Abstract:
A method for selecting a hammerhead ribozyme target site comprising the step of selecting a site comprising an XXUH/XX nucleotide sequence, where XX are strong duplex forming bases, H is U, A or C, and the slash represents the cleavage site.

Description:
This application is a continuation of application Ser. No. 07/884,074, filed May 14, 1992 now abandoned. 
    
    
     BACKGROUND OF THE INVENTION 
     This invention relates to hammerhead ribozymes and their interaction with substrate RNA. 
     Hammerhead ribozymes are generally described by Haseloff and Gerlach (1988) Nature, 334, 555. In this article, the design of new ribozymes and testing of a synthetic ribozyme is discussed, as well as their application in vitro and in vivo. FIG. 1 is a diagrammatic representation of a hammerhead ribozyme and its substrate (where N represents any nucleotide, H represents A, U or C, and I, II and III represent various stems of the ribozyme); the closed circles represent nucleotide bases in the substrate. 
     SUMMARY OF THE INVENTION 
     This invention features an improved method for designing active hammerhead ribozymes. Such ribozymes are chosen to include sequences which form &#34;strong&#34; base-pairing interactions at the positions closest to the internal loop formed by the ribozyme-substrate complex (parameters for sequence-specific duplex stability are found in Freier, et al. &#34;Improved Parameters for Predictions of RNA Duplex Stability&#34; (1986) Proc. Nat. Acad. Sci. (USA), 83, 9373-9377). Thus, such ribozymes have a substrate sequence XXUH/XX (where XX are &#34;strong&#34; duplex forming bases, H is U, A or C, and the slash represents the cleavage site) &#34;Strong&#34; duplex forming bases are chosen to be those which have dinucleotide free energies of helix propagation of -2.0 kcal/mole or less (i.e. GA, UC, GU, AC, CG, GC, GG, CC; see Freier, et el). Such ribozymes are more active than other ribozymes having &#34;weak&#34; duplex forming bases at the positions XX. These ribozymes are more efficient at cleaving the substrate RNA molecules since the ribozyme is able to bind to the substrate tightly enough to allow the catalytic components to be positioned for cleavage, but is still weakly enough bound to allow the reaction to be driven to completion by dissociation of the product RNA. Provision of strong ribozyme-substrate interactions at these positions allows for maximal cleavage activity by forming a rigid structure close to the central loop of the ribozyme. This prevents the interior portions of stems I and III of the ribozyme from separating prematurely due to local thermal fluctuations. FIG. 2 is a diagrammatic representation of the equilibrium between a tightly constrained structure (&#34;Proper configuration&#34;) and an undesirable loose structure (&#34;Improper configuration&#34;). The method of this invention is to select ribozymes and substrates which maximize the proper configuration. 
     Stem III is limited in this regard since the innermost base-pair must be AU with the U in the substrate. Stem I, however, has no such constraints and ribozymes can be chosen which include &#34;strong&#34; duplex forming bases immediately adjacent to the internal loop. 
     Thus, in a first aspect, the invention features a method for providing a more active hammerhead ribozyme by modifying the ribozyme to have &#34;strong&#34; duplex forming bases at the variable positions closest to the internal loop. 
     In a second related aspect, the invention features a method for selecting a substrate or target site at which a hammerhead ribozyme will be more active. The method includes the step of selecting a substrate site having the sequence XXUH/XX (where XX are &#34;strong&#34; duplex forming bases, H is U, A or C, and the slash represents the cleavage site). 
     Other features and advantages of the invention will be apparent from the following description of the preferred embodiments thereof, and from the claims. 
    
    
     DESCRIPTION OF THE PREFERRED EMBODIMENTS 
     The drawings will first briefly be described. 
     Drawings: 
     FIG. 1 is a diagramatic representation of a hammerhead ribozyme and its substrate (SEQ ID NO: 21). 
     FIG. 2 is a diagramatic representation of a hammerhead ribozyme (SEQ ID NO: 21) in equilibrium between a tightly constrained structure and an undesirable loose structure. 
    
