Stable recognition of TA interruptions by triplex forming oligonucleotides containing a novel nucleoside

Biochemistry

Volumn 44, Issue 15, 2005, Pages 5884-5892

  Wang, Yang ^a   Rusling, David A ^a   Powers, Vicki E C ^a   Lack, Oliver ^a,b   Osborne, Sadie D ^a,c   Fox, Keith R ^a   Brown, Tom ^a  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^b F HOFFMANN LA ROCHE LTD   (Switzerland)

^c UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ENZYMES; FLUORESCENCE; GAS CHROMATOGRAPHY; PH EFFECTS; ULTRAVIOLET RADIATION;

OLIGONUCLEOTIDES; OLIGOPURINE TRACT; STABLE TRIPLEX; UV MELTING;

BIOCHEMISTRY;

DNA BASE; DNA FRAGMENT; NUCLEOSIDE DERIVATIVE; OLIGONUCLEOTIDE; PHOSPHORAMIDOUS ACID DERIVATIVE; PURINE DERIVATIVE;

ARTICLE; BASE PAIRING; BINDING AFFINITY; COMPLEX FORMATION; MOLECULAR RECOGNITION; MOLECULAR STABILITY; NUCLEOTIDE SEQUENCE; PH; PRIORITY JOURNAL; SYNTHESIS; TEMPERATURE SENSITIVITY; THERMOSTABILITY;

BASE SEQUENCE; DEOXYRIBONUCLEASE I; DEOXYRIBONUCLEOTIDES; DNA FOOTPRINTING; HYDROGEN-ION CONCENTRATION; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; OLIGODEOXYRIBONUCLEOTIDES; SPECTROMETRY, FLUORESCENCE; SPECTROPHOTOMETRY, ULTRAVIOLET; THIONUCLEOTIDES;

EID: 17144377878     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi050013v     Document Type: Article

References (45)

