.274   ---   504.937   504.965   504.966   504.994                           .-----.                     /       \                /         \        279.155 *          *270.981                \         /                 \\    / /                  \\  / /           279.239  *.* 270.897                   \  /                      X                   /   \           270.895*  .  *279.252                 /  /  \ \                /  /    \ \               /           \       270.811*             *279.336             /               \          
 
 Description of a Symmetric Lower-Upper Connectron Pair in  A. thaliana  
 
         [0093]      A. thaliana  is a multi-celled eukaryotic organism—a plant.  
         [0094]     The connectron 3 has a C1-T1 binding length of 94 bases and a C2-T2 binding length of 79 bases. The shorter of the two matches of 79 bases is then halved with the first half becoming the A and the second half becoming the B in  FIG. 5   a  producing a producted connectron pair lifetime of 1521.  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         genome                  |      Connection id                  |      |   chromosome                  |      |   |   contig                  |      |   |   |      (.groups) id                  |      |   |   |      |   type                  |      |   |   |      |   |           match start                  |      |   |   |      |   |           |          match stop                  |      |   |   |      |   |           |           |     type of Connectron                  |      |   |   |      |   |           |           |     |   source of Connection                  |      |   |   |      |   |           |           |     |   |   length of match                sequence of match   |      |   |           |           |     |   |    |                | |      |   |   |      |   |           |           |     |   |    |           ath      3   5   1   29822   CN   21590.870   21590.960   l/u   g   94                TGTTGAAAGTTAAACTTGATTTTGAATCAAGTTTAATTATTGGATCAATT           ATCCAATAATTAATTATGGCCAAATCCAAGTTCTAGAGTTTTCT                    ath      3   1   1    7951   TP   3780.765   3780.858   l/u   g   94                TGTTGAAAGTTAAACTTGATTTTGAATCAAGTTTAATTATTGGATCAATT           ATCCAATAATTAATTATGGCCAAATCCAAGTTCTAGAGTTTTCT                    ath      3   5   1   29822   CN   21590.870   21590.950   l/u   g   79                TGTTGAAAGTTAAACTTGATTTTGAATCAAGTTTAATTATTGGATCAATT           ATCCAATAATTAATTATGGCCAAATCCAA                    ath      3   1   1    7985   TP   3785.281   3785.359   l/u   g   79                TGTTGAAAGTTAAACTTGATTTTGAATCAAGTTTAATTATTGGATCAATT           ATCCAATAATTAATTATGGCCAAATCCAA               Can form an AB symmetric pair of l/u Connectrons with a       lifetime = 39 × 39 = 1521                        79                TGTTGAAAGTTAAACTTGATTTTGAATCAAGTTTAATTATTGGATCAATT           ATCCAATAATTAATTATGGCCAAATCCAA                        79                TGTTGAAAGTTAAACTTGATTTTGAATCAAGTTTAATTATTGGATCAATT           ATCCAATAATTAATTATGGCCAAATCCAA                    3780.765   3780.803   3780.820   3780.858   ---   3785.281   3785.319   3785.321   3785.359                           .-----.                     /       \                /         \        279.155 *          *270.981                \         /                 \\    / /                  \\  / /           279.239  *.* 270.897                    \  /                     X                   /   \           270.895*  .  *279.252                 /  /  \ \                /  /    \ \               /           \       270.811*             *279.336             /               \          
 
 Description of an Asymmetric Lower-Upper Connectron Pair in  E. coli  
 
         [0095]     The connectron 14918 has a C1-T1 binding length of 27 bases and a C2-T2 binding length of 35 bases. The shorter of the two matches at 27 bases produces the lifetime for this connectron. The connectron 15118 has a C1-T1 binding length of 20 bases and a C2-T2 binding length of 22 bases. The shorter of the two matches at 20 bases produces the lifetime for this connectron. The lifetime of this pair of anti-dominant—dominant connectrons as shown in  FIG. 9   d  is 540.  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           genome                  |      Connection id                  |       |   chromosome                  |       |   |   contig                  |       |   |   |      (.groups) id                  |       |   |   |      |   type                  |       |   |   |      |   |          match start                  |       |   |   |      |   |          |          match stop                  |       |   |   |      |   |          |          |     type of Connectron                  |       |   |   |      |   |          |          |     |   source of Connection                  |       |   |   |      |   |          |          |     |   |    length of match                sequence of match   |      |   |          |          |     |   |    |                | |       |   |   |      |   |          |          |     |   |    |                   eco   14918   1   1   7316   CN   4454.807   4454.833   l/u   g   27                AAATGCCGGATGCGGCGTGAACGCCTT                        eco   14918   1   1   6955   TN   4242.757   4242.783   l/u   g   27                AAATGCCGGATGCGGCGTGAACGCCTT                        eco   14918   1   1   7316   CN   4454.810   4454.844   l/u   g   35                TGCCGGATGCGGCGTGAACGCCTTATCCGGCCTAC                        eco   14918   1   1   6937   TN   4233.017   4233.051   l/u   g   35                TGCCGGATGCGGCGTGAACGCCTTATCCGGCCTAC                        eco   15118   1   1   1544   CP   831.575   831.594   l/u   g   20                TGTAGGCCGGATAAGGCGTT                        eco   15118   1   1   6939   TP   4232.999   4233.018   l/u   g   20                TGTAGGCCGGATAAGGCGTT                        eco   15118   1   1   1544   CP   831.596   831.617   l/u   g   22                ACGCCGCATCCGGCATTTCACA                        eco   15118   1   1   6957   TP   4242.783   4242.804   l/u   g   22                ACGCCGCATCCGGCATTTCACA                   Found L/U AD AB-CD Connectron pair for 14918 and 15118 with a       lifetime = 27 × 20 = 540                        .000   .001                                                        4242.757   4242.783   4233.017   4233.051   ---   4232.999   4233.018   4242.783   4242.804                           .-----.                     /       \                /         \        279.155 *          *270.981                \         /                 \\    / /                  \\  / /           279.239  *.* 270.897                   \  /                     X                   /   \           270.895*  .  *279.252                 /  /  \ \                /  /    \ \               /           \       270.811*             *279.336             /               \          
 
