On the stability of peptide nucleic acid duplexes in the presence of organic solvents

Nucleic Acids Research

Volumn 35, Issue 10, 2007, Pages 3367-3374

  Sen, Anjana ^a   Nielsen, Peter E ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

DIOXANE; DNA; N,N DIMETHYLFORMAMIDE; ORGANIC SOLVENT; PEPTIDE NUCLEIC ACID; THYMINE; 1,4-DIOXANE; DIOXANE DERIVATIVE; SOLVENT; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; DIELECTRIC CONSTANT; HYDRATION; MATHEMATICAL COMPUTING; MELTING POINT; MOLECULAR INTERACTION; MOLECULAR STABILITY; PRIORITY JOURNAL; THERMODYNAMICS; THERMOSTABILITY; ULTRAVIOLET SPECTROPHOTOMETRY; BASE MISPAIRING; CHEMISTRY; DNA DENATURATION;

BASE PAIR MISMATCH; DIMETHYLFORMAMIDE; DIOXANES; DNA; NUCLEIC ACID DENATURATION; PEPTIDE NUCLEIC ACIDS; SOLVENTS; THERMODYNAMICS; THYMINE;

EID: 34250878985     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm210     Document Type: Article

References (44)

1. Watson,J.D. and Crick,F.H. (1953) Genetical implications of the structure of deoxyribonucleic acid. Nature, 171, 964-967.
2. Saenger,W. (1988) Principles of Nucleic acid Structure. Springer, New York.
3. Kool,E.T. (2001) Hydrogen bonding, base stacking, and steric effects in DNA replication. Annu. Rev. Biophys. Biomol. Struct., 30, 1-22.
4. Oostenbrink,C. and van Gunsteren,W.F. (2005) Efficient calculation of many stacking and pairing free energies in DNA from a few molecular dynamics simulations. Chemistry, 11, 4340-4348.
5. Sundaralingam,M. and Ponnuswamy,P.K. (2004) Stability of DNA duplexes with Watson-Crick base pairs: A predicted model. Biochemistry, 43, 16467-16476.
6. Protozanove,E., Yakovchuk,P. and Frank-Kamenetskii,M.D. (2004) Stacked-unstacked equilibrium at the nick site of DNA. J. Mol. Biol. 342, 775-785.
7. Yakovchuk,P., Protozanove,E. and Frank-Kamenetskii,M.D. (2006) Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic. Acids Res., 34, 564-574.
8. Miller,P.S, Yano,J., Yano,E., Carroll,C., Jayaraman,K. and Ts'o,P.O. (1979) Nonionic nucleic acid analogues. Synthesis and characterization of dideoxyribonucleoside methylphosphonates. Biochemistry, 18 5134-5143.
9. Tosquellas,G., Alvarez,K., Dell'Aquila,C., Morvan,F., Vasseur,J-J., Imbach,J-L. and Rayner,B. (1998) The pro-oligonucleotide approach: Solid phase synthesis and preliminary evaluation of model pro-dodecathymidylates. Nucleic Acids Res., 26, 2069-2074.
10. Summerton,J. (1999) Morpholino antisense oligomers: The case for an RNase H-independent structural type. Biochim. Biophys. Acta, 1489, 141-158.
11. Nielsen,P.E., Egholm,M., Berg,R.H. and Buchardt,O. (1991) Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science, 254, 1497-1500.
12. Nielsen,P.E. (1999) Peptide nucleic acid. A molecule with two identities. Acc. Chem. Res., 32, 624-630.
13. Egholm,M., Buchardt,O., Christensen,L., Behrens,C., Freier,S.M., Driver,D.A. et al. (1993) PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules. Nature, 365, 566-568.
14. Wittung,P., Nielsen,P.E., Buchardt,O., Egholm,M. and Nordén,B. (1994) DNA-like double helix formed by peptide nucleic acid. Nature, 368, 561-563.
15. Jensen,K.K., Ørum,H., Nielsen,P.E. and Nordén,B. (1997) Kinetics for hybridization of peptide nucleic acids (PNA) with DNA and RNA studied with the BIAcore technique. Biochemistry, 36, 5072-5077.
16. Brown,S.C., Thomson,S.A., Veal,J.M. and Davis,D.G. (1994) NMR solution structure of a peptide nucleic acid complexed with RNA. Science, 265, 777-780.
17. Eriksson,M. and Nielsen,P.E. (1996) Solution structure of a peptide nucleic acid-DNA duplex. Nature Struct. Biol., 3, 410-413.
18. Rasmussen,H., Kastrup,J.S., Nielsen,J.N., Nielsen,J.M. and Nielsen,P.E. (1997) Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7A resolution. Nature Struct. Biol., 4, 98-101.
19. Sen,A. and Nielsen,P.E. (2006) Unique properties of purine/pyrimidine asymmetric PNA.DNA duplexes: Differential stabilization of PNA.DNA duplexes by purines in the PNA strand. Biophys. J., 90, 1329-1337.
20. Christensen,L., Fitzpatrick,R., Gildea,B., Petersen,K., Hansen,H.F., Koch,T., Egholm,M., Buchardt,O., Nielsen,P.E. et al. (1995) Solid-phase synthesis of peptide nucleic acids. J. Pept. Sci., 1, 175-183.
