In vitro selection identifies key determinants for loop-loop interactions: RNA aptamers selective for the TAR RNA element of HIV-1

RNA

Volumn 5, Issue 12, 1999, Pages 1605-1614

  Ducongé, Frédéric ^a   Toulmé, Jean Jacques ^a  

^a UNIVERSITÉ DE BORDEAUX   (France)

Author keywords

GA mismatch; Kissing complex; RNA hairpin; SELEX

Indexed keywords

MAGNESIUM; RNA;

ARTICLE; BASE PAIRING; BINDING AFFINITY; COMPLEX FORMATION; CONSENSUS SEQUENCE; CONTROLLED STUDY; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN INTERACTION; RNA SEQUENCE; RNA STRUCTURE; TRANSACTIVATION; VIRUS GENOME;

BASE PAIRING; BASE SEQUENCE; BINDING SITES; CONSENSUS SEQUENCE; DNA PRIMERS; HIV LONG TERMINAL REPEAT; HIV-1; HUMANS; KINETICS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OLIGORIBONUCLEOTIDES; POLYMERASE CHAIN REACTION; RNA, VIRAL; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0032795088     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838299991318     Document Type: Article

References (44)

1. Bartel DP, Szostak JW. 1993. Isolation of new ribozymes from a large pool of random sequences. Science 261:1411-1418.
2. Blommers MJJ, Pieles U, Demesmaeker A. 1994. An approach to the structure determination of nucleic acid analogues hybridized to RNA. NMR studies of a duplex between 2′-OMe RNA and an oligonucleotide containing a single amide backbone modification. Nucleic Acids Res 22:4187-4194.
3. Bohjanen PR, Liu Y, Garcia-Blanco MA. 1997. TAR RNA decoys inhibit tat-activated HIV-1 transcription after preinitiation complex formation. Nucleic Acids Res 25:4481-4486.
4. Boiziau C, Dausse E, Mishra R, Ducongé F, Toulmé JJ. 1997. Identification of aptamers against the DNA template for the HIV-1 TAR element. Antisense Nucleic Acid Drug Dev 7:369-380.
5. Boiziau C, Dausse E, Yurchenko L, Toulmé JJ. 1999. DNA aptamers selected against the HIV-1 TAR RNA element form RNA/DNA kissing complexes. J Biol Chem 274:12730-12737.
6. Brierley I, Digard P, Inglis SC. 1989. Characterization of an efficient coronavirus ribosomal frameshifting signal: Requirement for an RNA pseudoknot. Cell 57:537-547.
7. Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Szewczak AA, Kundrot CE, Cech TR, Doudna JA. 1996. RNA tertiary structure mediation by adenosine platforms [see comments]. Science 273:1696-1699.
8. Chang KY, Tinoco I. 1994. Characterization of a "kissing" hairpin complex derived from the human immunodeficiency virus genome. Proc Natl Acad Sci USA 91:8705-8709.
9. Chang KY, Tinoco I. 1997. The structure of an RNA "kissing" hairpin complex of the HIV TAR hairpin loop and its complement. J Mol Biol 269:52-66.
10. Colvin RA, Garcia-Blanco MA. 1992. Unusual structure of the human immunodeficiency virus type 1 trans-activation response element. J Virol 66:930-935.
11. Dandekar T, Sharma K. 1998. Regulatory RNA. Berlin: Springer Verlag.
12. Dassonneville L, Hamy F, Colson P, Houssier C, Bailly C. 1997. Binding of Hoechst 33258 to the TAR RNA of HIV-1. Recognition of a pyrimidine bulge-dependent structure. Nucleic Acids Res 25:4487-4492.
13. 7 RNA polymerase. Proc Natl Acad Sci USA 81:2035-2039.
14. Ecker DJ, Vickers TA, Bruice TW, Freier SM, Jenison RD, Manoharan M, Zounes M. 1992. Pseudo-half-knot formation with RNA. Science 257:958-961.
15. Eguchi Y, Tomizawa JI. 1990. Complex formed by complementary RNA stem-loops and its stabilization by a protein: Function of CoIE1 Rom protein. Cell 60:199-209.
16. Eguchi Y, Tomizawa JI. 1991. Complexes formed by complementary RNA stem-loops. Their formation, structures, and interactions with CoIE1 Rom protein. J Mol Biol 220:831-842.
17. Ellington AD, Conrad R. 1995. Aptamers as potential nucleic acid pharmaceuticals. Biotechnol Annu Rev 1:185-215.
18. Gait MJ, Karn J. 1993. RNA recognition by the human immuno-deficiency virus Tat and Rev proteins. Trends Biochem Sci 18: 255-259.
19. Gatignol A, Buckler-White A, Berkhout B, Jeang KT. 1993. Characterization of a human TAR RNA-binding protein that activates the HIV-1 LTR. Science 1251:1597-1600.
