Inhibition of HIV replication by cyclic and hairpin PNAs targeting the HIV-1 TAR RNA loop

Journal of Nucleic Acids

Volumn 2012, Issue , 2012, Pages

  Upert, Gregory ^a   Di Giorgio, Audrey ^a   Upadhyay, Alok ^b   Manvar, Dinesh ^b   Pandey, Nootan ^b   Pandey, Virendra N ^b   Patino, Nadia ^a  

^a UNIVERSITÉ DE NICE SOPHIA ANTIPOLIS   (France)

^b RUTGERS NEW JERSEY MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIC PEPTIDE NUCLEIC ACID; HAIRPIN PEPTIDE NUCLEIC ACID; NUCLEOTIDE DERIVATIVE; PEPTIDE NUCLEIC ACID; PHOSPHONIUM DERIVATIVE; TRANSACTIVATOR PROTEIN; UNCLASSIFIED DRUG;

ANTIVIRAL ACTIVITY; ARTICLE; CELL CULTURE; CONTROLLED STUDY; CYTOPLASM; EXPRESSION VECTOR; GENE EXPRESSION; HUMAN IMMUNODEFICIENCY VIRUS 1; IN VITRO STUDY; PRIORITY JOURNAL; RNA HAIRPIN LOOP; RNA STRUCTURE; TRANSACTIVATION; TRANSACTIVATION RESPONSIVE ELEMENT; VIRUS INHIBITION;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 84868279972     PISSN: 20900201     EISSN: 2090021X     Source Type: Journal    
DOI: 10.1155/2012/591025     Document Type: Article

References (36)

