Melting studies of short DNA hairpins: Influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability

Biopolymers

Volumn 50, Issue 4, 1999, Pages 425-442

  Vallone, Peter M ^a   Paner, Teodoro M ^b   Hilario, Jovencio ^a   Lane, Michael J ^b,c   Faldasz, Brian D ^b   Benight, Albert S ^a,b  

^a UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^b Tm Technologies Inc   (United States)

^c STATE UNIVERSITY OF NEW YORK   (United States)

Author keywords

Differential scanning calorimetry; DNA; Hairpin; Intramolecular; Model independent; Optical melting; Thermodynamics; Two state

Indexed keywords

CHEMICALS; ENTHALPY; ENTROPY; GIBBS FREE ENERGY; MATHEMATICAL MODELS; MELTING; MOLECULAR STRUCTURE; THERMODYNAMIC STABILITY; ULTRAVIOLET SPECTROSCOPY;

DNA HAIRPINS; OPTICAL MELTING;

DNA;

DNA; DNA BASE; OLIGOMER; SODIUM ION; SOLVENT;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; DIFFERENTIAL SCANNING CALORIMETRY; DNA SEQUENCE; DNA STRUCTURE; ENERGY; ENTHALPY; ENTROPY; MELTING POINT; MOLECULAR STABILITY; THERMODYNAMICS; ULTRAVIOLET SPECTROSCOPY;

BASE SEQUENCE; DNA; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; THERMODYNAMICS;

EID: 0033527321     PISSN: 00063525     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0282(19991005)50:4<425::AID-BIP8>3.0.CO;2-B     Document Type: Article

References (39)

1. Dai, X.; Greizerstein, M. B.; Nadas-Chinni, K.; Rothman-Denes, L. B. Proc Natl Acad Sci USA 1997, 94, 2174-2179.
2. Maniatis, T.; Ptashne, M.; Backman, K.; Kield, D.; Flashman, S.; Jeffrey, A.; Maurer, R. Cell 1975, 5, 109-113.
3. Gacy, A. M.; McMurray, C. T. Biochemistry 1994, 33, 11951-11959.
4. McMurray, C. T.; Wilson, W. D.: Douglass, J. O. Proc Natl Acad Sci USA 1991, 88, 666-670.
5. Müller, U. R.; Fitch, W. M. Nature 1982, 298, 582-585.
6. Spiro, C.; McMurray, C. T. J Biol Chem 1997, 272, 33145-33152.
7. McMurray, C. T.; Juranic, N.; Chandrasekaran, S.; Macura, S.; Li, Y.; Jones, R. L.; Wilson, W. D. Biochemistry 1994, 33, 11960-11970.
8. Zazopoulos, E.; Lalli, E.; Stocco, D. M.; Sassone-Corsi, P. Nature 1997, 390, 311-315.
9. Spiro, C.; Richards, J. P.; Chandrasekaran, S.; Brennan, R. G.; McMurray, C. T. Proc Natl Acad Sci USA 1993, 90, 4606-4610.
10. Grosschedl, R.; Hobom, G. Nature 1979, 277, 621-627.
11. Willwand, K.; Mumtsidu, E.; Kuntz-Simon, G.; Rommelaere, J. J Biol Chem 1998, 273, 1165-1174.
12. Chan, C. L.; Wang, D.; Landick, R. J Mol Biol 1997, 268, 54-68.
13. Chen, K. C.; Tyson, J. J.; Lederman, M.; Stout, E. R.; Bates, R. C. J Mol Biol 1989, 208, 283-296.
14. Gonzalez, A.; Talavera, A.; Almendral, J. M.; Vinuela, E. Nucleic Acids Res 1986, 14, 6835-6844.
15. Hobom, G.; Grosschedl, R.; Lusky, M.; Scherer, G.; Schwarz, E.; Kossel, H. Cold Spring Harb Symp Quant Biol 1979, 43, Pt 1, 165-178.
16. Rosenberg, M.; Court, D. Annu Rev Genet 1979, 13, 319-353.
17. Tyson, J. J.; Chen, K. C.; Lederman, M.; Bates, R. C. J Theor Biol 1990, 144, 155-169.
18. Wells, R. D.; Goodman, T. C.; Hillen, W.; Horn, G. T.; Klein, R. D.; Larson, J. E.; Müller, U. R.; Neuendorf, S. K.; Panayotatos, N.; Stirdivant, S. M. Prog Nucleic Acid Res Mol Biol 1980, 24, 167-267.
19. Zengel, J. M.; Lindahl, L. J Bacteriol 1996, 178, 2383-2387.
20. Wadkins, R. M.; Vladu, B.; Tung, C. S. Biochemistry 1998, 37, 11915-11923.
21. Poddevin, B.; Meguenni, S.; Elias, I.; Vasseur, M.; Blumenfeld, M. Antisense Res Dev 1994, 4, 147-154.
22. Carpenter, W. R.; Schutzbank, T. E.; Tevere, V. J.; Tocyloski, K. R.; Dattagupta, N.; Yeung, K. K. Clin Chem 1993, 39, 1934-1938.
23. Senior, M. M.; Jones, R. A.; Breslauer, K. J. Biochemistry 1988, 27, 3879-3885.
24. Senior, M. M.; Jones, R. A.; Breslauer, K. J. Proc Natl Acad Sci USA 1988, 85, 6242-6246.
25. Paner, T. M.; Amaratunga, M.; Doktycz, M. J.; Benight, A. S. Biopolymers 1990, 29, 1715-1734.
26. Doktycz, M. J.; Paner, T. M.; Amaratunga, M.; Benight, A. S. Biopolymers 1990, 30, 829-845.
27. Caruthers, M. H. Chemical and Enzymatic Synthesis of Gene Fragments; Verlag-Chemie: Weinheim, Germany, 1982.
28. Maniatis, T.; Fritsch, E. F.; Sambrook, J. Molecular Cloning; Cold Spring Harbor Laboratory: Cold Spring Harbor, NY, 1992.
29. Cantor, C. R.; Warshaw, M. M.; Shapiro, H. Biopolymers 1970, 9, 1059-1077.
30. Marky, L. A.; Breslauer, K. J. Biopolymers 1987, 26, 1601-1620.
31. Doktycz, M. J.; Goldstein, R. F.; Paner, T. M.; Gallo, F. J.; Benight, A. S. Biopolymers 1992, 32, 849-864.
32. Owczarzy, R.; Vallone, P. M.; Gallo, F. J.; Paner, T. M.; Lane, M. J.; Benight, A. S. Biopolymers 1997, 44, 217-239.
33. Benight, A. S.; Gallo, F. J.; Paner, T. M.; Bishop, K. D.; Faldasz, B. D.; Lane, M. J. Adv Biophys Chem 1995, 55, 1-55.
34. Press, W. H.; Flannery, B. P.; Teukolsky, S. A.; Vetterling, W. T. (1988) Numerical Recipes; Cambridge University Press: New York, 1988.
35. Antao, V. P.; Lai, S. Y.; Tinoco, I., Jr. Nucleic Acids Res 1991, 19, 5901-5905.
36. Antao, V. P.; Tinoco, I., Jr. Nucleic Acids Res 1992, 20, 819-824.
37. Turner, D. H.; Sugimoto, N. Annu Rev Biophys Biophys Chem 1988, 17, 167-192.
38. Paner, T. M.; Riccelli, P. V.; Owczarzy, R.; Benight, A. S. Biopolymers 1996, 39, 779-793.
39. Kaiser, J. F.; Reed, W. A. Rev Sci Instrum 1977, 48, 1447-1457.