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Effects of Sodium Ions on DNA Duplex Oligomers:  Improved Predictions of Melting Temperatures

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Integrated DNA Technologies, 1710 Commercial Park, Coralville, Iowa 52241
Cite this: Biochemistry 2004, 43, 12, 3537–3554
Publication Date (Web):March 5, 2004
https://doi.org/10.1021/bi034621r
Copyright © 2004 American Chemical Society
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Abstract

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 °C 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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Methods for calculation of the nearest-neighbor Tm salt correction, nearest-neighbor salt correction parameters (Table S-1), results of differential scanning calorimetry experiments (Table S-2), analysis of Tm prediction errors as a function of oligomer length (Table S-3), and Figure S-1 showing reproducibility of our melting experiments. This material is available free of charge via the Internet at http://pubs.acs.org.

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