 Description of an Asymmetric Lower-Upper Connectron Pair in  S. tokodaii  
 
         [0096]     The connectron 6416 has a C1-T1 binding length of 59 bases and a C2-T2 binding length of 60 bases. The shorter of the two matches at 59 bases produces the lifetime for this connectron. The connectron 6477 has a C1-T1 binding length of 189 bases and a C2-T2 binding length of 36 bases. The shorter of the two matches at 36 bases produces the lifetime for this connectron. The lifetime of this pair of dominant—anti-dominant connectrons as shown in  FIG. 9   d  is 2124.  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           genome                  |      Connection id                  |      |   chromosome                  |      |   |   contig                  |      |   |   |      (.groups) id                  |      |   |   |      |   type                  |      |   |   |      |   |          match start                  |      |   |   |      |   |          |          match stop                  |      |   |   |      |   |          |          |     type of Connectron                  |      |   |   |      |   |          |          |     |   source of Connection                  |      |   |   |      |   |          |          |     |   |    length of match                sequence of match   |      |   |          |          |     |   |    |                | |      |   |   |      |   |          |          |     |   |    |           sto   6416   1   1   3245   CP   1036.523   1036.581   l/u   g   59                ACTCCCAGTGAGGGATAGGGGTAACGGACTGAAGACCCAGCCCGTGGTCT           ACCGCTGGA                    sto   6416   1   1   3439   TP   1079.594   1079.652   l/u   g   59                ACTCCCAGTGAGGGATAGGGGTAACGGACTGAAGACCCAGCCCGTGGTCT           ACCGCTGGA                    sto   6416   1   1   3250   CP   1036.635   1036.694   l/u   g   60                ATGAAGGTGGTAAACCACAAACCTATGAACCGCCCTAAGGGAACCCTCGC           CCTTTAGGGC                    sto   6416   1   1   3714   TP   1146.360   1146.419   l/u   g   60                ATGAAGGTGGTAAACCACAAACCTATGAACCGCCCTAAGGGAACCCTCGC           CCTTTAGGGC                    sto   6477   1   1   618   CN   120.361   120.549   l/u   g   189                CTATCCCTCACCAAGAGTTGCCCTCTGCTCTTGGCTCTTGGGGACTCGGG           GATATGTAGTTCTGTGCGGGGACACATATCTTCAGTATGCCCACCTTTGT       GGGCTTCCCCGCACTTTATTAATAGTTTTAAGCTAAGATTAAAAACTTTA       CCCCGCCTTAAAAGGCGAGGCTTGCCCCGCGTTTTGTCA                    sto   6477   1   1   3709   TN   1146.169   1146.357   l/u   g   189                CTATCCCTCACCAAGAGTTGCCCTCTGCTCTTGGCTCTTGGGGACTCGGG           GATATGTAGTTCTGTGCGGGGACACATATCTTCAGTATGCCCACCTTTGT       GGGCTTCCCCGCACTTTATTAATAGTTTTAAGCTAAGATTAAAAACTTTA       CCCCGCCTTAAAAGGCGAGGCTTGCCCCGCGTTTTGTCA                    sto   6477   1   1   622   CN   120.590   120.625   l/u   g   36                CACCCACCCCGCTCCGTTCGTCCAGCGGTAGACCAC                        sto   6477   1   1   3446   TN   1079.651   1079.688   l/u   g   36                CACCCACCCCGCTCCGTTCGTCCAGCGGTAGACCAC                   Found L/U DA AB-CD Connectron pair for 6416 and 6477 with a       lifetime = 59 × 36 = 2124                        .001   .003                        1079.594   1079.652   1146.360   1146.419   ---   1146.169   1146.357   1079.651   1079.686                           .-----.                     /       \                /         \        279.155 *          *270.981                \         /                 \\    / /                  \\  / /           279.239  *.* 270.897                   \  /                     X                   /   \           270.895*  .  *279.252                 /  /  \ \                /  /    \ \               /           \       270.811*             *279.336             /               \          
 
