Selection of RNA aptamers that bind HIV-1 LTR DNA duplexes: Strand invaders

Nucleic Acids Research

Volumn 38, Issue 22, 2010, Pages 8306-8315

  Srisawat, Chatchawan ^a   Engelke, David R ^b  

^a MAHIDOL UNIVERSITY   (Thailand)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; DOUBLE STRANDED DNA; RNA APTAMER; UNCLASSIFIED DRUG;

ARTICLE; BASE PAIRING; CONSENSUS SEQUENCE; CONTROLLED STUDY; DNA STRAND; GENE INTERACTION; GENE TARGETING; GENETIC SELECTION; HUMAN IMMUNODEFICIENCY VIRUS 1; INTERACTIONS WITH NUCLEIC ACID; LONG TERMINAL REPEAT; MOLECULAR CLONING; NONHUMAN; NUCLEIC ACID ANALYSIS; NUCLEOTIDE BINDING SITE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RNA STRUCTURE; TRANSCRIPTION REGULATION;

APTAMERS, NUCLEOTIDE; BASE SEQUENCE; BINDING SITES; CLONING, MOLECULAR; CONSENSUS SEQUENCE; DNA, VIRAL; HIV LONG TERMINAL REPEAT; HIV-1; RNA; SELEX APTAMER TECHNIQUE;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 78650482160     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq696     Document Type: Article

References (46)