1. Zhou Q., Chen D., Pierstorff E., Luo K., Transcription elongation factor P-TEFb mediates Tat activation of HIV-1 transcription at multiple stages. EMBO Journal 1998 17 13 3681 3691 2-s2.0-0032127436 10.1093/emboj/17.13.3681 (Pubitemid 28327386)
2. Richter S., Cao H., Rana T. M., Specific HIV-1 TAR RNA loop sequence and functional groups are required for human cyclin T1-Tat-TAR ternary complex formation. Biochemistry 2002 41 20 6391 6397 2-s2.0-0037150091 10.1021/bi0159579 (Pubitemid 34526004)
3. Richter S., Ping Y. H., Rana T. M., TAR RNA loop: a scaffold for the assembly of a regulatory switch in HIV replication. Proceedings of the National Academy of Sciences of the United States of America 2002 99 12 7928 7933 2-s2.0-0037062495 10.1073/pnas.122119999 (Pubitemid 34650982)
4. Yang M., Discoveries of Tat-TAR interaction inhibitors for HIV-1. Current Drug Targets 2005 5 4 433 444 2-s2.0-29444440832 10.2174/156800505774912901 (Pubitemid 43008515)
5. Richter S. N., Palù G., Inhibitors of HIV-1 Tat-mediated transactivation. Current Medicinal Chemistry 2006 13 11 1305 1315 2-s2.0-33646534201 10.2174/092986706776872989
6. Ducongé F., Toulmé J. J., In vitro selection identifies key determinants for loop-loop interactions: RNA aptamers selective for the TAR RNA element of HIV-1. RNA 1999 5 12 1605 1614 2-s2.0-0032795088 10.1017/S1355838299991318
7. Ducongé F., Di Primo C., Toulmé J. J., Is a closing GA pair a rule for stable loop-loop RNA complexes? Journal of Biological Chemistry 2000 275 28 21287 21294 2-s2.0-0034647516 10.1074/jbc.M002694200 (Pubitemid 30481826)
8. Van Melckebeke H., Devany M., Di Primo C., Beaurain F., Toulmé J. J., Bryce D. L., Boisbouvier J., Liquid-crystal NMR structure of HIV TAR RNA bound to its SELEX RNA aptamer reveals the origins of the high stability of the complex. Proceedings of the National Academy of Sciences of the United States of America 2008 105 27 9210 9215 2-s2.0-48249122367 10.1073/pnas.0712121105
9. Beaurain F., Di Primo C., Toulmé J. J., Laguerre M., Molecular dynamics reveals the stabilizing role of loop closing residues in kissing interactions: comparison between TAR-TAR and TAR-aptamer. Nucleic Acids Research 2003 31 14 4275 4284 2-s2.0-0242317674 10.1093/nar/gkg467 (Pubitemid 37448498)
10. Darfeuille F., Reigadas S., Hansen J. B., Orum H., Di Primo C., Toulmé J. J., Aptamers targeted to an RNA hairpin show improved specificity compared to that of complementary oligonucleotides. Biochemistry 2006 45 39 12076 12082 2-s2.0-33749359169 10.1021/bi0606344 (Pubitemid 44497833)
11. Darfeuille F., Cazenave C., Gryaznov S., Ducongé F., Di Primo C., Toulmé J. J., RNA and N3′ → P5′ kissing aptamers targeted to the trans-activation responsive (TAR) RNA of the human immunodeficiency virus-1. Nucleosides, Nucleotides and Nucleic Acids 2001 20 47 441 449 2-s2.0-0034741675 10.1081/NCN-100002318 (Pubitemid 32821809)
12. Darfeuille F., Arzumanov A., Gryaznov S., Gait M. J., Di Primo C., Toulmé J. J., Loop-loop interaction of HIV-1 TAR RNA with N3′ → P5′ deoxyphosphoramidate aptamers inhibits in vitro Tat-mediated transcription. Proceedings of the National Academy of Sciences of the United States of America 2002 99 15 9709 9714 2-s2.0-0037162493 10.1073/pnas.122247199 (Pubitemid 34831112)
13. Darfeuille F., Arzumanov A., Gait M. J., Di Primo C., Toulmé J. J., 2′-O-methyl-RNA hairpins generate loop-loop complexes and selectively inhibit HIV-1 tat-mediated transcription. Biochemistry 2002 41 40 12186 12192 2-s2.0-0037044192 10.1021/bi025974d
14. Zapata L., Bathany K., Schmitter J. M., Moreau S., Metal-assisted hybridization of oligonucleotides, evaluation of circular 2′-O-Me RNA as ligands for the TAR RNA target. European Journal of Organic Chemistry 2003 6 1022 1028 2-s2.0-0037353743
15. Kolb G., Reigadas S., Boiziau C., Van Aerschot A., Arzumanov A., Gait M. J., Herdewijn P., Toulmé J. J., Hexitol nucleic acid-containing aptamers are efficient ligands of HIV-1 TAR RNA. Biochemistry 2005 44 8 2926 2933 2-s2.0-14344257609 10.1021/bi048393s (Pubitemid 40293667)
16. Darfeuille F., Hansen J. B., Orum H., Di Primo C., Toulmé J. J., LNA/DNA chimeric oligomers mimic RNA aptamers targeted to the TAR RNA element of HIV-1. Nucleic Acids Research 2004 32 10 3101 3107 2-s2.0-2942631142 10.1093/nar/gkh636 (Pubitemid 39023001)
17. Di Primo C., Rudloff I., Reigadas S., Arzumanov A. A., Gait M. J., Toulmé J. J., Systematic screening of LNA/2′-O-methyl chimeric derivatives of a TAR RNA aptamer. FEBS Letters 2007 581 4 771 774 2-s2.0-33846821787 10.1016/j.febslet.2007.01.047 (Pubitemid 46216303)
18. Lebars I., Richard T., Di Primo C., Toulmé J. J., LNA derivatives of a kissing aptamer targeted to the trans-activating responsive RNA element of HIV-1. Blood Cells, Molecules, and Diseases 2007 38 3 204 209 2-s2.0-34047151422 10.1016/j.bcmd.2006.11.008 (Pubitemid 46518173)
