Site-resolved stabilization of a DNA triple helix by magnesium ions

Nucleic Acids Research

Volumn 32, Issue 3, 2004, Pages 878-883

  Coman, Daniel ^a   Russu, Irina M ^a  

^a WESLEYAN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CYTOSINE; DNA; DNA BASE; GUANINE; IMINE; MAGNESIUM ION; OLIGONUCLEOTIDE; SODIUM ION; THYMINE; DIVALENT CATION; MAGNESIUM; PROTON; TRIPLEX DNA;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; DNA CONFORMATION; DNA HELIX; DNA STRUCTURE; MOLECULAR STABILITY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTON TRANSPORT; STRUCTURE ANALYSIS; TRIPLE HELIX; CHEMISTRY; CONFORMATION; DRUG EFFECT; NUCLEAR MAGNETIC RESONANCE; NUCLEOTIDE SEQUENCE;

BASE PAIRING; BASE SEQUENCE; CATIONS, DIVALENT; DNA; MAGNESIUM; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; PROTONS;

EID: 2342641429     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh228     Document Type: Article

References (31)

1. Soyfer,V.N. and Potaman,V.N. (1995) Triple-Helical Nucleic Acids. Springer-Verlag, New York, NY.
2. Potaman,V.N. (2003) Applications of triple-stranded nucleic acid structures to DNA purification, detection and analysis. Expert Rev. Mol. Diagn., 3, 481-496.
3. Mirkin,S.M. and Frank-Kamenetskii,M.D. (1994) H-DNA and related structures. Annu. Rev. Biophys. Biomol. Struct., 23, 541-576.
4. Cheng,Y.-K. and Pettitt,B.M. (1992) Stabilities of double- and triple-strand helical nucleic acids. Prog. Biophys. Mol. Biol., 58, 225-257.
5. 3) triple helices. Nucleic Acids Res., 18, 5743-5750.
6. 12 sequences bridged by two hexaethylene glycol chains. Biochemistry, 31, 9197-9204.
7. Rougee,M., Faucon,B., Mergny,J.L., Barcelo,F., Giovannangeli,C., Garestier,T. and Helene,C. (1992) Kinetics and thermodynamics of triple-helix formation: effects of ionic strength and mismatches. Biochemistry, 31, 9269-9278.
8. Singleton,S.F. and Dervan,P.B. (1993) Equilibrium association constants for oligonucleotide-directed triple helix formation at single DNA sites: linkage to cation valence and concentration. Biochemistry, 32, 13171-13179.
9. Sugimoto,N., Wu,P., Hara,H. and Kawamoto,Y. (2001) pH and cation effects on the properties of parallel pyrimidine motif DNA triplexes. Biochemistry, 40, 9396-9405.
10. James,P.L., Brown,T. and Fox,K.R. (2003) Thermodynamic and kinetic stability of intermolecular triple helices containing different proportions of C+·GC and T·AT triplets. Nucleic Acids Res., 31, 5598-5606.
11. Bond,J.P., Anderson,C.F. and Record,M.T.J. (1994) Conformational transitions of duplex and triplex nucleic acid helices: thermodynamic analysis of effects of salt concentration on stability using preferential interaction coefficients. Biophys. J., 67, 825-836.
12. Record,M.T.,Jr, Zhang,W. and Anderson,C.F. (1998) Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects and osmotic effects of salts. Adv. Protein Chem., 51, 281-352.
13. Volker,J. and Klump,H.H. (1994) Electrostatic effects in DNA triple helices. Biochemistry, 33, 13502-13508.
14. 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, 811-822.
15. Leitner,D., Schroder,W. and Weisz,K. (2000) Influence of sequence-dependent cytosine protonation and methylation on DNA triplex stability. Biochemistry, 39, 5886-5892.
16. Coman,D. and Russu,I.M. (2002) Site-resolved energetics in DNA triple helices containing G.TA and T.CG triads. Biochemistry, 41, 4407-4414.
17. Cantor,C.R., Warshaw,M.M. and Shapiro,H. (1970) Oligonucleotide interactions. III. Circular dichroism studies of the conformation of deoxyoligonucleotides. Biopolymers, 9, 1059-1077.
18. Plateau,P. and Gueron,M. (1982) Exchangeable proton NMR without base-line distortion, using new strong-pulse sequences. J. Am. Chem. Soc., 104, 7310-7311.
19. Powell,S.W., Jiang,L. and Russu,I.M. (2001) Proton exchange and base-pair opening in a DNA triple helix. Biochemistry, 40, 11065-11072.
20. 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.
21. Englander,S.W. and Kallenbach,N.R. (1984) Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q. Rev. Biophys., 16, 521-655.
22. Gueron,M. and Leroy,J.L. (1995) Studies of base pair kinetics by NMR measurement of proton exchange. Methods Enzymol., 261, 383-413.
23. Cain,R.J. and Glick,G.D. (1998) Use of cross-links to study the conformational dynamics of triplex DNA. Biochemistry, 37, 1456-1464.
24. Benight,A.S., Schurr,J.M., Flynn,P.F., Reid,B.R. and Wemmer,D.E. (1988) Melting of a self-complementary DNA minicircle. Comparison of optical melting theory with exchange broadening of the nuclear magnetic resonance spectrum. J. Mol. Biol., 200, 377-399.
25. 2+ binding to RNA. Proc. Natl Acad. Sci. USA, 98, 12456-12461.
26. Sharp,K.A. and Honig,B. (1995) Salt effects on nucleic acids. Curr. Opin. Struct. Biol., 5, 323-328.
27. Plum,G.E. and Breslauer,K.J. (1995) Thermodynamics of an intramolecular DNA triple helix: a calorimetric and spectroscopic study of the pH and salt dependence of thermally induced structural transitions. J. Mol. Biol., 248, 679-695.
28. Roberts,R.W. and Crothers,D.M. (1996) Prediction of stability of DNA triplexes. Proc. Natl Acad. Sci. USA, 93, 4320-4325.
29. Wu,P., Kawamoto,Y., Hara,H. and Sugimoto,N. (2002) Effect of divalent cations and cytosine protonation on thermodynamic properties of intermolecular DNA double and triple helices. J. Inorg. Chem., 91, 277-285.
30. + base triplet stacks. J. Am. Chem. Soc., 124, 14355-14363.
31. Frank-Kamenetskii,M.D. and Mirkin,S.M. (1995) Triplex DNA structures. Annu. Rev. Biochem., 64, 65-95.