Selectivity and affinity of triplex-forming oligonucleotides containing 2′-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine for recognizing AT base pairs in duplex DNA

Nucleic Acids Research

Volumn 32, Issue 15, 2004, Pages 4439-4447

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

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^b UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

2' AMINOETHOXY 5 (3 AMINOPROP 1 YNYL)URIDINE; DEOXYRIBONUCLEASE I; DNA FRAGMENT; DOUBLE STRANDED DNA; OLIGONUCLEOTIDE; UNCLASSIFIED DRUG; URIDINE DERIVATIVE; 2'-AMINOETHOXY-5-(3-AMINOPROP-1-YNYL)URIDINE; ADENINE; DNA; DRUG DERIVATIVE; OLIGODEOXYRIBONUCLEOTIDE; THYMINE; TRIPLEX DNA; URIDINE;

AMINO ACID SUBSTITUTION; ARTICLE; BASE PAIRING; CHEMICAL STRUCTURE; CIRCULAR DICHROISM; CONTROLLED STUDY; DNA BINDING; DNA DENATURATION; DNA FOOTPRINTING; DNA SEQUENCE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; CHEMISTRY; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SPECTROFLUOROMETRY; ULTRAVIOLET SPECTROPHOTOMETRY;

ADENINE; BASE PAIRING; BASE SEQUENCE; CIRCULAR DICHROISM; DEOXYRIBONUCLEASE I; DNA; DNA FOOTPRINTING; MOLECULAR SEQUENCE DATA; OLIGODEOXYRIBONUCLEOTIDES; SPECTROMETRY, FLUORESCENCE; SPECTROPHOTOMETRY, ULTRAVIOLET; THYMINE; URIDINE;

EID: 4243150790     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh776     Document Type: Article

References (40)

