Effect of DNA target sequence on triplex formation by oligo-2′-deoxy- and 2′-O-methylribonucleotides

Nucleic Acids Research

Volumn 31, Issue 14, 2003, Pages 4099-4108

  Cassidy, Rachel A ^a   Puri, Nitin ^a,b   Miller, Paul S ^a  

^a JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^b Amnion Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

5 METHYLCYTOSINE; ADENINE; ADENINE DERIVATIVE; CYTOSINE; DNA; ESTER DERIVATIVE; EXODEOXYRIBONUCLEASE III; GUANINE; METHYLPHOSPHONIC ACID; OLIGOMER; OLIGORIBONUCLEOTIDE; PHOSPHORUS DERIVATIVE; PSORALEN DERIVATIVE; PURINE; PYRIMIDINE DERIVATIVE; THYMINE; URACIL; GAG PROTEIN; OLIGODEOXYRIBONUCLEOTIDE; ORGANOPHOSPHORUS COMPOUND; TRIPLEX DNA; VIRUS ENVELOPE PROTEIN;

ARTICLE; CONTROLLED STUDY; DNA DEGRADATION; DNA SEQUENCE; MOLECULAR INTERACTION; MOLECULAR STABILITY; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PH MEASUREMENT; PRIORITY JOURNAL; TEMPERATURE MEASUREMENT; CHEMISTRY; CONFORMATION; DNA DENATURATION; GENETICS; NUCLEOTIDE SEQUENCE; PH; TEMPERATURE;

BASE SEQUENCE; DNA; GENE PRODUCTS, ENV; GENE PRODUCTS, GAG; HYDROGEN-ION CONCENTRATION; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; OLIGODEOXYRIBONUCLEOTIDES; OLIGORIBONUCLEOTIDES; ORGANOPHOSPHORUS COMPOUNDS; TEMPERATURE;

EID: 0242317685     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg436     Document Type: Article

References (66)