1. Demidov, V.V. and Frank-Kamenetskii, M.D. (2001) Sequence-specific targeting of duplex DNA by peptide nucleic acids via triplex strand invasion. Methods, 23, 108-122.
2. Duca, M., Vekhoff, P., Oussedik, K., Halby, L. and Arimondo, P.B. (2008) The triple helix: 50 years later, the outcome. Nucleic Acids Res., 36, 5123-5138.
3. Frank-Kamenetskii, M.D. and Mirkin, S.M. (1995) Triplex DNA structures. Annu. Rev. Biochem., 64, 65-95.
4. Grunweller, A. and Hartmann, R.K. (2007) Locked nucleic acid oligonucleotides: the next generation of antisense agents? BioDrugs, 21, 235-243.
5. Koizumi, M. (2006) ENA oligonucleotides as therapeutics. Curr. Opin. Mol. Ther., 8, 144-149.
6. Lohse, J., Dahl, O. and Nielsen, P.E. (1999) Double duplex invasion by peptide nucleic acid: a general principle for sequence-specific targeting of double-stranded DNA. Proc. Natl Acad. Sci. USA, 96, 11804-11808.
7. Nielsen, P.E. and Egholm, M. (2001) Strand displacement recognition of mixed adenine-cytosine sequences in double stranded DNA by thymine-guanine PNA (peptide nucleic acid). Bioorg. Med. Chem., 9, 2429-2434.
8. Diviacco, S., Rapozzi, V., Xodo, L., Helene, C., Quadrifoglio, F. and Giovannangeli, C. (2001) Site-directed inhibition of DNA replication by triple helix formation. FASEB J., 15, 2660-2668.
9. Guntaka, R.V., Varma, B.R. and Weber, K.T. (2003) Triplex-forming oligonucleotides as modulators of gene expression. Int. J. Biochem. Cell Biol., 35, 22-31.
10. Shen, C., Rattat, D., Buck, A., Mehrke, G., Polat, B., Ribbert, H., Schirrmeister, H., Mahren, B., Matuschek, C. and Reske, S.N. (2003) Targeting bcl-2 by triplex-forming oligonucleotide- a promising carrier for gene-radiotherapy. Cancer Biother. Radiopharm., 18, 17-26.
11. Wang, G. and Xu, X.S. (2004) Peptide nucleic acid (PNA) binding-mediated gene regulation. Cell. Res., 14, 111-116.
12. Chin, J.Y. and Glazer, P.M. (2009) Repair of DNA lesions associated with triplex-forming oligonucleotides. Mol. Carcinog., 48, 389-399.
13. Rogers, F.A., Vasquez, K.M., Egholm, M. and Glazer, P.M. (2002) Site-directed recombination via bifunctional PNA-DNA conjugates. Proc. Natl Acad. Sci. USA, 99, 16695-16700.
14. Simon, P., Cannata, F., Concordet, J.P. and Giovannangeli, C. (2008) Targeting DNA with triplex-forming oligonucleotides to modify gene sequence. Biochimie, 90, 1109-1116.
15. Suzuki, T. (2008) Targeted gene modification by oligonucleotides and small DNA fragments in eukaryotes. Front. Biosci., 13, 737-744.
16. Torigoe, H., Katayama, T. and Tsukamoto, Y. (2007) Triplex formation-based artificial transcription factor to regulate target gene expression. Nucleosides Nucleotides Nucleic Acids, 26, 1463-1466.
17. Christensen, L.A., Finch, R.A., Booker, A.J. and Vasquez, K.M. (2006) Targeting oncogenes to improve breast cancer chemotherapy. Cancer Res., 66, 4089-4094.
18. Jain, A., Wang, G. and Vasquez, K.M. (2008) DNA triple helices: biological consequences and therapeutic potential. Biochimie, 90, 1117-1130.
19. Ray, A. and Norden, B. (2000) Peptide nucleic acid (PNA): its medical and biotechnical applications and promise for the future. FASEB J., 14, 1041-1060.
20. Uil, T.G., Haisma, H.J. and Rots, M.G. (2003) Therapeutic modulation of endogenous gene function by agents with designed DNA-sequence specificities. Nucleic Acids Res., 31, 6064-6078.
21. McDonald, C.D. and Maher, L.J. 3rd (1995) Recognition of duplex DNA by RNA polynucleotides. Nucleic Acids Res., 23, 500-506.
22. Soukup, G.A., Ellington, A.D. and Maher, L.J. 3rd (1996) Selection of RNAs that bind to duplex DNA at neutral pH. J. Mol. Biol., 259, 216-228.
23. Belotserkovskii, B.P., De Silva, E., Tornaletti, S., Wang, G., Vasquez, K.M. and Hanawalt, P.C. (2007) A triplex-forming sequence from the human c-MYC promoter interferes with DNA transcription. J. Biol. Chem., 282, 32433-32441.
24. Carbone, G.M., McGuffie, E.M., Collier, A. and Catapano, C.V. (2003) Selective inhibition of transcription of the Ets2 gene in prostate cancer cells by a triplex-forming oligonucleotide. Nucleic Acids Res., 31, 833-843.
25. Karympalis, V., Kalopita, K., Zarros, A. and Carageorgiou, H. (2004) Regulation of gene expression via triple helical formations. Biochemistry, 69, 855-860.
26. Semerad, C.L. and Maher, L.J. 3rd (1994) Exclusion of RNA strands from a purine motif triple helix. Nucleic Acids Res., 22, 5321-5325.
27. Ellington, A.D. and Szostak, J.W. (1990) In vitro selection of RNA molecules that bind specific ligands. Nature, 346, 818-822.
28. Fitzwater, T. and Polisky, B. (1996) A SELEX primer. Meth. Enzymol., 267, 275-301.
29. Robertson, D.L. and Joyce, G.F. (1990) Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature, 344, 467-468.
30. Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249, 505-510.
31. Naghavi, M.H., Schwartz, S., Sonnerborg, A. and Vahlne, A. (1999) Long terminal repeat promoter/enhancer activity of different subtypes of HIV type 1. AIDS Res. Hum. Retroviruses, 15, 1293-1303.
32. Engelke, D.R., Krikos, A., Bruck, M.E. and Ginsburg, D. (1990) Purification of Thermus aquaticus DNA polymerase expressed in Escherichia coli. Anal. Biochem., 191, 396-400.
33. Laing, L. (1993) Thermodynamic study of the folding and ligand interactions for the 23S rRNA GTPase center. Doctoral dissertation. Johns Hopkins University.
34. Tabor, S. and Richardson, C.C. (1989) Selective inactivation of the exonuclease activity of bacteriophage T7 DNA polymerase by in vitro mutagenesis. J. Biol. Chem., 264, 6447-6458.
35. Srisawat, C. and Engelke, D.R. (2001) Streptavidin aptamers: affinity tags for the study of RNAs and ribonucleoproteins. RNA, 7, 632-641.
36. Srisawat, C., Goldstein, I.J. and Engelke, D.R. (2001) Sephadex-binding RNA ligands: rapid affinity purification of RNA from complex RNA mixtures. Nucleic Acids Res., 29, E4.
37. Benn, S., Rutledge, R., Folks, T., Gold, J., Baker, L., McCormick, J., Feorino, P., Piot, P., Quinn, T. and Martin, M. (1985) Genomic heterogeneity of AIDS retroviral isolates from North America and Zaire. Science, 230, 949-951.
38. Gendelman, H.E., Phelps, W., Feigenbaum, L., Ostrove, J.M., Adachi, A., Howley, P.M., Khoury, G., Ginsberg, H.S. and Martin, M.A. (1986) Trans-activation of the human immunodeficiency virus long terminal repeat sequence by DNA viruses. Proc. Natl Acad. Sci. USA, 83, 9759-9763.
39. Mathews, D.H., Disney, M.D., Childs, J.L., Schroeder, S.J., Zuker, M. and Turner, D.H. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl Acad. Sci. USA, 101, 7287-7292.
40. 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.
41. De Rijk, P. and De Wachter, R. (1997) RnaViz, a program for the visualisation of RNA secondary structure. Nucleic Acids Res., 25, 4679-4684.
42. Zeichner, S.L., Kim, J.Y. and Alwine, J.C. (1991) Linker-scanning mutational analysis of the transcriptional activity of the human immunodeficiency virus type 1 long terminal repeat. J. Virol., 65, 2436-2444.
43. Pohorille, A., Ross, W.S. and Tinoco, I. Jr (1990) DNA dynamics in aqueous solution: opening the double helix. Int J Supercomput Appl, 4, 81-96.
44. Nonin, S., Leroy, J.L. and Gueron, M. (1995) Terminal base pairs of oligodeoxynucleotides: imino proton exchange and fraying. Biochemistry, 34, 10652-10659.
45. Andreatta, D., Sen, S., Perez Lustres, J.L., Kovalenko, S.A., Ernsting, N.P., Murphy, C.J., Coleman, R.S. and Berg, M.A. (2006) Ultrafast dynamics in DNA: "fraying" at the end of the helix. J. Am. Chem. Soc., 128, 6885-6892. (Pubitemid 43830575)
46. Smolina, I.V., Demidov, V.V., Soldatenkov, V.A., Chasovskikh, S.G. and Frank-Kamenetskii, M.D. (2005) End invasion of peptide nucleic acids (PNAs) with mixed-base composition into linear DNA duplexes. Nucleic Acids Res., 33, e146.