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Article

Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability^†

Supporting Info

John SantaLucia, Jr.,* Hatim T. Allawi, and P. Ananda Seneviratne

Department of Chemistry, Wayne State University, Detroit, Michigan 48202

Biochemistry, 1996, 35 (11), pp 3555–3562

DOI: 10.1021/bi951907q

Publication Date (Web): March 19, 1996

†

This work was supported by Hitachi Chemical Research.

Author to whom correspondence should be addressed.

Abstract

Thermodynamic data were determined from UV absorbance vs temperature profiles of 23 oligonucleotides. These data were combined with data from the literature for 21 sequences to derive improved parameters for the 10 Watson−Crick nearest neighbors. The observed trend in nearest-neighbor stabilities at 37 °C is GC > CG > GG > GA ≈ GT ≈ CA > CT > AA > AT > TA (where only the top strand is shown for each nearest neighbor). This trend suggests that both sequence and base composition are important determinants of DNA duplex stability. On average, the improved parameters predict ΔG°₃₇, ΔH°, ΔS°, and T_M within 4%, 7%, 8%, and 2 °C, respectively. The parameters are optimized for the prediction of oligonucleotides dissolved in 1 M NaCl.

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History

Published In Issue March 19, 1996
Received August 14, 1995
Revised Manuscript Received December 1, 1995

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Article

Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability^†