1. Knauert,M.P. and Glazer,P.M. (2001) Triplex forming oligonucleotides: sequence-specific tools for gene targeting. Hum. Mol. Genet., 10, 2243-2251.
2. 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.
3. Postel,E.H., Flint,S.J., Kessler,D.J. and Hogan,M.E. (1991) Evidence that a triplex-forming oligodeoxyribonucleotide binds to the c-myc promoter in HeLa cells, thereby reducing c-myc mRNA levels. Proc. Natl Acad. Sci. USA, 88, 8227-8231.
4. Young,S.L., Krawczyk,S.H., Matteucci,M.D. and Toole,J.J. (1991) Triple helix formation inhibits transcription elongation in vitro. Proc. Natl Acad. Sci. USA, 88, 10023-10026.
5. Duval-Valentin,G., Thuong,N.T. and Helene,C. (1992) Specific inhibition of transcription by triple helix-forming oligonucleotides. Proc. Natl Acad. Sci. USA, 89, 504-508.
6. Alunnifabbroni,M., Manfioletti,G., Manzini,G. and Xodo,L.E. (1994) Inhibition of T7 RNA polymerase transcription by phosphate and phosphorothioate triplex-forming oligonucleotides targeted to a R.Y site downstream from the promoter. Eur. J. Biochem., 226, 831-839.
7. Xodo,L., Alunnifabbroni,M., Manzini,G. and Quadrifoglio,F. (1994) Pyrimidine phosphorothioate oligonucleotides form triple-stranded helices and promote transcription inhibition. Nucleic Acids Res., 22, 3322-3330.
8. Tu,G.-C., Cao,Q.-N. and Isreal,Y. (1995) Inhibition of gene expression by triple helix formation in hepatoma cells. J. Biol. Chem., 270, 28402-28407.
9. Kim,H.-G., Reddoch,J.F., Mayfield,C., Ebbinghaus,S., Vigneswaran,N., Thomas,S., David E. Jones,J. and Miller,D.M. (1998) Inhibition of transcription of the human c-myc protooncogene by intermolecular triplex. Biochemistry, 37, 2299-2304.
10. Faria,M., Wood,C.D., Perrouault,L., Nelson,J.S., Winter,A., White,M.R., Helene,C. and Giovannangeli,C. (2000) Targeted inhibition of transcription elongation in cells mediated by triplex-forming oligonucleotides. Proc. Natl Acad. Sci. USA, 97, 3862-3867.
11. Intody,Z., Perkins,B.D., Wilson,J.H. and Wensel,T.G. (2000) Blocking transcription of the human rhodopsin gene by triplex-mediated DNA photocrosslinking. Nucleic Acids Res., 28, 4283-4290.
12. Liu,J., Xu,R.-H., Jin,Y.-X. and Wang,D.-B. (2001) Triplex targeting of human PDGF-B (c-sis, proto-oncogene) promoter specifically inhibits factors binding and PDGF-B transcription. Nucleic Acids Res., 29, 783-791.
13. Stutz,A.M., Hoeck,J., Natt,F., Cuenoud,B. and Woestschlager,M. (2001) Inhibition of interleukin-4 and CD40-induced IgE germline gene promoter activity by 2′-aminoethoxy-modified triplex-forming oligonucleotides. J. Biol. Chem., 276, 11759-11765.
14. McGuffie,E.M., Pacheco,D., Carbone,G.M.R. and Catapano,C.V. (2001) Antigene and antiproliferative effects of a c-myc-targeting phosphorothioate triple helix-forming oligonucleotide in human leukemia cells. Cancer Res., 60, 3790-3799.
15. Besch,R., Giovannangeli,C., Kammerbauer,C. and Degitz,K. (2002) Specific inhibition of ICAM-1 expression mediated by gene targeting with triplex-forming oligonucleotides. J. Biol. Chem., 277, 32473-32479.
16. Rapozzi,V., Cogoi,S., Spessotto,P., Risso,A., Bonora,G.M., Quadrifoglio,F. and Xodo,L.E. (2002) Antigene effect in k562 cells of a PEG-conjugated triplex-forming oligonucleotide targeted to the bcr/abl oncogene. Biochemistry, 41, 502-510.
17. 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.
18. Wang,G. and Glazer,P.M. (1995) Altered repair of targeted psoralen photoadducts in the context of an oligonucleotide-mediated triple helix. J. Biol. Chem., 270, 22595-22601.
19. Wang,G., Levy,D.D., Seidman,M.M. and Glazer,P.M. (1995) Targeted mutagenesis in mammalian cells mediated by intracellular triple helix formation. Mol. Cell Biol., 15, 1759-1768.
20. Wang,G., Seidman,M.M. and Glazer,P.M. (1996) Mutagenesis in mammalian cells induced by triple helix formation and transcription-coupled repair. Science, 271, 802-805.
21. Majumdar,A., Khorlin,A., Dyatkina,N., Lin,F., Powell,J., Liu,J., Fei,Z., Khripine,Y., Watanabe,K., George,J. et al. (1998) Targeted gene knockout mediated by triple helix forming oligonucleotides. Nature Genet., 20, 212-214.
22. Vasquez,K., Wang,G., Havre,P. and Glazer,P. (1999) Chromosomal mutations induced by triplex-forming oligonucleotides in mammalian cells. Nucleic Acids Res., 27, 1176-1181.
23. Barre,F.-X., Ait-Si-Ali,S., Giovannageli,C., Luis,R., Robin,P., Pritchard,L.L., Helene,C. and Harel-Bellan,A. (2000) Unambiguous demonstration of triple-helix-directed gene modification. Proc. Natl Acad. Sci. USA, 97, 3084-3088.