 Description of an Asymmetric Lower-Upper Connectron Pair in  S. cerevisiae  
 
         [0097]     The connectron 3814 has a C1-T1 binding length of 72 bases and a C2-T2 binding length of 72 bases. The either of the two matches at 72 bases produces the lifetime for this connectron. The connectron 3847 has a C1-T1 binding length of 81 bases and a C2-T2 binding length of 89 bases. The shorter of the two matches at 81 bases produces the lifetime for this connectron. The lifetime of this pair of anti-dominant—dominant connectrons as shown in  FIG. 9   d  is 5832.  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           genome                  |      Connection id                  |      |   chromosome                  |      |   |   contig                  |      |   |   |      (.groups) id                  |      |   |   |      |   type                  |      |   |   |      |   |         match start                  |      |   |   |      |   |         |         match stop                  |      |   |   |      |   |         |         |     type of Connectron                  |      |   |   |      |   |         |         |     |   source of Connection                  |      |   |   |      |   |         |         |     |   |    length of match                sequence of match   |      |   |         |         |     |   |    |                | |      |   |   |      |   |         |         |     |   |    |           yst   3814   13   13   23498   CP   362.701   382.772   l/u   g   72                ATGGAATCTATATTTCTACATACTAATATTACGATTATTCCTCATTCCGT           TTTATATGTTTCATTATCCTAT                    yst   3814   2   2   1896   TN   265.267   265.338   l/u   g   72                ATGGAATCTATATTTCTACATACTAATATTACGATTATTCCTCATTCCGT           TTTATATGTTTCATTATCCTAT                    yst   3814   13   13   23498   CP   362.701   362.772   l/u   g   72                ATGGAATCTATATTTCTACATACTAATATTACGATTATTCCTCATTCCGT           TTTATATGTTTCATTATCCTAT                    yst   3814   2   2   1495   TN   226.820   226.891   l/u   g   72                ATGGAATCTATATTTCTACATACTAATATTACGATTATTCCTCATTCCGT           TTTATATGTTTCATTATCCTAT                    yst   3847   13   13   23551   CN   372.772   372.852   l/u   g   81                AAACATATAAAACGGAATGAGGAATAATCGTAATATTAGTATGTAGAAAT           ATAGATTCCATTTTGAGGATTCCTATATCCT                    yst   3847   2   2   1496   TP   226.739   226.819   l/u   g   81                AAACATATAAAACGGAATGAGGAATAATCGTAATATTAGTATGTAGAAAT           ATAGATTCCATTTTGAGGATTCCTATATCCT                    yst   3847   13   13   23551   CN   372.836   372.924   l/u   g   89                GAGGATTCCTATATCCTCGAGGAGAACTTCTAGTATATTCTGTATACCTA           ATATTATAGCCTTTATCAACAATGGAATCCCAACAATTA                    yst   3847   2   2   1923   TP   265.340   265.428   l/u   g   89                GAGGATTCCTATATCCTCGAGGAGAACTTCTAGTATATTCTGTATACCTA           ATATTATAGCCTTTATCAACAATGGAATCCCAACAATTA               Found L/U AD AB-CD Connectron pair for 3814 and 3847 with a       lifetime = 72 × 81 = 5832                        .002   .001                                                        265.267   265.338   226.820   226.891   ---   226.739   226.819   265.340   265.428                           .-----.                     /       \                /         \        279.155 *          *270.981                \         /                 \\    / /                  \\  / /           279.239  *.* 270.897                   \  /                     X                   /   \           270.895*  .  *279.252                 /  /  \ \                /  /    \ \               /           \       270.811*             *279.336             /               \          
 
 Description of an Asymmetric Lower-Upper Connectron Pair in  C. elegans  
 
         [0098]     The connectron 23175 has a C1-T1 binding length of 15 bases and a C2-T2 binding length of 18 bases. The shorter of the two matches at 15 bases produces the lifetime for this connectron. The connectron 23179 has a C1-T1 binding length of 16 bases and a C2-T2 binding length of 19 bases. The shorter of the two matches at 16 bases produces the lifetime for this connectron. The lifetime of this pair of dominant—anti-dominant connectrons as shown in  FIG. 9   c  is 240.  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           genome                  |       Connection id                  |       |   chromosome                  |       |   |   contig                  |       |   |   |       (.groups) id                  |       |   |   |       |   type                  |       |   |   |       |   |         match start                  |       |   |   |       |   |         |         match stop                  |       |   |   |       |   |         |         |     type of Connectron                  |       |   |   |       |   |         |         |     |   source of Connection                  |       |   |   |       |   |         |         |     |   |    length of match                sequence of match   |       |   |         |         |     |   |    |                | |       |   |   |       |   |         |         |     |   |    |           wrm   23175   4   2   22854   CP   708.778   708.792   l/u   g   15                TGGTCTGCTAAATCG                        wrm   23175   4   2   21925   TP   415.203   415.217   l/u   g   15                TGGTCTGCTAAATCG                        wrm   23175   4   2   22854   CP   708.793   708.810   l/u   g   18                AAACTTGTAGTTTGTAGT                        wrm   23175   4   2   22166   TP   486.479   486.496   l/u   g   18                AAACTTGTAGTTTGTAGT                        wrm   23179   4   2   24763   CN   1373.569   1373.584   l/u   g   16                ATTTAGCAGACCCAAA                        wrm   23179   4   2   22165   TN   486.461   486.476   l/u   g   16                ATTTAGCAGACCCAAA                        wrm   23179   4   2   24763   CN   1373.554   1373.572   l/u   g   19                AAACTACTACAAATTTCGATTT                        wrm   23179   4   2   21926   TN   415.212   415.230   l/u   g   19                AAACTACAAATTTCGATTT                   Found L/U DA AB-CD Connectron pair for 23175 and 23179 with a       lifetime = 15 × 16 = 240                        .005   .003                                                        415.203   415.217   486.479   486.496   ---   486.461   486.476   415.212   415.230                           .-----.                     /       \                /         \        279.155 *          *270.981                \         /                 \\    / /                  \\  / /           279.239  *.* 270.897                    \  /                     X                   /   \           270.895*  .  *279.252                 /  /  \ \                /  /    \ \               /           \       270.811*             *279.336             /               \          
 