1. Hélène, C., and Toulmé, J. (1990) Specific regulation of gene expression by antisense, sense, and antigene nucleic acids, Biochim. Biophys. Acta 1049, 99-125.
2. Fox, K. R. (2000) Targeting DNA with triplexes, Curr. Med. Chem. 7, 7-17.
3. Buchini, S., and Leuman, C. J. (2003) Recent improvements in antigene technology, Curr. Opin. Chem. Biol. 7, 717-726.
4. Seidman, M. M., and Glazer, P. (2003) The potential for gene repair via triple helix formation, J. Clin. Invest. 112, 487-494.
5. Felsenfield, G., Davies, R., and Rich, A. (1957) Formation of a three stranded polynucleotide molecule, J. Am. Chem. Soc. 79, 2023-2024.
6. Gowers, D. M., and Fox, K. R (1999) Towards mixed sequence recognition by triple helix formation, Nucleic Acids Res. 27, 1569-1577.
7. Griffin, L., and Dervan, P. (1989) Recognition of thymine.adenine base pairs by guanine in a pyrimidine triple helix motif, Science 245, 967-971.
8. Fossella, A., Kim, Y. J., Shih, H., Richards, E. G., and Fresco, J. R. (1993) Relative specificities in binding of Watson-Crick base pairs by third strand residues in a DNA pyrimidine triplex motif, Nucleic Acids Res. 21, 4511-4515.
9. Radhakrishnan, I., and Patel, D. J. (1994) Solution structure of a pyrimidine.purine.pyrimidine DNA triplex containing T.AT, C.GC, and G.TA triples, Structure 15, 17-32.
10. Gowers, D. M., and Fox, K. (1997) DNA triple helix formation at oligopurine sites containing multiple contiguous pyrimidines, Nucleic Acids Res. 25, 3787-3794.
11. Soto, M., and Marky, L. A. (2002) Thermodynamic contributions for the incorporation of GTA triplets within canonical TAT/TAT and CGC/CGC base-triplet stacks of DNA triplexes, Biochemistry 41, 12475-12482.
12. Jiang, L., and Russu, I. M. (2001) Proton exchange and local stability in a DNA triple helix containing a G.TA triad, Nucleic Acids Res. 29, 4231-4237.
13. Griffin, L. C., Kiessling, L. L., Seal, P. A., Gillespie, P., and Dervan, P. (1992) Recognition of all four base pairs of double helical DNA by triple helix formation, J. Am. Chem. Soc. 114, 7976-7982.
14. 3 incorporated in an intramolecular DNA triplex binds sequence specifically by intercalation, J. Am. Chem. Soc. 115, 7908-7909.
15. 3, J. Mol. Biol. 257, 1057-1069.
16. Mokhir, A. A., Connors, W. H., and Richert, C. (2001) Synthesis and monitored selection of nucleotide surrogates for binding T:A base pairs in homopurine-homopyrimidine DNA triple helices, Nucleic Acids Res. 29, 3674-3684.
17. Eldrup, A. B., and Nielson, P. E. (1997) A novel peptide nucleic acid monomer for recognition of thymine in triple-helix structures, J. Am. Chem. Soc. 119, 11116-11117.
18. Olsen, A., Dahl, O., and Nielsen, P. E. (2004) Synthesis and evaluation of a conformationally constrained pyridazinone PNA-monomer for recognition of thymine in triple-helix structures, Bioorg. Med. Chem. Lett. 22, 1551-1554.
19. Li, J. S., Fan, Y., Zhang, Y., Marky, L. A., and Gold, B. (2003) Design of triple helix forming C-glycoside molecules, J. Am. Chem. Soc. 125, 2084-2093.
20. Li, J. S., Shikiya, R., Marky, L. A., and Gold, B. (2004) Triple helix forming TRIPside molecules that target mixed purine/pyrimidine DNA sequences, Biochemistry 43, 1440-1448.
21. Sasaki, S., Taniguchi, Y., Takahashi, R., Senko, Y., Kodama, K., Nagatsugi, F., and Maeda, M. (2004) Selective formation of stable triplexes including a TA or a CG interrupting site with new bicyclic nucleoside analogues (WNA), J. Am. Chem. Soc. 126, 516-528.
22. Sollogoub, M., Darby, R. A. J., Cuenoud, B., Brown, T., and Fox, K. (2002) Stable DNA triple helix formation using oligonucleotides containing 2′-aminoethoxy,5-propargylamino-U, Biochemistry 41, 7224-7231.
23. Osborne, S. D., Powers, V. E. C., Rusling, D. A., Lack, O., Fox, K. R., and Brown, T. (2004) Selectivity and affinity of triplex-forming oligonucleotides containing 2′-aminoethoxy-5-(3-amino-prop-1-ynyl)uridine for recognising AT base pairs in duplex DNA, Nucleic Acids Res. 32, 4439-4447.
24. Blommers, M. J. J., Natt, F., Jahnke, W., and Cuenoud, B. (1998) Dual recognition of double stranded DNA by 2′-aminoethoxy-modified oligonucleotides: The solution structure of an intramolecular triplex obtained by NMR spectroscopy, Biochemistry 37, 17714-17725.