20. Gold L, Polisky B, Uhlenbeck O, Yarus M. 1995. Diversity of oligonucleotide functions. Annu Rev Biochem 64:763-797.
21. Gregorian RS, Crothers DM. 1995. Determinants of RNA hairpin loop-loop complex stability. J Mol Biol 248:968-984.
22. Grosjean H, Soll DG, Crothers D. 1976. Studies of the complex formed between transfer RNAs with complementary anticodons. J Mol Biol 103:499-519.
23. Haasnoot CAG, Hilbers CW, Van der Marel GA, Van Boom JH, Singh UC, Pattabiraman N, Kollman PA. 1986. On loopfolding in nucleic acid hairpin-type structures. J Biomol Struct Dyn 3:843-855.
24. Hamy F, Felder ER, Heizmann G, Lazdins J, Aboul-ela F, Varani G, Karn J, Klimkait T. 1997. An inhibitor of the Tat/TAR RNA interaction that effectively suppresses HIV-1 replication. Proc Natl Acad Sci USA 94:3548-3553.
25. Harper JW, Logsdon NJ. 1991. Refolded HIV-1 tat protein protects both bulge and loop nucleotides in TAR RNA from ribonucleolytic cleavage. Biochemistry 30:8060-8066.
26. Jaeger JA, Tinoco IJ. 1993. An NMR study of the HIV-1 TAR element hairpin. Biochemistry 32:12522-12530.
27. Le Tinévez R, Mishra RK, Toulmé JJ. 1998. Selective inhibition of cell-free translation by oligonucleotides targeted to a mRNA structure. Nucleic Acids Res 26:2273-2278.
28. Lee AJ, Crothers DM. 1998. The solution structure of an RNA loop-loop complex: The CoIE1 inverted loop sequence. Structure 6:993-1005.
29. Marino JP, Gregorian RSJ, Csankovszki G, Crothers DM. 1995. Bent helix formation between RNA hairpins with complementary loops. Science 268:1448-1454.
30. Mhashilkar AM, Biswas DK, LaVecchio J, Pardee AB, Marasco WA. 1997. Inhibition of human immunodeficiency virus type 1 replication in vitro by a novel combination of anti-Tat single-chain intra-bodies and NF-kappa B antagonists. J Virol 71:6486-6494.
31. Milligan JF, Groebe DR, Witherell GW, Uhlenbeck OC. 1987. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res 15:8783-8798.
32. Mishra RK, Le Tinévez R, Toulmé JJ. 1996. Targeting nucleic acid secondary structures by antisense oligonucleotides designed through in vitro selection. Proc Natl Acad Sci USA 93:10679-10684.
33. Mishra RK, Toulmé JJ. 1994. In vitro selection of antisense oligonucleotides targeted to a hairpin structure. C R Acad Sci Paris 317:977-982.
34. Lai RNA dimerization process in vitro. Biochemistry 35:5075-5082.
35. Paillart JC, Westhof E, Ehresmann C, Ehresmann B, Marquet R. 1997. Non-canonical interactions in a kissing loop complex: The dimerization initiation site of HIV-1 genomic RNA. J Mol Biol 270:36-49.
36. SantaLucia J Jr, Kierzek R, Turner DH. 1991. Stabilities of consecutive A · C, C · C, G · G, U · C, and U · U mismatches in RNA internal loops: Evidence for stable hydrogen-bonded U · U and C · C · + pairs. Biochemistry 30:8242-8251.
37. Serra MJ, Lyttle MH, Axenson TJ, Schadt CA, Turner DH. 1993. RNA hairpin loop stability depends on closing base pair. Nucleic Acids Research 21:3845-3849.
38. Skripkin E, Paillart JC, Marquet R, Ehresmann B, Ehresmann C. 1994. Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro. Proc Natl Acad Sci USA 91:4945-4949.
39. Sullenger BA, Gallardo HF, Ungers GE, Gilboa E. 1990. Overexpression of TAR sequences renders cells resistant to human immunodeficiency virus. Cell 63:601-608.
40. Tomizawa JI. 1990. Control of CoIE1 plasmid replication: Intermediates in the binding of RNA I and RNA II. J Mol Biol 212:683-694.
41. Wagner RW, Matteucci MD, Grant D, Huang T, Froehler BC. 1996. Potent and selective inhibition of gene expression by an anti-sense heptanucleotide. Nat Biotechnol 14:840-844.
42. Walczak R, Carbon P, Krol A. 1998. An essential non-Watson-Crick base pair motif in 3′-UTR to mediate selenoprotein translation. RNA 4:74-84.
43. Wu-Baer F, Lane WS, Gaynor RB. 1995. The cellular factor TRP-185 regulates RNA polymerase II binding to HIV-1 TAR RNA. EMBO J 14:5995-6009.
44. Zhou Q, Sharp PA. 1996. Tat-SF1: Co-factor for stimulation of transcriptional elongation by HIV-1 Tat. Science 274:605-610.