 Description of an Asymmetric Lower-Upper Connectron Pair in  H. sapiens  
 
         [0099]     The connectron 383992 has a C1-T1 binding length of 39 bases and a C2-T2 binding length of 41 bases. The shorter of the two matches at 39 bases produces the lifetime for this connectron. The connectron 383993 has a C1-T1 binding length of 40 bases and a C2-T2 binding length of 34 bases. The shorter of the two matches at 34 bases produces the lifetime for this connectron. The lifetime of this pair of dominant—anti-dominant connectrons as shown in  FIG. 9   c  is 1326.  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             genome                  |       Connection id                  |       |   chromosome                  |       |   |   contig                  |       |   |   |       (.groups) id                  |       |   |   |       |   type                  |       |   |   |       |   |         match start                  |       |   |   |       |   |         |         match stop                  |       |   |   |       |   |         |         |     type of Connectron                  |       |   |   |       |   |         |         |     |   source of Connection                  |       |   |   |       |   |         |         |     |   |    length of match                sequence of match   |       |   |         |         |     |   |    |                | |       |   |   |       |   |         |         |     |   |    |                hsd   383992   920   19   756303   CP   21789.055   21789.092   u/d   g   39                AGCCCGAGCCCCACCTCTCCCTTAGGGACCTCCGCCCAC                        hsd   383992   920   19   756563   TP   21820.715   21820.754   u/d   9   39                AGCCCGAGCCCCACCTCTCCCTTAGGGACCTCCGCCCAC                        hsd   383992   920   19   756303   CP   21789.080   21789.121   u/d   g   41                ACCTCCGCCCACCCTACCCTCAAGCCAGGATCCCCGGAGCG                        hsd   383992   920   19   756615   TP   21827.379   21827.420   u/d   g   41                ACCTCCGCCCACCCTACCCTCAAGCCAGGATGCCCGGAGCG                        hsd   383993   920   19   756433   CN   21808.781   21808.820   u/d   g   40                CCTAAGGGAGAGGTGGGGCTCGGGCTGAATCCCTCGTTGG                        hsd   383993   920   19   756614   TN   21827.338   21827.377   u/d   g   40                CCTAAGGGAGAGGTGGGGCTCGGGCTGAATCCCTCGTTGG                        hsd   383993   920   19   756433   CN   21808.740   21808.773   u/d   g   34                GCTCCGGGCATCCTGGCTTGAGGGTAGAGTGGGC                        hsd   383993   920   19   756564   TN   21820.748   21820.781   u/d   g   34                GCTCCGGGCATCCTGGCTTGAGGGTAGAGTGGGC                   Found L/U DA AB-CD Connectron pair for 383992 and 383993 with a       lifetime = 39 × 34 = 1326                        0.006   0.002                                                        21820.715   21820.754   21827.379   21827.420   ---   21827.338   21827.377   21820.748   21820.781                           .-----.                     /       \                /         \        279.155 *          *270.981                \         /                 \ \    / /                  \ \  / /           279.239  *.* 270.897                    \  /                     X                   /    \           270.895*  .  *279.252                 /  / \ \                /  /    \ \               /           \       270.811*             *279.336             /               \          
 
 Description of an Asymmetric Lower-Upper Connectron Pair in  A. thaliana  
 
         [0100]     The connectron 188312 has a C1-T1 binding length of 20 bases and a C2-T2 binding length of 30 bases. The shorter of the two matches at 20 bases produces the lifetime for this connectron. The connectron 188397 has a C1-T1 binding length of 30 bases and a C2-T2 binding length of 16 bases. The shorter of the two matches at 16 bases produces the lifetime for this connectron. The lifetime of this pair of dominant—anti-dominant connectrons as shown in  FIG. 9   c  is 340.  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           genome                  |       Connection id                  |       |   chromosome                  |       |   |   contig                  |       |   |   |       (.groups) id                  |       |   |   |       |   type                  |       |   |   |       |   |         match start                  |       |   |   |       |   |         |         match stop                  |       |   |   |       |   |         |         |     type of Connectron                  |       |   |   |       |   |         |         |     |   source of Connection                  |       |   |   |       |   |         |         |     |   |    length of match                sequence of match   |       |   |         |         |     |   |    |                | |       |   |   |       |   |         |         |     |   |    |                   ath   188312   18   4   269631   CP   5320.517   5320.536   u/d   g   20                TTGTAGACGTATGGTGGTGG                        ath   188312   18   4   269507   TP   5311.160   5311.179   u/d   g   20                TTGTAGACGTATGGTGGTGG                        ath   188312   18   4   269631   CP   5320.519   5320.548   u/d   g   30                GTAGACGTATGGTGGTGGTGGAGACTTGTA                        ath   188312   18   4   269890   TP   5340.361   5340.390   u/d   g   30                GTAGACGTATGGTGGTGGTGGAGACTTGTA                        ath   188397   18   4   269741   CN   5324.883   5324.921   u/d   g   39                GCTCTCCACCACCACCATACTACAGTCCATCTCCAAAGG                        ath   188397   18   4   269881   TN   5340.322   5340.360   u/d   g   39                GCTCTCCACCACCACCATACTACAGTCCATCTCCAAAGG                        ath   188397   18   4   269741   CN   5324.867   5324.882   u/d   g   16                CCACCATACGTCTACA                        ath   188397   18   4   269509   TN   5311.176   5311.191   u/d   g   16                CCACCATACGTCTACA                   Found L/U DA AB-CD Connectron pair for 188312 and 188397 with a       lifetime = 20 × 16 = 320                        0.003   0.001                                                        5311.160   5311.179   5340.361   5340.390   ---   5340.322   5340.360   5311.176   5311.191                           .-----.                     /       \                /         \        279.155 *          *270.981                \         /                 \\    / /                  \\  / /           279.239  *.* 270.897                    \  /                     X                   /   \           270.895*  .  *279.252                 /  /  \ \                /  /    \ \               /           \       270.811*             *279.336             /               \          
 