1. Chan,P.P. and Glazer,P.M. (1997) Triplex DNA: fundamentals, advances and potential applications for gene therapy. J. Mol. Med., 75, 267-282.
2. Gorman,L. and Glazer,P.M. (2001) Directed gene modification by triple helix formation. Curr. Mol. Med., 1, 391-399.
3. Praseuth,D., Guieysse,A.L. and Hélène,C.,(1999) Triple helix formation and the antigene strategy for sequence-specific control of gene expression. Biochim. Biophys. Acta, 1489, 181-206.
4. Neidle,S. (1997) Recent developments in triple-helix regulation of gene expression. Anticancer Drug Des., 12, 433-442.
5. Vasquez,K.M. and Wilson,J.H. (1998) Triplex-directed modification of genes and gene activity. Trends Biochem. Sci., 23, 4-9.
6. Knauert,M.P. and Glazer,P.M. (2001) Triplex forming oligonucleotides: sequence-specific tools for gene targeting. Hum. Mol. Gen., 10, 2243-2251.
7. Thuong,N.T. and Hélène,C. (1993) Sequence specific recognition and modification of double helical DNA by oligonucleotides. Angew. Chem. Int. Ed. Engl., 32, 666-690.
8. Soyfer,V.N. and Potoman,V.N. (1996) Triple-Helical Nucleic Acids. Springer-Verlag, New York.
9. Fox,K.R. (2000) Targeting DNA with triplexes. Curr. Med. Chem., 7, 17-37.
10. Gowers,D.M. and Fox,K.R. (1999) Towards mixed sequence recognition by triple helix formation. Nucleic Acids Res., 27, 1569-1577.
11. Asensio,J.L., Lane,A.N., Dhesi,J., Bergvist,S. and Brown,T. (1998) The contribution of cytosine protonation to the stability of parallel DNA triple helices. J. Mol. Biol., 275, 811-822.
12. Völker,J. and Klump,H.K. (1994) Electrostatic effects in DNA triple helices. Biochemistry, 33, 13502-13508.
13. +.GC triplets. Nucleic Acids Res., 25, 4644-4649.
14. + base triplet stacks. J. Am. Chem. Soc., 124, 14355-14363.
15. Roberts,R.W. and Crother,D.M. (1996) Prediction of the stability of DNA triplexes. Proc. Natl Acad. Sci. USA, 93, 4320-4325.
16. +.GC and T.AT triplets. Nucleic Acids Res., 31, 5598-5606.
17. Hampel,K.J., Crosson,P. and Lee,J.S. (1991) Polyamines favour DNA triplex formation at neutral pH. Biochemistry, 30, 4455-4459.
18. Thomas,T. and Thomas,T.J. (1993) Selectivity of polyamines in triplex DNA stabilization. Biochemistry, 32, 14068-14074.
19. 4 with spermine and tetraethyleneoxyamine. Nucleic Acids Res., 25, 4187-4193.
20. Roig,V. and Asseline,U. (2003) Oligo-2′-deoxyribonucleotides containing uracil modified at the 5-position with linkers ending with guanidinium groups. J. Am. Chem. Soc., 125, 4416-4417.
21. p): a novel thymidine analogue for generating DNA triplexes with increased stability. Nucleic Acids Res., 27, 1802-1809.
22. 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.
23. Cuenoud,B., Casset,F., Husken,D., Natt,F., Wolf,R.M., Altmann,K.-H., 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.
24. Sollogoub,M., Darby,R.A.J., Cuenoud,B., Brown,T. and Fox,K.R. (2002) Stable DNA triple helix formation using oligonucleotides containing 2′-aminoethoxy,5-propargylamino-U. Biochemistry, 41, 7224-7231.
25. Sollogoub,M., Dominguez,B., Fox,K.R. and Brown,T. (2000) Synthesis of a novel bis-amino-modified thymidine monomer for use in DNA triplex stabilisation. Chem. Commun., 2315-2316.
26. 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-α-L-talofuranosyl)uracil. Coll. Czech Chem. Commun., 40, 1860-1865.
27. Mitsunobu,O. (1981) The use of diethyl azodicarboxylate and triphenylphosphine in synthesis and transformation of natural-products. Synthesis, 1, 1-28.
28. 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.
29. Vorbruggen,H., Krolikiewicz,K. and Bennua,B. (1981) Nucleoside syntheses. 22. Nucleoside synthesis with trimethylsilyl triflate and perchlorate as catalysts. Chem. Ber. Recl., 114, 1234-1255.
30. Cruickshank,K.A. and Stockwell,D.L. (1988) Oligonucleotide labelling: a concise synthesis of a modified thymidine phosphoramidite. Tetrahedron Lett., 29, 5221-5224.
31. Hobbs,F.W. (1989) Palladium-catalyzed synthesis of alkynylamino nucleosides - a universal linker for nucleic-acids. J. Org. Chem., 54, 3420-3422.
32. Takahashi,S., Kuroyama,K., Sonogashira,N. and Hagihara,N. (1980) A convenient synthesis of ethynylarenes and diethynylarenes. Synthesis, 627-630.
33. Langley,G.J., Herniman,J.M., Davies,N.L. and Brown,T. (1999) Simplified sample preparation for the analysis of oligonucleotides by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom., 13, 1717-1723.
34. Darby,R.A.J., Sollogoub,M., McKeen,C., Brown,L., Risitano,A., Brown,N., 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.
35. Brown,P.M., Madden,C.A. and Fox,K.R. (1998) Triple helix formation at different positions on nucleosomal DNA. Biochemistry, 37, 16139-16151.
36. Dabrowiak,J.C. and Goodisman,J. (1989) Quantitative footprinting analysis of drug-DNA interactions. In: Kallenbach,N.R. (ed.), Chemistry and Physics of DNA-Ligand Interactions. Adenine Press, NY, pp.143-174.
37. 2 by two-dimensional NMR and simulated annealing. Biochemistry, 35, 14077-14089.
38. Gralla,J. and Crothers,D.M. (1973) Free energy of imperfect nucleic acid helices. III. Small internal loops resulting from mismatches. J. Mol. Biol., 78, 301-319.
39. Gray,D.M., Hung,S.-H. and Johnson,K.H. (1995) Absorption and circular dichroism spectroscopy of nucleic acid duplexes and triplexes. Meth. Enzymol., 246, 19-34.
40. Gray,D.M., Morgan,A.R. and Ratliff,R.L. (1978) A comparison of the circular dichroism spectra of synthetic DNA sequences of the homopurine homopyrimidine and mixed purine-pyrimidine types. Nucleic Acids Res., 5, 3679-3695.