19. Lebars I., Richard T., Diprimo C., Toulmé J. J., NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA-modified aptamer. Nucleic Acids Research 2007 35 18 6103 6114 2-s2.0-35649014422 10.1093/nar/gkm655 (Pubitemid 350019242)
20. Toulmé J. J., Di Primo C., Moreau S., Modulation of RNA function by oligonucleotides recognizing RNA structure. Progress in Nucleic Acid Research and Molecular Biology 2001 69 1 46 2-s2.0-0035225969 (Pubitemid 33804675)
21. Toulmé J. J., Darfeuille F., Kolb G., Chabas S., Staedel C., Modulating viral gene expression by aptamers to RNA structures. Biology of the Cell 2003 95 3-4 229 238 2-s2.0-0037780516 10.1016/S0248-4900(03)00036-4 (Pubitemid 36889224)
22. Kolb G., Reigadas S., Castanotto D., Faure A., Ventura M., Rossi J. J., Toulmé J. J., Endogenous expression of an anti-TAR aptamer reduces HIV-1 replication. RNA Biology 2006 3 4 150 156 2-s2.0-33947623718 (Pubitemid 46495343)
23. Upert G., Mehiri M., Giorgio A. D., Condom R., Patino N., Solid-phase synthesis and thermal denaturation study of cyclic PNAs targeting the HIV-1 TAR RNA loop. Bioorganic and Medicinal Chemistry Letters 2007 17 21 6026 6030 2-s2.0-34548841109 10.1016/j.bmcl.2007.07.030 (Pubitemid 47446191)
24. Nielsen P. E., Gene targeting and expression modulation by peptide nucleic acids (PNA). Current Pharmaceutical Design 2010 16 28 3118 3123 2-s2.0-78649822317 10.2174/138161210793292546
25. Pandey V. N., Upadhyay A., Chaubey B., Prospects for antisense peptide nucleic acid (PNA) therapies for HIV. Expert Opinion on Biological Therapy 2009 9 8 975 989 2-s2.0-67650690673 10.1517/14712590903052877
26. Abes R., Arzumanov A. A., Moulton H. M., Abes S., Ivanova G. D., Iversen P. L., Gait M. J., Lebleu B., Cell-penetrating-peptide-based delivery of oligonucleotides: an overview. Biochemical Society Transactions 2007 35 4 775 779 2-s2.0-34548150237 (Pubitemid 47310366)
27. Zhilina Z. V., Ziemba A. J., Ebbinghaus S. W., Peptide nucleic acid conjugates: synthesis, properties and applications. Current Topics in Medicinal Chemistry 2005 5 12 1119 1131 2-s2.0-27844465935 10.2174/156802605774370892 (Pubitemid 41644887)
28. Muratovska A., Lightowlers R. N., Taylor R. W., Turnbull D. M., Smith R. A. J., Wilce J. A., Martin S. W., Murphy M. P., Targeting peptide nucleic acid (PNA) oligomers to mitochondria within cells by conjugation to lipophilic cations: implications for mitochondrial DNA replication, expression and disease. Nucleic Acids Research 2001 29 9 1852 1863 2-s2.0-0035339611 (Pubitemid 32433269)
29. Filipovska A., Eccles M. R., Smith R. A. J., Murphy M. P., Delivery of antisense peptide nucleic acids (PNAs) to the cytosol by disulphide conjugation to a lipophilic cation. FEBS Letters 2004 556 13 180 186 2-s2.0-0346725016 10.1016/S0014-5793(03)01403-0 (Pubitemid 38058576)
30. Mehiri M., Upert G., Tripathi S., Di Giorgio A., Condom R., Pandey V. N., Patino N., An efficient biodelivery system for antisense polyamide nucleic acid (PNA). Oligonucleotides 2008 18 3 245 255 2-s2.0-51849110440 10.1089/oli.2008.0126
31. Armitage B., Ly D., Koch T., Frydenlund H., Orum H., Schuster G. B., Hairpin-forming peptide nucleic acid oligomers. Biochemistry 1998 37 26 9417 9425 2-s2.0-0032580965 10.1021/bi9729458 (Pubitemid 28307697)
32. Planelles V., Bachelerie F., Jowett J. B. M., Haislip A., Xie Y., Banooni P., Masuda T., Chen I. S. Y., Fate of the human immunodeficiency virus type 1 provirus in infected cells: a role for vpr. Journal of Virology 1995 69 9 5883 5889 2-s2.0-0029126614
33. Riguet E., Tripathi S., Chaubey B., Désiré J., Pandey V. N., Décout J. L., A peptide nucleic acid-neamine conjugate that targets and cleaves HIV-1 TAR RNA inhibits viral replication. Journal of Medicinal Chemistry 2004 47 20 4806 4809 2-s2.0-4544328474 10.1021/jm049642d (Pubitemid 39238253)
34. Kashanchi F., Shibata R., Ross E. K., Brady J. N., Martin M. A., Second-site long terminal repeat (LTR) revertants of replication-defective human immunodeficiency virus: effects of revertant TATA box motifs on virus infectivity, LTR-directed expression, in vitro RNA synthesis, and binding of basal transcription factors TFIID and TFIIA. Journal of Virology 1994 68 5 3298 3307 2-s2.0-0028300393
35. Chou T. C., Relationships between inhibition constants and fractional inhibition in enzyme catalyzed reactions with different numbers of reactants, different reaction mechanisms, and different types and mechanisms of inhibition. Molecular Pharmacology 1974 10 2 235 247 2-s2.0-0016379917
36. Chou T. C., On the determination of availability of ligand binding sites in steady state systems. Journal of Theoretical Biology 1977 65 2 345 356 2-s2.0-0017617685 (Pubitemid 8054907)