 Description of an Asymmetric Left-Right Connectron Pair in  E. coli  
 
         [0101]     The connectron 3707 has a C1-T1 binding length of 21 bases and a C2-T2 binding length of 19 bases. The shorter of the two matches at 19 bases produces the lifetime for this connectron. The connectron 3763 has a C1-T1 binding length of 42 bases and a C2-T2 binding length of 37 bases. The shorter of the two matches at 37 bases produces the lifetime for this connectron. The lifetime of this pair of dominant—dominant connectrons as shown in  FIG. 10   a  is 703.  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           genome                  |       Connection id                  |       |   chromosome                  |       |   |   contig                  |       |   |   |       (.groups) id                  |       |   |   |       |   type                  |       |   |   |       |   |         match start                  |       |   |   |       |   |         |         match stop                  |       |   |   |       |   |         |         |     type of Connectron                  |       |   |   |       |   |         |         |     |   source of Connection                  |       |   |   |       |   |         |         |     |   |    length of match                sequence of match   |       |   |         |         |     |   |    |                | |       |   |   |       |   |         |         |     |   |    |           eco    3707   1   1    3906   CN   2338.350   2338.370   l/r   g   21                AACGCCTTLTCCGGCCTLCGG                        eco   3707   1   1   689   TP   374.169   374.189   l/r   g   21                AACGCCTTLTCCGGCCTLCGG                        eco   3707   1   1   3906   CN   2338.380   2338.398   l/r   g   19                GTLGGCCTGATLAGACGCG                        eco   3707   1   1   707   TN   376.619   376.637   l/r   g   19                GTLGGCCTGATLAGACGCG                        eco   3763   1   1   709   CP   376.712   376.753   l/r   g   42                GTLGGCCGGATLAGGCGTTCACGCCGCATCCGGCAGTCGTGC                        eco   3763   1   1   690   TN   374.152   374.193   l/r   g   42                GTLGGCCGGATLAGGCGTTCACGCCGCATCCGGCAGTCGTGC                        eco   3763   1   1   709   CP   376.717   376.753   l/r   g   37                CCGGATLAGGCGTTCACGCCGCATCCGGCAGTCGTGC                        eco   3763   1   1   706   TP   376.617   376.653   l/r   g   37                CCGGATLAGGCGTTCACGCCGCATCCGGCAGTCGTGC                   Found L/R DD AB-CD Connectron pair for 3707 and 3763 with a       lifetime = 19 × 37 = 703                        .004   .002                                                        374.169   374.189   376.619   376.637   ---   374.152   374.193   376.617   376.653                           .-----.                     /       \                /         \        279.155 *          *270.981                \         /                 \\    / /                  \\  / /           279.239  *.* 270.897                    \  /                     X                  /    \           270.895*  .  *279.252                 /  /  \ \                /  /    \ \               /           \       270.811*             *279.336             /               \          
 
 Description of an Asymmetric Left-Right Connectron Pair in  S. cerevisiae  
 
         [0102]     The connectron 6834 has a C1-T1 binding length of 105 bases and a C2-T2 binding length of 38 bases. The shorter of the two matches at 38 bases produces the lifetime for this connectron. The connectron 6944 has a C1-T1 binding length of 152 bases and a C2-T2 binding length of 143 bases. The shorter of the two matches at 143 bases produces the lifetime for this connectron. The lifetime of this pair of dominant—anti-dominant connectrons as shown in  FIG. 10   c  is 5434.  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           genome                  |       Connection id                  |       |   chromosome                  |       |   |   contig                  |       |   |   |       (.groups) id                  |       |   |   |       |   type                  |       |   |   |       |   |         match start                  |       |   |   |       |   |         |         match stop                  |       |   |   |       |   |         |         |     type of Connectron                  |       |   |   |       |   |         |         |     |   source of Connection                  |       |   |   |       |   |         |         |     |   |    length of match                sequence of match   |       |   |         |         |     |   |    |                | |       |   |   |       |   |         |         |     |   |    |           yst    6834   7   7   10928   CN   111.321   111.425   l/r   g   105                CGGTGTTAGAAGATGACGCAAATGATGAGAAATAGTCATCTAAATTAGTG           GAAGCTGAAACGCAAGGATTGATAATGTAATAGCATCAATGAATATTAAC       ATATA                    yst   6834   3   3   2988   TP   84.359   84.463   l/r   g   105                CGGTGTTAGAAGATGACGCAAATGATGAGAAATAGTCATCTAAATTAGTG           GAAGCTGAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATTAAC       ATATA                    yst   6834   7   7   10945   CN   111.449   111.486   l/r   g   38                TCATCTACTAACTAGTATTTACGTTACTAGTATATTAT                        yst   6834   3   3   3500   TN   168.765   168.802   l/r   g   38                TCATCTACTAACTAGTATTTACGTTACTAGTATATTAT                        yst   6944   4   4   5116   CN   645.641   645.792   l/r   g   152                TCATCTACTAACTAGTATTTACGTTACTAGTATATTATCATATACGGTGT           TAGAAGATGACGCAAATGATGAGAAATAGTCATCTAAATTAGTGGAAGCT       GAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATTAACATATAA       AA                    yst   6944   3   3   2991   TP   84.315   84.466   l/r   g   152                TCATCTACTAACTAGTATTTACCTTACTAGTATATTATCATATACGGTGT           TAGAAGATGACGCAAATGATGAGAAATAGTCATCTAAATTAGTGGAAGCT       GAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATTAACATATAA       AA                    yst   6944   4   4   5116   CN   645.641   645.783   l/r   g   143                TCATCTACTAACTAGTATTTACGTTACTAGTATATTATCATATACGGTGT           TAGAAGATGACGCAAATGATGAGAAATAGTCATCTAAATTAGTGGAAGCT       GAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATTAA                    yst   6944   3   3   3496   TN   168.762   168.904   l/r   g   143                TCATCTACTAACTAGTATTTACGTTACTAGTATATTATCATATACGGTGT           TAGAAGATGACGCAAATGATGAGAAATAGTCATCTAAATTAGTGGAAGCT       GAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATTAA               Found L/R DA AB-CD Connectron pair for 6834 and 6944 with a       lifetime = 38 × 143 = 5434                        .003   .003                                                        84.359   84.463   168.765   168.802   ---   84.315   84.466   168.762   168.904                           .-----.                     /       \                /         \        279.155 *          *270.981                \         /                 \\    / /                  \\  / /           279.239  *.* 270.897                    \  /                     X                   /   \           270.895*  .  *279.252                 /  /  \ \                /  /    \ \               /           \       270.811*             *279.336             /               \          
 
