DNA melting temperature - How to calculate it?
A simplified explanation can be found in
IDT Tech Bulletin that
reviews calculation of melting temperatures for DNA duplex oligonucleotides.
I helped to develop on-line Tm calculations at Integrated DNA
Technologies.
Find OligoAnalyzer in
this link to calculate Tm of your duplex.
Comparison of various sets of thermodynamic parameters and their accuracy in predictions of DNA melting temperatures can be found in
Owczarzy et al. (1998) Predicting Sequence-Dependent Melting Stability of Short Duplex DNA Oligomers,
Biopolymers, Vol. 44, pp. 217-239. See abstract
and full text in PDF file.
Our latest contribution to thermodynamic model is the most accurate correction for effects of sodium ions on DNA melting temperatures, which was
published in Owczarzy, et al. (2004) Biochemistry 43, 3537-3554.
(abstract)
My Ph.D. thesis (full text in PDF file, 1.7 MB)
contains exhaustive theoretical descriptions and investigations of various models.
References for sets of nearest-neighbor parameters
- Thermodynamic parameters determined in 20-200 mM Na+
- Owczarzy, R., Vallone, P.M., Goldstein, R.F., Benight, A.S. (1999)
Studies of DNA Dumbbells VII: Evaluation of the Next-Nearest-Neighbor
Sequence-Dependent Interactions in Duplex DNA.
Biopolymers, 52, 29-56.
- Doktycz, M.J., Goldstein, R.F., Paner, T.M., Gallo, F.J., Benight, A.S. (1992)
Studies of DNA Dumbbells I: Melting curves of 17 DNA dumbbells with the
different duplex stem sequences linked by T4 end-loops: Evaluation of the
nearest-neighbor stacking interactions in DNA.
Biopolymers, 32, 849-864.
- Delcourt, S.G., Blake, R.D. (1991) Stacking energies in DNA.
J. Biol. Chem., 266, 15160-15169.
- Wartell, R.M., Benight, A.S. (1985) Thermal denaturation of DNA molecules:
A comparison of theory with experiment. Phys. Rep., 126, 67-107.
- Vologodskii, A.V., Amirikyan, B.R., Lyubchenko, Y.L., Frank-Kamenetskii, M.D.
(1984) Allowance for heterogeneous stacking in the DNA helix-coil transition
theory. J. Biomol. Struct. Dynam., 2, 131-148.
- Gotoh, O., Tagashira, Y. (1981) Stabilities of nearest-neighbor doublets
in double-helical DNA determined by fitting calculated melting profiles to
observed profiles. Biopolymers, 20, 1033-1042.
- McCampbell, C.R., Wartell, R.M., Plaskon, R.R (1989) Inverted repeat
sequences can influence the melting transitions of linear DNAs.
Biopolymers, 28, 1745-1758.
- Thermodynamic parameters determined in 1 M Na+
- SantaLucia, J. Jr. (1998) A unified view of polymer, dumbbell, and
oligonucleotide DNA nearest-neighbor thermodynamics.
Proc. Natl. Acad. Sci. USA, 95, 1460-1465.
- Sugimoto, N., Nakano, S., Yoneyama, M., Honda, K. (1996) Improved
thermodynamic parameters and helix initiation factor to predict
stability of DNA duplexes. Nucleic Acids Res. 24, 4501-4505.
- Breslauer, K.J., Frank, R., Blocker, H., Marky, L.A. (1986) Predicting DNA
duplex stability from the base sequence.
Proc. Natl. Acad. Sci. USA, 83, 3746-3750.
Copyright 2004, Updated January 5, 2004.