Elucidation and characterization of oligonucleotide-accessible sites on HIV-2 leader region RNA

Antisense and Nucleic Acid Drug Development

Volumn 13, Issue 1, 2003, Pages 45-55

  Deer, Emily L ^a   Douk, Boramee ^a   Lanchy, Jean Marc ^a   Lodmell, J Stephen ^a  

^a UNIVERSITY OF MONTANA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE; RNA; VIRUS RNA; PRIMER RNA; RIBONUCLEASE H;

ARTICLE; DIMERIZATION; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 2; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RETROVIRUS; REVERSE TRANSCRIPTION; RNA ANALYSIS; RNA BINDING; VIRUS GENOME; VIRUS INFECTIVITY; VIRUS REPLICATION; 5' UNTRANSLATED REGION; ANTIVIRAL ACTIVITY; DRUG BINDING SITE; DRUG EFFICACY; IN VITRO STUDY; NUCLEIC ACID HYBRIDIZATION; RNA STRUCTURE; VIRAL GENETICS;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 2; RNA VIRUSES; UNIDENTIFIED RETROVIRUS;

EID: 24144474574     PISSN: 10872906     EISSN: None     Source Type: Journal    
DOI: 10.1089/108729003764097331     Document Type: Article

References (27)

1. ALLAWI, H.T., DONG, F., IP, H.S., NERI, B.P., and LYAMICHEV, V.I. (2001). Mapping of RNA accessible sites by extension of random oligonucleotide libraries with reverse transcriptase. RNA 7, 314-327.
2. BERKHOUT, B. (1992). Structural features in TAR RNA of human and simian immunodeficiency viruses: A phylogenetic analysis. Nucleic Acids Res. 20, 27-31.
3. BERKHOUT, B., and SCHONEVELD, I. (1993). Secondary structure of the HIV-2 leader RNA comprising the tRNA-primer binding site. Nucleic Acids Res. 21, 1171-1178.
4. BERKHOUT, B., and VAN WAMEL, J.L. (1996). Role of the DIS hairpin in replication of human immunodeficiency virus type 1. J. Virol. 70, 6723-6732.
5. CLEVER, J.L., and PARSLOW, T.G. (1997). Mutant human immunodeficiency virus type 1 genomes with defects in RNA dimerization or encapsidation. J. Virol. 71, 3407-3414.
6. DIRAC, A.M., HUTHOFF, H., KJEMS, J., and BERKHOUT, B. (2001). The dimer initiation site hairpin mediates dimerization of the human immunodeficiency virus, type 2 RNA genome. J. Biol. Chem. 276, 32345-32352.
7. DIRAC, A.M., HUTHOFF, H., KJEMS, J., and BERKHOUT, B. (2002). Regulated HIV-2 dimerization by means of alternative RNA conformations. Nucleic Acids Res. 30, 2647-2655.
8. HADDRICK, M., LEAR, A.L., CANN, A.J., and HEAPHY, S. (1996). Evidence that a kissing loop structure facilitates genomic RNA dimerisation in HIV-1. J. Mol. Biol. 259, 58-68.
9. HIROTA, M., KOYANAGI, Y., AN, D.S., IWANAGA, Y., YAMAMOTO, N., and SHIMOTOHNO, K. (1997). Mutational analysis of the 5′ noncoding region of human immunodeficiency virus type 1 genome. Leukemia 3, 102-105.
10. HO, S.P., BAO, Y., LESHER, T., MALHOTRA, R., MA, L.Y., FLUHARTY, S.J., and SAKAI, R.R. (1998). Mapping of RNA accessible sites for antisense experiments with oligonucleotide libraries. Nat. Biotechnol. 16, 59-63.
11. HO, S.P., BRITTON, D.H., BAO, Y., and SCULLY, M.S. (2000). RNA mapping: Selection of potent oligonucleotide sequences for antisense experiments. Methods Enzymol. 314, 168-183.
12. JOSSINET, F., LODMELL, J.S., EHRESMANN, C., EHRESMANN, B., and MARQUET, R. (2001). Identification of the in vitro HIV-2/SIV RNA dimerization site reveals striking differences with HIV-1. J. Biol. Chem. 276, 5598-5604.