    
     EXAMPLE 
     HIV-1 HSV AND ANF TARGETED RIBOZYMES 
     The following is data obtained from various ribozymes demonstrating the desirability of ribozymes having strong duplex forming bases at the variable positions closest to the internal loop. 
     Tables I, II and IIl contain sequence and activity information for ribozymes designed against targets found in the HIV-1 genome, the HSV genome, and the rat ANF gene, respectively. Activities (as kcat/k M ) were determined by incubating 2-100nM ribozyme with approximately 1 nM radioactively labeled substrate for different times in 75 mM Tris-HCl pH 8.0, 10 mM MgCl 2 . The products are separated by denaturing polyacrylamide electrophoresis and quantitated by a beta emission scanner (Ambis Systems, San Diego, Calif.). The data are treated per Michaelis-Menton for excess enzyme, specifically, the negative log of the fraction substrate remaining is plotted as a function of time. The resulting slope is then plotted as a function of ribozyme concentration. The slope of this line is then kcat/k M . 
     Ribozymes which meet the strong base-pair criteria for stem I are marked with a &#34;I&#34; in the left margin. The average activity of these ribozymes is 33×10 6  /M·min, which is well above the average for all the represented ribozymes (22×10 6  /M·min) and the average for ribozymes not meeting this criteria (15×10 6  /M·min). Ribozymes which meet the strong base-pair criteria for stem III are marked with a &#34;III&#34; in the left margin. The average activity of these ribozymes is 28×10 6  /M·min, and for those not meeting this criteria is 8×10 6  M·min. Six ribozymes have the appropriate strong inner bases in both stems. Their average activity is 37×10 6  /M·min. See, McSwiggen, entitled &#34;Hammerhead Ribozymes&#34;, filed on the same day as the present application, and assigned to the same assignee, the whole of which (including drawings) is hereby incorporated by reference herein, which describes a method for determining ribozyme activity. This application has been assigned Ser. No. 07/884,422. 
     
                                           TABLE I__________________________________________________________________________Summary of HIV ribozyme activity     Stem III (3&#39; RZ)  Stem I (5&#39; RZ)      Total ΔG of     length         ΔG°                       length                           ΔG°                                           Binding                                                  kcal/kMRibozyme  (bp)         (kcal/mole)               Sequence                       (bp)                           (kcal/mole)                                 Sequence  (kcal/mole)                                                  (/10 6 M                                                  ·__________________________________________________________________________                                                  min)    HCH-r36     5   -7    ACUUC   5   -9.7  (GG)AGGCU -6.0   0.17    HCH-r38     6   -9.9  ACUUCC  6   -10.8 (GG)UAGGCU                                           -10.1  6.0    HCH-r40     7   -11.6 ACUUCCU 7   -11.7 (GG)UUAGGCU                                           -12.8  5.4    HCH-r42     8   -13.4 ACUUCCUG                       8   -12.6 (GG)UUUAGGCU                                           -15.4  3.3    HCH-r37-5&#39;     6   -9.9  ACUUCC  5   -9.7  (GG)AGGCU -9.1   0.54    HCH-r37-3&#39;     5   -9.2  ACUUC   6   -10.8 (GG)UAGGCU                                           -7.0   &lt;0.01    HCH-r39-5&#39;     7   -11.5 ACGCU   6   -10.8 (GG)UAGGCU                                           -11.9  7.0    HCH-r39-3&#39;     6   -9.9  ACUUCC  7   -11.7 (GG)UUAGGCU                                           -11.0  14    HBH-r I     5   -9.2  ACGCU   4   -5.7  (GGAG)UACU                                           -3.4   0.006    HBH-r II     5   -7    ACGCU   8   -8.7  UUAAUACU  -7.3   0.58    HBH-r III     6   -11.6 ACUUCCU 8   -8.7  UUAAUACU  -9.4   7.0III HBH-r IV     6   -11.5 ACGCUC  6   -6.7  AAUACU    -7.3   15.7    HBH-r V     6   -11.5 ACGCUC  7   -7.8  UAAUACU   -8.5   5.6    HBH-r VI     6   -11.5 ACGCUC  5   -5.8  AUACU     -6.4   3.15    HDH-34-     6   -11.9 ACUGCC  6   -10.1 GAGUCU    -10.2  16    MF    HEH-34-     6   -9.6  AGUCUG  6   -7.6  CUUGAU    -5.4   1.1    MF    HFH-34-     6   -7.7  AUAGAG  6   -8.7  UGCUUU    -4.6   1.2    MF__________________________________________________________________________Substrate Sequence__________________________________________________________________________HCS-r29ch GGAGCAUCCAGGAAGUCAGCCUAAAACUG (SEQ ID NO: 1)HBS-r21 UGCGAGAGCGUCAGUAUUAAG (SEQ ID NO: 2)HDS-r13 GGCAGUCAGACUC (SEQ ID NO: 3)HES-r13 CAGACUCAUCAAG (SEQ ID NO: 4)HFS-r13 CUCUAUCAAAGCA (SEQ ID NO: 5)__________________________________________________________________________ 
    