24. Vasquez,K.M., Narayanan,L. and Glazer,P.M. (2000) Specific mutations induced by triplex-forming oligonucleotides in mice. Science, 290, 530-533.
25. Puri,N., Majumdar,A., Cuenoud,B., Natt,F., Martin,P., Boyd,A., Miller,P.S. and Seidman,M.M. (2001) Targeted gene knockout by 2′-O-aminoethyl modified triplex forming oligonucleotides. J. Biol. Chem., 276, 28991-28998.
26. Majumdar,A., Puri,N., Cuenoud,B., Natt,F., Martin,P., Khorlin,A., Dyatkina,N., George,A.J., Miller,P.S. and Seidman,M.M. (2003) Cell cycle modulation of gene targeting by a triple helix forming oligonucleotide. J. Biol. Chem., 278, 11072-11077.
27. Radhakrishnan,I. and Patel,D.J. (1994) DNA triplexes: solution structures, hydration sites, energetics, interactions and function. Biochemistry, 33, 11405-11416.
28. Singleton,S.F. and Dervan,P.B. (1992) Influence of pH on the equilibrium association constants for oligodeoxyribonucleotide-directed triple helix formation at single DNA sites. Biochemistry, 31, 10995-11003.
29. Ono,A., Ts'o,P.O.P. and Kan,L.S. (1991) Triplex formation of oligonucleotides containing 2′-O-methylpesudoisocytidine in substitution for 2′-deoxycytidine. J. Am. Chem. Soc., 113, 4032-4033.
30. Ono,A., Ts'o,P. and Kan,L. (1992) Triplex formation of an oligonucleotide containing 2′-O-methylpseudoisocytidine with a DNA duplex at neutral pH. J. Org. Chem., 57, 3225-3230.
31. Ono,A., Ts'o,P. and Kan,L.-S. (1997) Triplex formation of an oligonucleotide containing 2′-O-methylpseudoisocytidine with single and double stranded nucleic acids at neutral pH. J. Chin. Chem. Soc., 44, 601-607.
32. Chin,T.M., Lin,S.B., Lee,S.Y., Chang,M.L., Cheng,A.Y., Chang,F.C., Paternack,L., Huang,D.H. and Kan,L.S. (2000) 'Paper-clip' type triple helix formation by 5′-d-(TC)3Ta(CT)3Cb(AG)3 (a and b = 0-4) as a function of loop size with and without the pseudoisocytosine base in the Hoogsteen strand. Biochemistry, 39, 12457-12464.
33. Xiang,G.B., Soussou,W. and McLaughlin,L.W. (1994) A new pyrimidine nucleoside (m(5ox)C) for the pH-independent recognition of G-C base pairs by oligonucleotide-directed triplex formation. J. Am. Chem. Soc., 116, 11155-11156.
34. Xiang,G., Bogacki,R. and McLaughlin,L.W. (1996) Use of a pyrimidine nucleoside that functions as a bidentate hydrogen bond donor for the recognition of isolated or contiguous G-C base pairs by oligonucleotide-directed triplex formation. Nucleic Acids Res., 24, 1963-1970.
35. Hildebrand,S., Blaser,A., Parel,S.P. and Leumann,C.J. (1997) 5-Substituted 2-aminopyridine C-nucleosides as protonated cytidine equivalents: increasing efficiency and selectivity in DNA triple-helix formation. J. Am. Chem. Soc., 119, 5499-5511.
36. Miller,P.S., Bhan,P., Cushman,C.D. and Trapane,T.L. (1992) Recognition of a guanine-cytosine base pair by 8-oxoadenine. Biochemistry, 31, 6788-6793.
37. Jetter,M.C. and Hobbs,F.W. (1993) 7,8-Dihydro-8-oxoadenine as a replacement for cytosine in the third strand of triple helices. Triplex formation without hypochromicity. Biochemistry, 32, 3249-3254.
38. Davison,E.C. and Johnsson,E. (1993) Triple helix binding of oligodeoxyribonucleotides containing 8-oxo-2′-deoxyadenosine. Nucl. Nucl., 12, 237-243.
39. Wang,Q., Tsukahara,S., Yamakawa,H., Takai,K. and Takaku,H. (1994) pH-independent inhibition of restriction endonuclease cleavage via triple helix formation by oligonucleotides containing 8-oxo-2′-deoxyadenosine. FEBS Lett., 355, 11-14.
40. Ishibashi,T., Yamakawa,H., Wang,Q., Tsukahara,S., Takai,K., Maryyama,T. and Takaku,H. (1995) Triple helix formation with oligodeoxyribonucleotides containing 8-oxo-2′-deoxyadenosine and 2′-modified nucleoside derivatives. Nucleic Acids Res. Symp. Ser., 34, 127-128.
41. Ishibashi,T., Yamakawa,H., Wang,Q., Tsukahara,S., Takai,K., Maruyama,T. and Takaku,H. (1996) Properties of triple helix formation with oligodeoxyribonucleotides containing 8-oxo-2′-deoxyadenosine and 2′-modified nucleoside derivatives. Bioorg. Med. Chem., 4, 2029-2034.
42. Tsukahara,S., Suzuki,J.,K.,U., Takai,K. and Takaku,H. (1996) Nonenzymatic sequence-specific cleavage of duplex DNA via triple-helix formation by homopyrimidine phosphorothioate oligonucleotides. Bioorg. Med. Chem., 4, 2219-2224.
43. Ushijima,K., Ishibashi,T., Yamakawa,H., Tsukahara,S., Takai,K., Maruyama,T. and Takaku,H. (1999) Inhibition of restriction endonuclease cleavage by triple helix formation with RNA and 2′-O-methyl RNA oligonucleotides containing 8-oxo-adenosine in place of cytidine. Biochemistry, 38, 6570-6575.