 Description of an Asymmetric Left-Right Connectron Pair in  C. elegans  
 
         [0103]     The connectron 40849 has a C1-T1 binding length of 34 bases and a C2-T2 binding length of 34 bases. The either of the two matches at 34 bases produces the lifetime for this connectron. The connectron 40850 has a C1-T1 binding length of 48 bases and a C2-T2 binding length of 39 bases. The shorter of the two matches at 39 bases produces the lifetime for this connectron. The lifetime of this pair of anti-dominant—dominant connectrons as shown in  FIG. 10   d  is 1326.  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             genome                  |       Connection id                  |       |   chromosome                  |       |   |   contig                  |       |   |   |       (.groups) id                  |       |   |   |       |   type                  |       |   |   |       |   |         match start                  |       |   |   |       |   |         |         match stop                  |       |   |   |       |   |         |         |     type of Connectron                  |       |   |   |       |   |         |         |     |   source of Connection                  |       |   |   |       |   |         |         |     |   |    length of match                sequence of match   |       |   |         |         |     |   |    |                | |       |   |   |       |   |         |         |     |   |    |                wrm   40849   6   2   51392   CN   13819.470   13819.500   l/r   g   34                ACCGAACCCAACGGCCCTCTTTAGGGCCACAAAT                        wrm   40849   6   2   51379   TN   13817.594   13817.630   l/r   g   34                ACCGAACCCAACGGCCCTCTTTAGGGCCACAAAT                        wrm   40849   6   2   51392   CN   13819.470   13819.500   l/r   g   34                ACCGAACCCAACGGCCCTCTTTAGGGCCACAAAT                        wrm   40849   6   2   51400   TP   13820.550   13820.583   l/r   g   34                ACCGAACCCAACGGCCCTCTTTAGGGCCACAAAT                        wrm   40850   6   2   51410   CN   13820.791   13820.840   l/r   g   48                CAACACACCTAACCGAACCCAACGGCCCTCTTTAGGGCCACAAATGTT                        wrm   40850   6   2   51379   TN   13817.583   13817.630   l/r   g   48                CAACACACCTAACCGAACCCAACGGCCCTCTTTAGGGCCACAAATGTT                        wrm   40850   6   2   51410   CN   13820.800   13820.840   l/r   g   39                CTAACCGAACCCAACGGCCCTCTTTAGGGCCACAAATGT                        wrm   40850   6   2   51400   TP   13820.550   13820.584   l/r   g   39                CTAACCGAACCCAACGGCCCTCTTTAGGGCCACAAATGT                   Found L/R AD AB-CD Connectron pair for 40849 and 40850 with a       lifetime = 34 × 39 = 1326                        .003   .003                                                        13817.595   13817.628   13820.550   13820.583   ---   13817.584   13817.631   13820.547   13820.585                           .-----.                     /       \                /         \        279.155 *          *270.981                \         /                 \ \   / /                  \ \ / /           279.239  *.* 270.897                    \  /                     X                   /   \           270.895*  .  *279.252                 /  /  \ \                /  /    \ \               /           \       270.811*             *279.336             /               \          
 
 Description of an Asymmetric Left-Right Connectron Pair in  H. sapiens  
 
         [0104]     The connectron 67620 has a C1-T1 binding length of 38 bases and a C2-T2 binding length of 33 bases. The shorter of the two matches at 33 bases produces the lifetime for this connectron. The connectron 67621 has a C1-T1 binding length of 41 bases and a C2-T2 binding length of 42 bases. The shorter of the two matches at 41 bases produces the lifetime for this connectron. The lifetime of this pair of dominant—anti-dominant connectrons as shown in  FIG. 10   c  is 1353.  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           genome                  |       Connection id                  |       |   chromosome                  |       |   |   contig                  |       |   |   |       (.groups) id                  |       |   |   |       |   type                  |       |   |   |       |   |         match start                  |       |   |   |       |   |         |         match stop                  |       |   |   |       |   |         |         |     type of Connectron                  |       |   |   |       |   |         |         |     |   source of Connection                  |       |   |   |       |   |         |         |     |   |    length of match                sequence of match   |       |   |         |         |     |   |    |                | |       |   |   |       |   |         |         |     |   |    |           hsd   67620   100   1   96091   CN   1705.996   1706.033   l/r   g   36                GTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGC                        hsd   67620   60   1   78101   TP   218.397   218.434   l/r   g   38                GTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGC                        hsd   67620   100   1   96101   CN   1705.970   1706.002   l/r   g   33                AGGTCAGGAGATCGAGACCATCCTGGCTAACAC                        hsd   67620   60   1   78110   TN   234.341   234.373   l/r   g   33                AGGTCAGGAGATCGAGACCATCCTGGCTAACAC                        hsd   67621   100   1   98781   CN   3142.085   3142.125   l/r   g   41                CGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCC                        hsd   67621   60   1   78101   TP   218.395   218.435   l/r   g   41                CGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCC                        hsd   67621   100   1   98781   CN   3142.052   3142.093   l/r   g   42                GAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAAC                        hsd   67621   60   1   78110   TN   234.340   234.381   l/r   g   42                GAGGTCAGCAGATCGAGACCATCCTGGCTAACACGGTGAAAC                   Found L/R DA AB-CD Connectron pair for 67620 and 67621 with a       lifetime = 33 × 41 = 1353                        0.001   0.001                                                        218.397   218.434   234.341   234.373   ---   218.395   218.435   234.340   234.381                           .-----.                     /       \                /         \        279.155 *          *270.981                \         /                 \\    / /                  \\  / /           279.239  *.* 270.897                    \  /                     X                   /   \           270.895*  .  *279.252                 /  /  \ \                /  /    \ \               /           \       270.811*             *279.336             /               \          
 