     
                                           TABLE II__________________________________________________________________________HSV Summary      Stem III (3&#39; RZ)                    Stem I (5&#39; RZ)          ΔG°                        ΔG°                                  Total ΔG of                                               Multiple                                                    Turnover      length          (kcal/    length                        (kcal/    Binding                                         kcat/Km                                               kcat KmRibozyme   (bp)          mole)              Sequence                    (bp)                        mole)                            Sequence                                  (kcal/mole)                                         (/M · min)                                               (/min)                                                    (nM)__________________________________________________________________________III  VAH-r36      6   -11.4              ACGGUC                    6   -11.5                            GCGUCU                                  -12.4  20I,IV VCH-r34      6   -12.8              ACCCCG                    6   -11.7                            CCCACG                                  -13.4  68    1.73 34VI   VEH-r34      6   -12.2              ACGCCA                    6   -10.1                            UUCUCC                                  -11.8  30I,IIIVEH-r32      5   -10.4              ACGCC 5   -9.2                            UCUCC -9.1   38III  VFH-r34      6   -11 ACGAGG                    6   -10.4                            GACGAG                                  -9.7   3.4I,IIIVGH-r35      6   -11 ACGAGG                    6   -9.3                            CGGAC -11.4  61    5.69 126III  VIH-r34      6   -13.7              ACCCCC                    6   -10.6                            CGCGAA                                  -13.3  50    2.2  69I    VJH-r33      6   -10.8              ACAGCA                    5   -9.9                            CCCGU -9.3   5.6                                         (X10 6)Substrate                 Sequence__________________________________________________________________________VAS-r17-2                 CAGACCGUCAGACGCUC (SEQ ID NO: 6)VCS-r17                   GUCGGGGUCCGUGGGUC (SEQ ID NO: 7)VES-r17                   GAUGGCGUCGGAGAACA (SEQ ID NO: 8VFS-r15                   GUCCUCGUCCUCGUC (SEQ ID NO: 9)VGS-r16                   GUCCUCGUCGUCCGCA (SEQ ID NO: 10)VIS-r17                   CCGGGGGUCUUCGCGCG (SEQ ID NO: 11)VJS-r14                   GGUGCUGUAACGGG (SEQ ID NO: 12)__________________________________________________________________________ 
    
     
                                           TABLE III__________________________________________________________________________Summary of ANF ribozyme activity    Stem III (3&#39; RZ)  Stem I (5&#39; RZ)    Total ΔG                                               kcal/kM    length        ΔG°                      length                          ΔG°                                        Binding                                               (/106Ribozyme (bp)        (kcal/mole)              Sequence                      (bp)                          (kcal/mole)                                Sequence                                        (kcal/mole)                                               M · min)                                                     Exp.__________________________________________________________________________   ACH-r32    5   -7    ACUUC   5   -8.8  GGGUU   -5.7   1.2   64-19   ACH-r33-5&#39;    6   -9.9  ACUUCC  5   -8.8  GGGUU   -8.6   0.54  64-23   ACH-r33-3&#39;    5   -7    ACUUC   6   -10.8 CGGGUU  -6.6   0.0011                                                     64-30   ACH-r34    6   -9.9  ACUUCC  6   -10.8 CGGGUU  -9.5   7.8   64-20   ACH-r35-5&#39;    7   -12.8 ACUUCCC 6   -10.8 CGGGUU  -12.4  1.0   64-25,27   ACH-r35-3&#39;    6   -9.9  ACUUCC  7   -12.9 ACGGGUU -11.0  7.5   64-26   ACH-r36    7   -12.8 ACUUCCC 7   -12.9 ACGGGUU -13.9  0.87  64-28   AHH-r34-    5   -9.9  ACGGG   7   -10.6 CACUGUA -9.8   8.5   64-35   57   AHH-r34-    6   -12.2 ACGGGA  6   -8.8  ACUGUA  -10.8  &lt;0.1  64-40   66   AHH-r35-    6   -12.2 ACGGGA  7   -10.6 CACUGUA -12.3  16    64-35   67   AHH-r38-    8   -14   ACGGGAUU                      8   -14.0 GCACUGUA                                        -18.8  21    64-36   88   AAH-r35-    6   -10.9 ACACCG  7   -10.5 UGUGUUG -10.6  0.1   64-42   67III   ABH-r33-    6   -10.8 ACCUCA  5   -10.7 GGCAU   -11.2  18    64-37   65I,III   ADH-r34-    5   -9.9  ACGGG   7   -12.1 UCUCUGA -11.6  9.3   64-44   57III   AEH-r35-    7   -11.9 ACCUUCG 6   -9.5  CAGCUU  -10.1  13    64-43   76I,III   AIH-r34-    6   -13.3 ACCGGC  6   -8.1  AUCUUC  -11.2  8.1   64-38   66I,III   AJH-r34-    5   -10.8 ACCCC   7   -11.1 UCAAUCC -10.8  46    64-41   57                                               k2 = .069                                                     113.2                                               /min__________________________________________________________________________Substrate Sequence__________________________________________________________________________ACS-r15 GGGAAGUCAACCCGU (SEQ ID NO: 13)AHS-r19 AAAUCCCGUAUACAGUGCG (SEQ ID NO: 14)AAS-r16 GCGGUGUCCAACACAG (SEQ ID NO: 15)ABS-r14 AUGAGGUCAUGCCU (SEQ ID NO: 16)ADS-r15 ACCCGUCUCAGAGAG (SEQ ID NO: 17)AES-r16 GCGAAGGUCAAGCUGC (SEQ ID NO: 18)AIS-r15 UGCCGGUAGAAGAUG (SEQ ID NO: 19)AJS-r15 GGGGGUAGGAUUGAC (SEQ ID NO: 20)__________________________________________________________________________ 
    