25. Cuenoud, B., Casset, F., Husken, D., Natt, F., Wolf, R. W., Altmann, K., Martin, P., and Moser, H. E. (1998) Dual recognition of double-stranded DNA by 2′-aminoethoxy-modified oligonucleotides, Angew. Chem., Int. Ed. 37, 1288-1291.
26. Puri, N., Majumdar, A., Cuenoud, B., Miller, P. S., and Seidman, M. M. (2004) Importance of clustered 2′-O-(2-aminoethyl) residues for gene targeting activity of triple helix formation, Biochemistry 43, 1343-1351.
27. Buchini, S., and Leumann, C. J. (2003) Dual recognition of a C-G pyrimidine-purine inversion site: Synthesis and binding properties of triplex-forming oligonucleotides containing 2′-aminoethoxy-5-methyl-H1- pyrimidin-2-one ribonucleosides, Tetrahedron Lett. 44, 5065-5068.
28. Buchini, S., and Leumann, C. J. (2004) Stable and selective recognition of three base pairs in the parallel triple-helical DNA binding motif, Angew. Chem., Int. Ed. 43, 3925-3928.
29. Guinvarc'h, D., Fourrey, J., Maurisse, R., Sun, J., and Benhida, R. (2001) Incorporation of a novel nucleobase allows stable oligonucleotide- directed triple helix formation at the target sequence containing a purine.pyrimidine interruption, Chem. Commun. 1814-1815.
30. Guinvarc'h, D., Fourrey, J., Maurisse, R., Sun, J., and Benhida, R. (2002) Synthesis, incorporation into triplex forming oligonucleotide, and binding properties of a novel 2′-deoxy-C-nucleoside featuring a 6-(thiazolyl-5)-benzimidazole nucleobase, Org. Lett. 4, 4209-4212.
31. Guinvarc'h, D., Fourrey, J., Maurisse, R., Sun, J., and Benhida, R. (2003) Design of nucleobase for the recognition of the AT inversion by triplex-forming oligonucleotides; a structure-stability relationship study and neighbour bases effects, Biorg. Med. Chem. 11, 2751-2759.
32. Reese, C. B., and Wu, Q. (2003) Conversion of 2-deoxy-D-ribose into 2-amino-5-(2-deoxy-β-D-ribofuanosyl)pyridine, 2′-deoxyp-seudouridine, and other C-(2-deoxyribonucleosides), Org. Biomol. Chem. 1, 3160-3172.
33. Markiewicz, W. T., Padyukova, N. S., Samek, Z., and Smrt, J. (1980) The reaction of 1,3-dichloro-1,1,3,3-tetraisopropyldisiloxane with cytosine arabinoside and 1-(6-deoxy-a-L-talofuranosyl)-uracil, Collect. Czech Chem. Commun. 40, 1869-1865.
34. Mitsunobo, O. (1981) The use of diethyl azodicarboxylate and triphenylphosphine in synthesis and transformation of natural-products, Synthesis 1, 1-14.
35. Kume, A., Sekine, M., and Hata, T. (1982) Phthaloyl group: A new amino protecting group of deoxyadenosine in oligonucleotide synthesis, Tetrahedron Lett. 23, 4365-4368.
36. Hovinen, J., and Salo, H. (1997) C-glycoside phosphoramidate building block for versatile functionalization of oligodeoxyribo-nucleotides, J. Chem. Soc., Perkin Trans, 1, 3017-3020.
37. Langley, G. J., Herniman, J. M., Davies, N. L., and Brown T. (1999) Simplified sample preparation for the analysis of oligonucleotide by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry, Rapid Commun. Mass Spectrom. 13, 1717-1723.
38. Darby, R. A. J., Sollogoub, M., McKeen, C., Brown, L., Risitano, A., Brown, N. M., Barton, C., Brown, T., and Fox, K. R. (2002) High throughput measurement of duplex, triplex, and quadruplex melting curves using molecular beacons and a LightCycler, Nucleic Acids Res. 30, e39.
39. +.GC and T.AT triplets, Nucleic Acids Res. 31, 5598-5506.
40. Brown, P. M., Madden, C. A., and Fox, K. R. (1998) Triple helix formation at different positions on nucleosomal DNA, Biochemistry 37, 16139-16151.
41. Dabrowiak, J. C., and Goodisman, J. (1989) Quantitative foot-printing analysis of drug-DNA interactions, in Chemistry and Physics of DNA - Ligand Interactions (Kallenbach, N. R., Ed.) pp 143-174, Adenine Press, New York.
42. Yoon, K., Hobbs, C. A., Koch, J., Sardaro, M., Kutny, R., and Weis, A. L. (1992). Elucidation of the sequence-specific third strand recognition of four Watson-Crick base pairs in a pyrimidine triple helix motif: T.AT, C.GC, G.TA, and T.CG, Proc. Natl. Acad. Sci. U.S.A. 89, 3840-3844.
43. 8, FEBS Lett. 332, 189-192.
44. Fosella, A., Kim, Y. J., Shih, H., Richards, E. G., and Fresco, J. R. (1993) Relative specificities in binding of Watson-Crick base pairs by third strand residues in a DNA pyrimidine triplex motif, Nucleic Acids Res. 21, 4511-4515.
45. Bernal-Méndez, C., and Leumann, C. J. (2002) Stability and kinetics of nucleic acid triplexes with chimaeric DNA/RNA third strands, Biochemistry 41, 12343-12340.