 Description of an Asymmetric Left-Right Connectron Pair in  A. thaliana  
 
         [0105]     The connectron 5 has a C1-T1 binding length of 28 bases and a C2-T2 binding length of 35 bases. The shorter of the two matches at 28 bases produces the lifetime for this connectron. The connectron 6 has a C1-T1 binding length of 37 bases and a C2-T2 binding length of 68 bases. The shorter of the two matches at 37 bases produces the lifetime for this connectron. The lifetime of this pair of anti-dominant—dominant connectrons as shown in  FIG. 10   d  is 1036.  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             genome                  |       Connection id                  |       |   chromosome                  |       |   |   contig                  |       |   |   |       (.groups) id                  |       |   |   |       |   type                  |       |   |   |       |   |         match start                  |       |   |   |       |   |         |         match stop                  |       |   |   |       |   |         |         |     type of Connectron                  |       |   |   |       |   |         |         |     |   source of Connection                  |       |   |   |       |   |         |         |     |   |    length of match                sequence of match   |       |   |         |         |     |   |    |                | |       |   |   |       |   |         |         |     |   |    |                ath       5   15   3   102175   CN   12540.150   12540.174   l/r   g   28                ATCATCAATGAACTCATTTGGCTAAGGT                        ath   5   15   3   102902   TN   13558.720   13558.750   l/r   g   28                ATCATCAATGAACTCATTTGGCTAAGGT                        ath   5   15   3   102176   CN   12540.184   12540.220   l/r   g   35                ACATTCATTAGTTCTGGAACGTGAATCAAGCAATG                        ath   5   15   3   103090   TP   13634.210   13634.240   l/r   g   35                ACATTCATTAGTTCTGGAACGTGAATCAAGCAATG                        ath   6   15   3   103067   CP   13626.660   13626.700   l/r   g   37                ATGCATCATCAATGAACTCATTTGGCTAAGGTGAAGG                        ath   6   15   3   102902   TN   13558.713   13558.750   l/r   g   37                ATGCATCATCAATGAACTCATTTGGCTAAGGTGAAGG                        ath   6   15   3   103067   CP   13626.624   13626.691   l/r   g   68                TTTAACATTCATTAGTTCTGGAACGTGAATCAAGCAATGCATCATCAATG           AACTCATTTGGCTAAGGT                    ath   6   15   3   103090   TP   13634.202   13634.270   l/r   g   68                TTTAACATTCATTAGTTCTGGAACGTGAATCAAGCAATGCATCATCAATG           AACTCATTTGGCTAAGGT               Found L/R AD AB-CD Connectron pair for 5 and 6 with a       lifetime = 28 × 37 = 1036                        .005   .004                                                        13558.718   13558.745   13634.206   13634.240   ---   13558.714   13558.750   13634.202   13634.269                           .-----.                     /       \                /         \        279.155 *          *270.981                \         /                 \\    / /                  \\  / /           279.239  *.* 270.897                    \  /                     X                   /   \           270.895*  .  *279.252                 /  /  \ \                /  /    \ \               /           \       270.811*             *279.336             /               \          
 