13. KUIKEN, C., FOLEY, B., HAHN, B., MARX, P., McCUTCHAN, F., MELLORS, J., WOLINSKY, S., and KORBER, B. (2001). HIV sequence compendium 2001. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos.
14. LANCHY, J.M., and LODMELL, J.S. (2002). Alternate usage of two dimerization sites in HIV-2 viral RNA in vitro. J. Mol. Biol. 319, 637-648.
15. LANCHY, J.M., RENTZ, C.A., IVANOVITCH, J.D., and LODMELL, J.S. (2003). Elements located upstream and downstream of the major splice donor site influence the ability of HIV-62 leader RNA to dimerize in vitro. Biochemistry 42, 2634-2642.
16. LAUGHREA, M., and JETTÉ, L. (1994). A 19-nucleotide sequence upstream of the 5′ major splice donor is part of the dimerization domain of human immunodeficiency virus 1 genomic RNA. Biochemistry 33, 13464-13474.
17. LAUGHREA, M., JETTÉ, L., MAK, J., KLEIMAN, L., LIANG, C., and WAINBERG, M.A. (1997). Mutations in the kissing-loop hairpin of human immunodeficiency virus type 1 reduce viral infectivity as well as genomic RNA packaging and dimerization. J. Virol 71, 3397-3406.
18. LAUGHREA, M., SHEN, N., JETTÉ, L., and WAINBERG, M.A. (1999). Variant effects of nonnative kissing-loop hairpin palindromes on HIV replication and HIV RNA dimerization: Role of stem-loop B in HIV replication and HIV RNA dimerization. Biochemistry 38, 226-234.
19. MATHEWS, D.H., SABINA, J., ZUKER, M., and TURNER, D.H. (1999). Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288, 911-940.
20. PAILLART, J.C., BERTHOUX, L., OTTMANN, M., DARLIX, J.L., MARQUET, R., EHRESMANN, B., and EHRESMANN, C. (1996). A dual role of the putative RNA dimerization initiation site of human immunodeficiency virus type 1 in genomic RNA packaging and proviral DNA synthesis. J. Virol. 70, 8348-8354.
21. PATZEL, V., and SCZAKIEL, G. (2000). In vitro selection supports the view of a kinetic control of antisense RNA-mediated inhibition of gene expression in mammalian cells. Nucleic Acids Res. 28, 2462-2466.
22. REEVES, J.D., and DOMS, R.W. (2002). Human immunodeficiency virus type 2. J. Gen. Virol. 83, 1253-1265.
23. RHIM, H., and RICE, A.P. (1994). Functional significance of the dinucleotide bulge in stem-loop 1 and stem-loop 2 of HIV-2 TAR RNA. Virology 202, 202-211.
24. ST. LOUIS, D., GOTTE, D., SANDERS-BUELL, E., RITCHEY, D., SALMINEN, M., CARR, J., and McCUTCHAN, F. (1998). Infectious molecular clones with the nonhomologous dimer initiation sequences found in different subtypes of human immunodeficiency virus type 1 can recombine and initiate a spreading infection in vitro. J. Mol. Biol. 72, 3991-3998.
25. SKRIPKIN, E., PAILLART, J.C., MARQUET, R., EHRESMANN, B., and 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.
26. WALTON, S.P., STEPHANOPOULOS, G.N., YARMUSH, M.L., and ROTH, C.M. (2002). Thermodynamic and kinetic characterization of antisense oligodeoxynucleotide binding to a structured mRNA. Biophys. J. 82, 366-377.
27. ZUKER, M., MATHEWS, D.H., and TURNER, D.H. (1999). Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide. In: RNA Biochemistry and Biotechnology. J. Barciszewski and B.F.C. Clark, eds. (Kluwer Academic Publishers, Dordrecht, The Netherlands), pp. 11-43.