44. Miller,P.S., Bi,G., Kipp,S.A., Fok,V. and DeLong,R.K. (1996) Triplex formation by a psoralen-conjugated oligodeoxyribonucleotide containing the base analog 8-oxo-adenine. Nucleic Acids Res., 24, 730-736.
45. Lin,S.-B., Wu,C.-M., Lin,W.-C. and Kan,L.-S. (1999) The formation of triple stranded helix of oligodeoxyribonucleotides containing 8-oxo-2′-deoxyadenosine. J. Chin. Chem. Soc., 46, 693-697.
46. Cassidy,R., Kondo,N. and Miller,P. (2000) Triplex-formation by psoralen-conjugated chimeric oligonucleoside methylphosphonates. Biochemistry, 39, 8683-8691.
47. Miller,P.S. and Cushman,C.D. (1993) Triplex formation by oligodeoxyribonucleotides involving the formation of X UA triads. Biochemistry, 32, 2999-3004.
48. Ratner,L., Haseltine,W., Patarca,R., Livak,K.J., Starcich,B., Josephs,S.F., Doran,E.R., Rafalski,J.A., Whitchorn,E.A., Baumeister,K. et al. (1985) Complete nucleotide sequence of the AIDS virus, HTLV-III. Nature, 313, 277-284.
49. Shimizu,M., Konishi,A., Shimada,Y., Inoue,H. and Ohtsuka,E. (1992) Oligo(2′-O-methyl)ribonucleotides. Effective probes for duplex DNA. FEBS Left., 302, 155-158.
50. Mills,M., Arimondo,P.B., Lacroix,L., Garestier,T., Klump,H. and Mergny,J.-L. (2002) Chemical modification of the third strand: differential effects on purine and pyrimidine triple helix formation. Biochemistry, 41, 357-366.
51. Puri,N., Majumdar,A., Cuenoud,B., Natt,F., Martin,P., Boyd,A., Miller,P.S. and Seidman,M.M. (2002) Minimum number of 2′-O-(2-aminoethyl) residues required for gene knockout activity by triple helix forming oligonucleotides. Biochemistry, 41, 7716-7724.
52. Callahan,D.E., Trapane,T.L., Miller,P.S., Ts'o,P.O.P. and Kan,L.-S. (1991) Comparative circular dichroism and fluorescence studies of oligodeoxyribonucleotide and oligodeoxyribonucleoside methylphosphonate pyrimidine strands in duplex and triplex formation. Biochemistry, 30, 1650-1655.
53. Volker,J. and Klump,H.H. (1994) Electrostatic effects in DNA triple helices. Biochemistry, 33, 13502-13508.
54. Asensio,J.L., Lane,A.N., Dhesi,J., Bergqvist,S. and Brown,T. (1998) The contribution of cytosine protonation to the stability of parallel triple helices. J. Mol. Biol., 275, 811-822.
55. Lee,J.S., Woodsworth,M.L., Latimer,L.J.P. and Morgan,A.R. (1984) Poly(pyrimidine)-poly(purine) synthetic DNAs containing 5-methylcytosine form stable triplexes at neutral pH. Nucleic Acids Res., 12, 6603-6614.
56. Plum,G.E., Singleton,S.F., Dervan,P.B. and Breslauer,K.J. (1990) Thermodynamic characterization of the stability and the melting behavior of a DNA triplex: a spectroscopic and calorimetric study. Proc. Natl Acad. Sci. USA, 87, 9436-9440.
57. Xodo,L.E., Manzini,G., Quadrifoglio,F., van der Marel,G.A. and van Boom,J.H. (1991) Effect of 5-methylcytosine on the stability of triple-stranded DNA - a thermodynamic study. Nucleic Acids Res., 19, 5625-5631.
58. Leitner,D., Schroder,W. and Weisz,K. (2000) Influence of sequence-dependent cytosine protonation and methylation on DNA triplex stability. Biochemistry, 39, 5886-5892.
59. Wang,S. and Kool,E.T. (1995) Relative stabilities of triple helices composed of combinations of DNA, RNA and 2′-O-methyl-RNA backbones: chimeric circular oligonucleotides as probes. Nucleic Acids Res., 23, 1157-1164.
60. Asenio,J.L., Carr,R., Brown,T. and Lane,A.N. (1999) Conformational and thermodynamic properties of parallel intramolecular triple helices containing a DNA, RNA, or 2′-O-MeDNA third strand. J. Am. Chem. Soc., 121, 11063-11070.
61. Shimizu,M., Koizumi,T., Inoue,H. and Ohtsuka,E. (1994) Effects of 5-methyl substitution in 2′-O-methyl oligo-(pyrimidine)nucleotides on triple-helix formation. Bioorg. Med. Chem. Lett., 4, 1029-1032.
62. Wang,S., Xu,Y. and Kool,E.T. (1997) Recognition of RNA by triplex formation: divergent effects of pyrimidine C-5 methylation. Bioorg. Med. Chem., 5, 1043-1050.
63. Asensio,J.L., Lane,A.N., Dhesi,J., Bergqvist,S. and Brown,T. (1998) The Contribution of cytosine protonation to the stability of parallel DNA triple helices. J. Mol. Biol., 275, 811-812.
64. Powell,S.W., Jiang,L. and Russo,I.M. (2001) Proton exchange and base pair opening in a DNA triple helix. Biochemistry, 40, 11065-11072.
65. Tarkoy,M., Phipps,A.K., Schultze,P. and Feigon,J. (1998) Solution structure of an intramolecular DNA triplex linked by hexakis(ethylene glycol) units: d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-TCTCTCTT). Biochemistry, 37, 5810-5819.
66. Rhee,S., Han,Z.-j., Liu,K., Miles,H.T. and Davies,D.R. (1999) Structure of a triple helical DNA with a triplex-duplex junction. Biochemistry, 38, 16810-16815.