MersV1, Main, Exploration, bibRecord, 003094

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

Identifieur interne : 003094 ( Main/Exploration ); précédent : 003093; suivant : 003095

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

Auteurs : Richard Owczarzy [États-Unis] ; Yong You [États-Unis] ; Bernardo G. Moreira [États-Unis] ; Jeffrey A. Manthey [États-Unis] ; Lingyan Huang [États-Unis] ; Mark A. Behlke [États-Unis] ; Joseph A. Walder [États-Unis]

Source :

Biochemistry [ 0006-2960 ] ; 2004.

RBID : ISTEX:649489F74DBB12280F9B38D74DBAA974B5DCA6E1

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.

Url:

https://api.istex.fr/ark:/67375/TPS-4ZCVNJTH-Z/fulltext.pdf

DOI: 10.1021/bi034621r

Affiliations:

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<front><div type="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.</div>
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Effects of Sodium Ions on DNA Duplex Oligomers: Improved Predictions of Melting Temperatures

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

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Abstract

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