Biochemistry, 2004, Vol. 43, No. 12, pp 3537-3554.
Effects of sodium ions on DNA duplex oligomers: Improved predictions of melting temperatures
Richard Owczarzy, Yong You, Bernardo G. Moreira, Jeffrey A. Manthey, Lingyan Huang, Mark A. Behlke, and Joseph A. Walder
Reprint
Supplementary data
Melting temperatures, Tm, were systematically studied for
a set of 92 DNA duplex oligomers in a variety of sodium ion concentrations
ranging from 69 mM to 1.02 M. The relationship between Tm
and ln [Na+] was nonlinear over this range of sodium ion
concentrations, and the observed melting temperatures were poorly predicted
by existing algorithms. A new empirical relationship was derived from UV
melting data that employs a quadratic function, which better models the
melting temperatures of DNA duplex oligomers as sodium ion concentration is
varied. Statistical analysis shows that this improved salt correction is
significantly more accurate than previously suggested algorithms and predicts
salt-corrected melting temperatures with an average error of only 1.6
oC when tested against an independent validation set of
Tm measurements obtained from the literature. Differential
scanning calorimetry studies demonstrate that this Tm salt
correction is insensitive to DNA concentration. The Tm salt
correction function was found to be sequence-dependent and varied with the
fraction of G-C base pairs, in agreement with previous studies of genomic and
polymeric DNAs. The salt correction function is independent of oligomer length,
suggesting that end-fraying and other end effects have little influence on the
amount of sodium counterions released during duplex melting. The results are
discussed in the context of counterion condensation theory.
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