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 T_m calculations at Integrated DNA Technologies.  Find OligoAnalyzer in this link to calculate T_m 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.