21. Peyret,N., Seneviratne,P.A., Allawi,H.T. and SantaLucia,J.Jr (1999) Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches. Biochemistry, 38, 3468-3477.
22. Eldrup,A., Nielsen,B.B., Haaima,G., Rasmussen,H., Kastrup,J.S., Christensen,C. and Nielsen,P.E. (2001) 1,8-Naphthyridin-2(1H)-ones - novel bicyclic and tricyclic analogues of thymine in peptide nucleic acids (PNAs). Eur. J. Org. Chem., 9, 1781-1790.
23. Patel,D.J., Shapiro,L. and Hare,D. (1987). In Eckstein,F. and Lilley,D.M.J. (eds), In Nucleic acid and Molecular Biology. Springer, Berlin, pp. 70-84.
24. Germann,M.W., Kalisch,B.W., Varnum,J.M., Vogel,H.J. and van de Sande,J.H. (1998) NMR spectroscopic and enzymatic studies of DNA hairpins containing mismatches in the EcoRI recognition site. Biochem. Cell Biol., 76, 391-402.
25. Allawi,H.T. and SantaLucia,J.Jr (1998) Thermodynamics of internal C.T mismatches in DNA. Nucleic. Acids Res., 26, 2694-2701.
26. Boulard,Y., Cognet,J.A.H. and Fazakerley,G.V. (1997) Solution structure as a function of pH of two central mismatches, C.T and C.C, in the 29 to 39 K-ras gene sequence, by nuclear magnetic resonance and molecular dynamics. J. Mol. Biol., 268, 331-347.
27. Nemecek,D., Stepanek,J., Turpin,P.Y. and Rosenberg,I. (2004) Raman study of potential 'antisense' drugs: Nonamer oligonucleotide duplexes with a central mismatch as a model system for the binding selectivity evaluation. Biopolymers, 74, 115-119.
28. Hunter,W.N., Brown,T., Kneale,G., Anand,N.N., Rabinovich,D. and Kennard,O. (1987) The structure of guanosine-thymidine mismatches in B-DNA at 2.5-A resolution. J. Biol. Chem., 262, 9962-9970.
29. Ke,S.-H. and Wartell,R.M. (1996) The thermal stability of DNA fragments with tandem mismatches at a d(CXYG).d(CY′X′G) site. Nucleic. Acids Res., 24, 707-712.
30. Gervais,V., Cognet,J.A., Le Bret,M.L., Sowers,C. and Fazakerley,G.V. (1995) Solution structure of two mismatches A.A and T.T in the K-ras gene context by nuclear magnetic resonance and molecular dynamics. Eur. J. Biochem., 228, 279-290.
31. Guckian,K.M., Schweitzer,B.A., Ren,R.X-F., Sheils,C.J., Tahmassebi,D.C. and Kool,E.T. (2000) Factors contributing to aromatic stacking in water: Evaluation in the context of DNA. J. Am. Chem. Soc., 122, 2213-2222.
32. Kim,T.W. and Kool,E.T. (2005) A series of nonpolar thymidine analogs of increasing size: DNA base pairing and stacking properties. J. Org. Chem., 70, 2048-2053.
33. 7p. Biochemistry, 24, 2086-2094.
34. Hutton,J.R. (1977) Renaturation kinetics and thermal stability of DNA in aqueous solutions of formamide and urea. Nucleic. Acids Res., 4 3537-3555.
35. Blake,R.D. and Delcourt,S.G. (1996) Thermodynamic effects of formamide on DNA stability. Nucleic. Acids Res., 24, 2095-2103.
36. Püschl,A., Sforza,S., Haaima,G., Dahl,O. and Nielsen,P.E. (1998) Peptide nucleic acids (PNAs) with a functional backbone. Tetrahedron Lett., 39, 4707-4710.
37. Schuster,G.B. (2004) In Long-Range Charge Transfer in DNA I-II. Springer, Heidelberg.
38. Delaney,S. and Barton,J.K. (2003) Long-range DNA charge transport. J. Org. Chem., 68, 6475-6483.
39. Fink,H.W. and Schonenberger,C. (1999) Electrical conduction through DNA molecules. Nature, 398, 407-410.
40. Wan,C., Fiebig,T., Schiemann,O., Barton,J.K. and Zewail,A.H. (2000) Femtosecond direct observation of charge transfer between bases in DNA. Proc. Natl Acad. Sci. USA, 97, 14052-14055.
41. Shao,F., Augustyn,K. and Barton,J.K. (2005) Sequence dependence of charge transport through DNA domains. J. Am. Chem. Soc., 127 17445-17452.
42. Armitage,B., Ly,D., Koch,T., Frydenlund,H., Orum,H., Batz,H.G. and Schuster,G.B. (1997) Peptide nucleic acid-DNA duplexes: Long range hole migration from an internally linked anthraquinone. Proc. Natl Acad. Sci. USA, 94, 12320-12325.
43. Tanabe,K., Yoshida,K., Dohno,C., Okamoto,A. and Saito,I. (2000) Control of electron transfer in DNA by peptide nucleic acids (PNA). Nucleic Acids Symp. Ser., 44, 35-36.
44. Gertner,Z.J., Tse,B.N., Grubina,R., Doyon,J.B., Snyder,T.M. and Liu,D.R. (2004) DNA-templated organic synthesis and selection of a library of macrocycles. Science, 305, 1601-1605.