Selection by phage display of peptides targeting the HIV-1 TAR element

RNA Biology

Volumn 2, Issue 1, 2005, Pages 28-33

  Kolb, Gaëlle ^a   Boiziau, Claudine ^a,b  

^a INSERM   (France)

^b UNIVERSITÉ DE BORDEAUX   (France)

Author keywords

Hiv 1 tar element; In vitro selection; Peptidic ligand; Phage display; Regulatory rna

Indexed keywords

LIGAND; MAGNESIUM; PEPTIDE; PEPTIDE LIBRARY; RNA; STREPTAVIDIN;

ARTICLE; CONCENTRATION RESPONSE; HUMAN IMMUNODEFICIENCY VIRUS 1; PHAGE DISPLAY; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; REGULATORY RNA SEQUENCE; RNA STRUCTURE; TRANSACTIVATION; TRANSCRIPTION REGULATION; VIRUS INHIBITION; VIRUS REPLICATION;

HIV 1; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 27744470157     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.2.1.1681     Document Type: Article

References (33)

1. Draper DE. Protein-RNA recognition. Annual Rev Biochem 1995; 64:593-620.
2. Karn J. Tackling Tat. J Mol Biol 1999; 293:235-54.
3. Garber ME, Wei P, Jones KA. HIV-1 Tat interacts with cyclin T1 to direct the P-TEFb CTD kinase complex to TAR RNA. Cold Spring Harb Symp Quant Biol 1998; 63:371-80.
4. Froeyen M, Herdewijn P. RNA as a target for drug design, the example of Tat-TAR interaction. Curr Top Med Chem 2002; 2:1123-45.
5. Hamy F, Felder ER, Heizmann G, Lazdins J, Aboul-ela F, Varani G, Karn J, Klimkait T. An inhibitor of the Tat/TAR RNA interaction that effectively suppresses HIV-1 replication. Proc Natl Acad Sci USA 1997; 94:3548-53.
6. Arzumanov AA, Walsh AP, Rajwanshi VK, Kumar R, Wengef J, Gait MJ. Inhibition of HIV-1 Tat-dependent trans activation by steric block chimeric 2′-O-methyl/LNA oligoribonucleotides. Biochemistry 2001; 40:14645-54.
7. Holmes SC, Arzumanov AA, Gait MJ. Steric inhibition of human immunodeficiency virus type-1 Tat-dependent trans-activation in vitro and in cells by oligonucleotides containing 2′-O-methyl G-clamp ribonucleoside analogues. Nucleic Acids Res 2003; 31:2759-68.
8. Smith GP, Petrenko VA. Phage Display. Chem Rev 1997; 97:391-410.
9. Agris PF, Marchbank MT, Newman W, Guenther R, Ingram P, Swallow J, Mucha P, Szyk A, Rekowski P, Peletskaya E, Deutscher SL. Experimental models of protein-RNA interaction: Isolation and analyses of tRNA(Phe) and U1 snRNA-binding peptides from bacteriophage display libraries. J Protein Chem 1999; 18:425-35.
10. Friesen WJ, Darby MK. Specific RNA binding proteins constructed from zinc fingers. Nat Struct Biol 1998; 5:543-6.
11. Boiziau C, Dausse E, Yurchenko L, Toulmé JJ. DNA aptamers selected against the HIV-1 TAR RNA element form RNA/DNA kissing complexes. J Biol Chem 1999; 274:12730-7.
12. Ducongé F, Toulmé JJ. In vitro selection identifies key determinants for loop-loop interactions: RNA aptamers selective for the TAR RNA element of HIV-1. RNA 1999; 5:1605-14.
13. Sekkai D, Dausse E, Di Primo C, Darfeuille F, Boiziau C, Toulmé JJ. In vitro selection of DNA aptamers against the HIV-1 TAR RNA hairpin. Antisense Res Nucleic Acid Drug Dev 2002; 12:265-74.
14. Devlin JJ, Panganiban LC, Devlin PE. Random peptide libraries: A source of specific protein binding molecules. Science 1990; 249:404-6.
15. Adey NB, Mataragnon AH, Rider JE, Carter JM, Kay BK. Characterization of phage that bind plastic from phage-displayed random peptide libraries. Gene 1995; 156:27-30.
16. Cheng AC, Calabro V, Frankel AD. Design of RNA-binding proteins and ligands. Curr Opin Struct Biol 2001; 11:478-84.
17. Miller J, McLachlan AD, Klug A. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J 1985; 4:1609-14.
18. Rebar EJ, Pabo CO. Zinc finger phage: Affinity selection of fingers with new DNA-binding specificities. Science 1994; 263:671-3.
19. Blancafort P, Steinberg SV, Paquin B, Klinck R, Scott JK, Cedergren R. The recognition of a noncanonical RNA base pair by a zinc finger protein. Chem Biol 1999; 6:585-97.
20. Isalan M, Patel SD, Balasubramanian S, Choo Y. Selection of zinc fingers that bind single-stranded telomeric DNA in the G-quadruplex conformation. Biochemistry 2001; 40:830-6.
21. Frugier M, Schimmel P. Subtle atomic group discrimination in the RNA minor groove. Proc Natl Acad Sci USA 1997; 94:11291-4.
22. Pustowka A, Dietz J, Ferner J, Baumann M, Landersz M, Konigs C, Schwalbe H, Dietrich U. Identification of peptide ligands for target RNA structures derived from the HIV-1 packaging signal psi by screening phage-displayed peptide libraries. Chem biochem 2003; 4:1093-7.
23. Jonas G, Hoffmann S, Willbold D. Binding of phage-displayed HIV-1 Tat to TAR RNA in the presence of cyclin T1. J Biomed Sci 2001; 8:430-6.
24. Wolcke J, Weinhold E. A DNA-binding peptide from a phage display library. Nucleosides Nucleotides Nucleic Acids 2001; 20:1239-41.
25. Naik R, Jones S, Murray C, McAuliffe J, Vaia R, Stone M. Peptide templates for nanoparticle synthesis derived from polymerase chain reaction-driven phage display. Adv Funct Materials 2004; 14:25-30.
26. Wiesehan K, Willbold D. Mirror-image phage display: Aiming at the mirror. Chem biochem 2003; 4:811-5.
27. Kim S, Ribas de Pouplana L, Schimmel P. Diversified sequences of peptide epitope for same-RNA recognition. Proc Natl Acad Sci USA 1993; 90:10046-50.
28. Das C, Frankel AD. Sequence and structure space of RNA-binding peptides. Biopolymers 2003; 70:80-5.
29. Battiste JL, Mao H, Rao NS, Tan R, Muhandiram DR, Kay LE, Frankel AD, Williamson JR. Alpha helix-RNA major groove recognition in an HIV-1 rev peptide-RRE RNA complex. Science 1996; 273:1547-51.
30. Zhang Q, Harada K, Cho HS, Frankel AD, Wemmer DE. Structural characterization of the complex of the Rev response element RNA with a selected peptide. Chem Biol 2001; 8:511-20.
31. Garnier J, Osguthorpe DJ, Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol 1978; 120:97-120.
32. Darfeuille F, Sekkai D, Dausse E, KoIb G, Yurchenko L, Boiziau C, Toulmé JJ. Driving in vitro selection of anti-HIV-1 TAR aptamers by magnesium concentration and temperature. Combinat Chem High Throughput Screen 2002; 5:313-25.
33. Gallego J, Varani G. The hepatitis C virus internal ribosome-entry site: A new target for antiviral research. Biochem Soc Trans 2002; 30:140-5.