 Design of an Asymmetric Lower-Upper Connectron Pair in  S. cerevisiae  
 
         [0106]     There are many ways to design a pair of connectrons. In this example we have chosen to replace the C1 source and the T1 target of the upper naturally occuring connectron with another sequence. Design of a connectron pair can be accomplished by anyone skilled the art by modifying and/or replacing any of the sources and targets in the four positions of either a lower-upper or a left-right connectron pair. A totally synthetic pair of dominant—anti-dominant connectrons could also be designed de-novo.  
         [0107]     The connectron 5441 has a C1-T1 binding length of 82 bases and a C2-T2 binding length of 35 bases. The shorter of the two matches at 34 bases produces the lifetime for this connectron. The connectron 5500 has a C1-T1 binding length of 16 bases and a C2-T2 binding length of 16 bases. Either of the two matches at 16 bases produces the lifetime for this connectron. The lifetime of this pair of anti-dominant—dominant connectrons as shown in  FIG. 9   c  is 544.  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           genome                  |       Connection id                  |       |   chromosome                  |       |   |   contig                  |       |   |   |       (.groups) id                  |       |   |   |       |   type                  |       |   |   |       |   |         match start                  |       |   |   |       |   |         |         match stop                  |       |   |   |       |   |         |         |     type of Connectron                  |       |   |   |       |   |         |         |     |   source of Connection                  |       |   |   |       |   |         |         |     |   |    length of match                sequence of match   |       |   |         |         |     |   |    |                | |       |   |   |       |   |         |         |     |   |    |           yst    5441   3   3    2944   CP    84.112   84.193   l/u   g   82                ATACGTTTGAAGAATCACTTTATGGATTGAAACAAAGTGGAGCGAACTG           GTACGAAACTATCAAATCATACCTGATAAAAC                    yst   5441   3   3   2901   TP   82.743   82.824   l/u   g   82                ATACGTTTGAAGAATCACTTTATGGATTGAAACAAAGTGGAGCGAACTG           GTACGAAACTATCAAATCATACCTGATAAAAC                    yst   5441   3   3   2965   CP   84.195   84.228   l/u   g   34                GAAACGTGACGGTACTCATAAAGCTAGATTTGTT                        yst   5441   3   3   3529   TP   169.327   169.360   l/u   g   34                GAAACGTCACGGTACTCATAAAGCTAGATTTGTT                        yst   5500   3   3   3387   CN   151.534   151.549   l/u   g   16                TAATTGTTGGGATTCG                        yst   5500   3   3   3526   TN   169.308   169.323   l/u   g   16                TAATTGTTGGGATTCC                        yst   5500   3   3   3387   CN   151.516   151.531   l/u   g   16                AAAGGCTATAATATTA                        yst   5500   3   3   2905   TN   82.825   82.840   l/u   g   16                AAAGGCTATAATATTA                   Found L/U DA AB-CD Connectron pair for 5441 and 5500 with a       lifetime = 34 × 16 = 544                        .001   .004                                                        82.743   82.824   169.327   169.360   ---   169.308   169.323   82.825   82.840                           .-----.                     /       \                /         \        279.155 *          *270.981                \         /                 \\    / /                  \\  / /           279.239  *.* 270.897                    \  /                     X                   /   \           270.895*  .  *279.252                 /  /  \ \                /  /    \ \               /           \       270.811*             *279.336             /               \          
 
 Design of an Asymmetric Lower-Upper Connectron Pair in  H. sapiens  
 
         [0108]     There are many ways to design a pair of connectrons. In this example we have chosen to replace the C1 source and the T1 target of the right naturally occuring connectron with another sequence. Design of a connectron pair can be accomplished by anyone skilled the art by modifying and/or replacing any of the sources and targets in the four positions of either a lower-upper or a left-right connectron pair. A totally synthetic pair of anti-dominant—dominant connectrons could also be designed de-novo.  
         [0109]     The connectron 395760 has a C1-T1 binding length of 32 bases and a C2-T2 binding length of 32 bases. Either of the two matches at 32 bases produces the lifetime for this connectron. The connectron 395762 has a C1-T1 binding length of 40 bases and a C2-T2 binding length of 39 bases. The shorter of the two matches at 39 bases produces the lifetime for this connectron. The lifetime of this pair of anti-dominant—dominant connectrons as shown in  FIG. 10   c  is 1248.  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             genome                  |       Connection id                  |       |   chromosome                  |       |   |   contig                  |       |   |   |       (.groups) id                  |       |   |   |       |   type                  |       |   |   |       |   |         match start                  |       |   |   |       |   |         |         match stop                  |       |   |   |       |   |         |         |     type of Connectron                  |       |   |   |       |   |         |         |     |   source of Connection                  |       |   |   |       |   |         |         |     |   |    length of match                sequence of match   |       |   |         |         |     |   |    |                | |       |   |   |       |   |         |         |     |   |    |                hsd   395760   920   19   747775   CP   17572.332   17572.363   l/r   g   32                CCAGCCCCTCCTCCCTCAGACCCAGGAGTCCA                        hsd   395760   922   19   765474   TN   27988.178   27988.209   l/r   g   32                CCAGCCCCTCCTCCCTCAGACCCAGGAGTCCA                        hsd   395760   920   19   747777   CP   17572.369   17572.400   l/r   g   32                CCAGCCCCTCCTCCCTCAGACCCAGGAGTCCA                        hsd   395760   922   19   765567   TP   28004.852   28004.883   l/r   g   32                CCAGCCCCTCCTCCCTCAGACCCAGGAGTCCA                        hsd   395762   920   19   747819   CP   17573.447   17573.486   l/r   g   40                CCCCAGCCCCTCCTCCCTCAGACCCAGGAGTCCAGACCCC                        hsd   395762   922   19   765474   TN   27988.176   27988.215   l/r   g   40                CCCCAGCCCCTCCTCCCTCAGACCCAGGAGTCCAGACCCC                        hsd   395762   920   19   747823   CP   17573.520   17573.557   l/r   g   39                GGCCCCAGCCCCTCCTCCCTCAGACCCAGGAGTCCAGGT                        hsd   395762   922   19   765567   TP   28004.848   28004.887   l/r   g   39                GGCCCCAGCCCCTCCTCCCTCAGACCCAGGAGTCCAGGT                   Found L/R AD AB-CD Connectron pair for 395760 and 395762 with a       lifetime = 32 × 39 = 1248                        0.006   0.004                                                        27988.178   27988.209   28004.852   28004.883   ---   27988.176   27988.215   28004.848   28004.887                           .-----.                     /       \                /         \        279.155 *          *270.981                \         /                 \\    / /                  \\  / /           279.239  *.* 270.897                    \  /                     X                   /   \           270.895*  .  *279.252                 /  /  \ \                /  /    \ \               /           \       270.811*             *279.336             /               \          
 
         [0110]