     Other embodiments are within the following claims. 
     
         __________________________________________________________________________SEQUENCE LISTING(1) GENERAL INFORMATION:(iii) NUMBER OF SEQUENCES: 21(2) INFORMATION FOR SEQ ID NO: 1:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 29(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 1:GGAGCAUCCAGGAAGUCAGCCUAAAACUG29(2) INFORMATION FOR SEQ ID NO: 2:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 21(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 2:UGCGAGAGCGUCAGUAUUAAG21(2) INFORMATION FOR SEQ ID NO: 3:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 13(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 3:GGCAGUCAGACUC13(2) INFORMATION FOR SEQ ID NO: 4:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 13(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 4:CAGACUCAUCAAG13(2) INFORMATION FOR SEQ ID NO: 5:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 13(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 5:CUCUAUCAAAGCA13(2) INFORMATION FOR SEQ ID NO: 6:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 17(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 6:CAGACCGUCAGACGCUC17(2) INFORMATION FOR SEQ ID NO: 7:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 17(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 7:GUCGGGGUCCGUGGGUC17(2) INFORMATION FOR SEQ ID NO: 8:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 17(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 8:GAUGGCGUCGGAGAACA17(2) INFORMATION FOR SEQ ID NO: 9:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 15(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 9:GUCCUCGUCCUCGUC15(2) INFORMATION FOR SEQ ID NO: 10:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 16(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 10:GUCCUCGUCGUCCGCA16(2) INFORMATION FOR SEQ ID NO: 11:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 17(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 11:CCGGGGGUCUUCGCGCG17(2) INFORMATION FOR SEQ ID NO: 12:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 14(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 12:GGUGCUGUAACGGG14(2) INFORMATION FOR SEQ ID NO: 13:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 15(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 13:GGGAAGUCAACCCGU15(2) INFORMATION FOR SEQ ID NO: 14:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 19(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 14:AAAUCCCGUAUACAGUGCG19(2) INFORMATION FOR SEQ ID NO: 15:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 16(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 15:GCGGUGUCCAACACAG16(2) INFORMATION FOR SEQ ID NO: 16:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 14(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 16:AUGAGGUCAUGCCU14(2) INFORMATION FOR SEQ ID NO: 17:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 15(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 17:ACCCGUCUCAGAGAG15(2) INFORMATION FOR SEQ ID NO: 18:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 16(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 18:GCGAAGGUCAAGCUGC16(2) INFORMATION FOR SEQ ID NO: 19:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 15(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 19:UGCCGGUAGAAGAUG15(2) INFORMATION FOR SEQ ID NO: 20:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 15(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 20:GGGGGUAGGAUUGAC15(2) INFORMATION FOR SEQ ID NO: 21:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 34(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ix) FEATURE:(D) OTHER INFORMATION: The letter &#34;N&#34;stands for any base.(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 21:NNNNNNCUGAUGAGGCCGAAAGGCCGAAANNNNN34__________________________________________________________________________