Thermodynamic dependence of DNA/DNA and DNA/RNA hybridization reactions on temperature and ionic strength

Biophysical Chemistry

Volumn 131, Issue 1-3, 2007, Pages 96-104

  Lang, Brian E ^a   Schwarz, Frederick P ^a  

^a NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

Author keywords

DNA DNA binding; DNA RNA hybridization; Thermodynamics

Indexed keywords

OLIGONUCLEOTIDE; SODIUM CHLORIDE;

ARTICLE; DIFFERENTIAL SCANNING CALORIMETRY; DNA HYBRIDIZATION; DNA STRAND; HYDROGEN BOND; IONIC STRENGTH; ISOTHERMAL TITRATION CALORIMETRY; MELTING POINT; PRIORITY JOURNAL; RNA HYBRIDIZATION; TEMPERATURE SENSITIVITY; THERMODYNAMICS;

BASE SEQUENCE; CALORIMETRY; DNA, COMPLEMENTARY; NUCLEIC ACID HYBRIDIZATION; OSMOLAR CONCENTRATION; RNA; THERMODYNAMICS; TRANSITION TEMPERATURE;

EID: 35648938629     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2007.09.007     Document Type: Article

References (27)

1. Gray D.M. Derivation of nearest-neighbor properties from data on nucleic acid oligomers. II. Thermodynamic parameters of DNA-RNA hybrids and DNA duplexes. Biopolymers 42 (1997) 795-810
2. Kallansrud G., and Ward B. A comparison of measured and calculated single- and double-stranded oligodeoxynucleotide extinction coefficients. Analytical Biochemistry 236 (1996) 134-138
3. SantaLucia Jr. J., Allawi H.T., and Seneviratne P.A. Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35 (1996) 3555-3562
4. Sugimoto N., Nakano S.-i., Misa K., Matsumura A., Nakamuta H., Ohmichi T., Yoneyama M., and Sasaki M. Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry 34 (1995) 11211-11216
5. Henderson J.T., Benight A.S., and Hanlon S. A semi-micro method for the determination of the extinction coefficients of duplex and single-stranded DNA. Analytical Biochemistry 201 (1992) 17-29
6. Freier S., Kierzek M.R., Jaeger J.A., Sugimoto N., Caruthers M.H., Neilson T., and Turner D.H. Improved free-energy parameters for predictions of RNA duplex stability. Proceedings of the National Academy of Sciences of the United States of America 83 (1986) 9373-9377
7. Breslauer K.J., Frank R., Blöcker H., and Marky L.A. Predicting DNA duplex stability. Proceedings of the National Academy of Sciences 83 (1986) 3746-3750
8. SantaLucia Jr. J. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest neighbor thermodynamics. Proceedings of the National Academy of Sciences 95 (1998) 1460-1465
9. Xia T., SantaLucia Jr. J., Burkard M.E., Kierzek R., Schroeder S.J., Jiao X., Cox C., and Turner D.H. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 37 (1998) 14719-14735
10. Zhou J., Gregurick S.K., Krueger S., and Schwarz F.P. Conformational changes in single strand DNA as a function of temperature by SANS. Biopolymers 81 (2006) 235-248
11. Owczarzy R., Dunietz I., Behlke M.A., Klotz I.M., and Walder J.A. Thermodynamic treatment of oligonucleotide duplex simplex equilibria. Proceedings of the National Academy of Sciences of the United States of America 100 (2003) 14840-14845
12. Cavaluzzi M.J., and Borer P.N. Revised UV extinction coefficients for nucleoside-5'-monophosphates and unpaired DNA and RNA. Nucleic Acids Research 32 (2004) e13
13. Wiseman T., Williston S., Brandts J.F., and Lin L.-N. Rapid measurement of binding constants and heats of binding using a new titration calorimeter. Analytical Biochemistry 179 (1989) 131-137
14. Schwarz F.P., Robinson S., and Butler J.M. Thermodynamic comparison of PNA/DNA and DNA/DNA hybridizations at ambient temperature. Nucleic Acids Research 27 (1999) 4792-4800
15. Kirchhoff W.H. Exam: a two-state thermodynamic analysis program. (NIST Technical Note 1401. NIST (1993), US Government Printing Office, Washington, DC 1-103
16. Pardi A., Martin F., and Tinoco Jr. I. Comparative study of riboncleotides, deoxyribonucleotide, and hybrid oligonucleotide helices by nuclear magnetic resonance. Biochemistry 20 (1981) 3986-3996
17. Walker G.T. Deoxycytidine methylation does not affect DNA RNA hybrid formation or B-A transitions of (dG)n(dC)n sequences. Nucleic acids Research 16 (1988) 3091-3099
18. Mikulecky P.J., and Feig A.L. Heat capacity changes associated with DNA duplex formation: salt- and sequence-dependent effects. Biochemistry 45 (2006) 604-616
19. Allawi H.T., and SantaLucia Jr. J. Thermodynamics and NMR of internal G-T mismatches in DNA. Biochemistry 36 (1997) 10581-10594
20. Petersheim M., and Turner D.H. Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formations with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp and ACCGGUp. Biochemistry 22 (1983) 256-263
21. Freier S., Sugimoto M.N., Sinclair A., Alkema D., Neilson T., Kierzek R., Caruthers M.H., and Turner D.H. Stability of XGCGCp, GCGCYp, and XGCGCYp helixes: an empirical estimate of the energetics of hydrogen bonds in nucleic acids. Biochemistry and Cell Biology 25 (1986) 3214-3219
22. Lewis G.N., Randall M., Pitzer K.S., and Brewer L. Thermodynamics. second ed., (1961), McGraw-Hill, New York p 723
23. Tan Z.-J., and Chen S.-J. Nucleic acid helix stability: effects of salt concentration, cation valence and size, and chain length. Biophysical Journal 90 (2006) 1175-1190
24. Yakovchuk P., Protozanova E., and Frank-Kamenetskii M.D. Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Research 34 (2006) 564-574
25. Robinson R.A., and Stokes R.H. Electrolyte Solutions. second (revised) ed., (1959), Butterworth Inc., Washington
26. Lumry R., and Rajender S. Enthalpy-entropy compensation phenomena in water solutions of proteins and small molecules: a ubiquitous property of water. Biopolymers 9 (1970) 1125-1227
27. Schwarz F.P., Puri K., Bhat R.G., and Surolia A. Thermodynamics of monosaccharide binding to concanavalin A, pea (Pisum sativum) lectin, and lentil (Lens culinaris) lectin. Journal of Biological Chemistry 268 (1993) 7668-7677