Patent Application: US-33967403-A

Abstract:
a computational method has been developed to detect the conditions whereby gene expression control mechanisms will stop the transcription of rna that would otherwise be used to form a connectron .

Description:
as shown in fig1 single - stranded rna is produced when a gene is transcribed . the rna transcript performs three roles . in role one , one or more copies of the rna transcript may be edited to form the open reading frame mrna for translation into protein . in role two , the single - stranded rna can be used for connectron formation . in role three , other copies of the single - stranded rna are cut into small fragment by the dicer enzyme . characteristically the dicer enzyme cuts rna into 21 - base fragments . two of these fragments are the c1 and the c2 sequences . these single - stranded rna fragments then bind to the respective double - strand cognate dna sequences to form two short triple - strand generalized hoogsteen helices . the double - strand dna sequences of c1 and c2 that are relevant are those that are in the 3 ′ utr of one or more genes . when the polymerase that is transcribing the double - stranded dna into rna comes to the c1 and c2 sequences that have the irna bound to them , the polymerase stops its transcribing action . the two generalized hoogsteen helices act as a block to the formation of more single - stranded rna of the c1 and c2 sequences . the hoogsteen helices of both connectrons and irna have lifetimes that vary directly with the length of the generalized hoogsteen helix . the effect of the irna ( generalized ) hoogsteen helices is to prevent the formation of more c1 - c2 rna during the lifetime of these helices . the total systematic effect is that the first gene to express a particulate c1 - c2 sequence inhibits all other genes with the same sequence from generating more c1 - c2 sequenced rna . this invention provides capabilities that are utilized in our application ser . no . ______ filed contemporaneously herewith and entitles “ simulation of gene expression control using connectrons , interference rnas ( irnas ) and small temporal rnas ( strnas ) in prokaryotic , archea and eukaryotic genomes ”. the irnas and strnas play a vital role in determining the simulation of cellular dynamics . this invention provides a way of utilizing irnas and strnas within the methodology of connectron control of gene expression . connectron 350 is an example of a transient connectron . it is described in e . coli genomic patent application identified above as c1 / c2 t1 - t2 global_id chromosome cl_id c2_id chromosome t1_id t2_id connectron_type 350 1 26 26 1 321 346 transient the c1 / c2 source of the transient connectron 350 is represented in as type num jobno chr start stop length genename cnt 26 1 1 19 . 796 19 . 859 . 064 --& gt ; | | | | | | | | | | | | | | the “ type ” descriptor of this transient c1 / c2 connectron source is “ cnt ”. the letter “ n ” indicates that the c1 / c2 connectron source occurs on the negative strand of the double - stranded dna of the genome . the letter “ p ” in this place would indicate a c1 / c2 connectron source on the positive strand of the genomic dna . the letter “ t ” in this descriptor indicates a “ transient ” connectron . similarly , the letter “ p ” would indicate a permanent connectron that is shown in a later example . the “ start ”, “ stop ” and “ length ” descriptors throughout these examples are given in kilo - bases ( kb ). connectron 19340 is an example of a transient connectron . it is described in e . coli genomic patent application identified above as c1 / c2 t1 - t2 global_id chromosome cl_id c2_id chromosome t1_id t2_id connectron_type 19340 1 1260 1260 1 321 346 transient the c1 / c2 source of the transient connectron 19340 is represented in as type num jobno chr start stop length genename cpt 1260 1 1 1049 . 705 1049 . 769 . 065 --& gt ; | | |||| |||||||||||||||| connectron 23879 is an example of a transient connectron . it is described in e . coli genomic patent application identified above as c1 / c2 t1 - t2 global_id chromosome cl_id c2_id chromosome t1_id t2_id connectron_type 23879 1 1927 1927 1 321 346 transient the c1 / c2 source of the transient connectron 23879 is represented in as type num jobno chr start stop length genename cpt 1927 1 1 1976 . 526 1976 . 590 . 065 --& gt ; || ||||||||||||||||||||| connectron 45018 is an example of a transient connectron . it is described in e . coli genomic patent application identified above as c1 / c2 t1 - t2 global_id chromosome cl_id c2_id chromosome t1_id t2_id connectron_type 45018 1 3424 3424 1 321 346 transient the c1 / c2 source of the transient connectron 45018 is represented in as type num jobno chr start stop length genename cpt 3424 1 1 3581 . 763 3581 . 827 . 065 --& gt ; || | | |||| ||||||||||| these four connectrons are driven by four c1 / c2 instances that share the same 64 - base sequence as shown in bold below . all of the data for the transient connectron 350 are pulled together in the following table that is the “ terse ” description of the connectron . connectron relationships global_id type 350 transient control sequences direction chromosome c1 / c2_id start stop length negative 1 26 19 . 859 19 . 796 . 064 trigger gene name cog_id start stop length insb_1 cog1662 . 508 19 . 811 . 698 target sequences direction chromosome t1_id start stop length negative 1 321 279 . 118 278 . 386 . 733 t2_id start stop length 346 290 . 589 289 . 833 . 757 controlled genes local_id chromosome group name cog_id direction start stop length 1 1 group0058 insb_2 cog1662 positive 278 . 402 279 . 099 . 698 2 1 group0059 yagb — positive 279 . 609 281 . 207 1 . 598 3 1 group0059 yaga cog1425 negative 281 . 207 280 . 053 1 . 155 4 1 group0060 yage cog0329 positive 281 . 481 284 . 392 2 . 911 5 1 group0060 yagf cog0129 positive 282 . 425 284 . 392 1 . 968 6 1 group0061 yagg cog2211 positive 284 . 619 287 . 623 3 . 004 7 1 group0061 yagh — positive 286 . 013 287 . 623 1 . 611 8 1 group0062 yagf cog1414 positive 287 . 628 289 . 529 1 . 901 9 1 group0062 argf cog0078 negative 289 . 529 288 . 525 1 . 005 controlled connectrons local_id chromosome c1 / c2_id direction start stop length 1 1 327 negative 279 . 335 279 . 136 . 200 2 1 337 negative 287 . 273 287 . 259 . 015 3 1 339 negative 287 . 296 287 . 282 . 015 4 1 342 negative 288 . 502 288 . 471 . 032 5 1 345 negative 290 . 589 289 . 833 . 757 when gene insb ( cog1662 ) is transcribed , the c1 / c2 sequence is produced in the 3 ′ utr . depending on how the dicer enzyme works there can be many different fragments . a few such fragments are shown below a given operation of the dicer enzyme will produce one of these examples or similar examples . the irna fragments will then bind as triple - stranded helices to the equivalent sequences in the c1 / c2 instances 1260 , 1927 , and 3424 . when the genes associated with these c1 / c2 sequences transcribe , the polymerase will find the sequence instances 1260 , 1927 and 3424 blocked by triple - stranded generalized hoogsteen helices formed by the irna from c1 / c2 26 . 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