DNA Hybridization Thermodynamics Calculation

Brought to you by the Research Group of Prof. Robert M. Corn
at the Dept. of Chemistry, University of California, Irvine.


Method 0(for perfectly matched dsDNA and its absorbance of 260 nm, parameters from Breslauer et al. *):

DNA sequence: DNA5'- -3'

Concentration of Na+(M): DN

Concentration of Mg2+(M):A

Absorbance of DNA:A


Method 1 (parameters from Breslauer et al.* -- nearest-neighbor calcaulation excluding any nearest-neighbor pairs that contain a mismatch base):

DNA sequence: DNAWord5'- -3'

Complement sequence: Co-3'- -5'

Concentration of Na+(M): DN

Concentration of Mg2+(M):A


Method 2 (parameters from Wetmur et al.** -- first calculate the duplex as if the mismatch had no effect then add an appropriate destabilization factor depending on the identity of the mismatch):

DNA sequence: DNAWord5'- -3'

Complement sequence :Co-3'- -5'

Concentration of Na+(M): DN

Concentration of Mg2+(M):A


* Breslauer, K. J., Frank, R., Blocker, H. and Marky, L. A.(1986) Proc. Natl. Acad. Sci. USA, 83, 3746-3750

** Wetmur, J. G. (1996) In Myers, R. A. (ed.), Encyclopedia of Molecular Biology and Molecular Medicine. VCH Press, New York, Vol. 4, pp. 235-243.