Biopolymers, 1997, Vol. 44, No. 3, pp 217-239.
Predicting sequence-dependent melting stability of short duplex DNA oligomers
Richard Owczarzy, Peter M. Vallone, Frank J. Gallo, Teodoro M. Paner, Michael J. Lane, and Albert S. Benight
Reprint
Many important applications of DNA sequence-dependent hybridization reactions
have recently emerged. This has sparked a renewed interest in analytical calculations of
sequence-dependent melting stability of duplex DNA. In particular, for many applications it is
often desirable to accurately predict the transition temperature, or tm, of short duplex DNA
oligomers (∼ 20 base pairs or less) from their sequence and concentration. The thermodynamic
analytical method underlying these predictive calculations is based on the nearest-neighbor
model. At least 11 sets of nearest-neighbor sequence-dependent thermodynamic parameters
for DNA have been published. These sets are compared. Use of the nearest-neighbor sets in
predicting tm from the DNA sequence is demonstrated, and the ability of the nearest-neighbor
parameters to provide accurate predictions of experimental tm's of short duplex DNA oligomers
is assessed.
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