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Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability†

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Department of Chemistry, Wayne State University, Detroit, Michigan 48202
Cite this: Biochemistry 1996, 35, 11, 3555–3562
Publication Date (Web):March 19, 1996
https://doi.org/10.1021/bi951907q
Copyright © 1996 American Chemical Society
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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 TM within 4%, 7%, 8%, and 2 °C, respectively. The parameters are optimized for the prediction of oligonucleotides dissolved in 1 M NaCl.

†

 This work was supported by Hitachi Chemical Research.

*

 Author to whom correspondence should be addressed.

✗

 Abstract published in Advance ACS Abstracts, February 15, 1996.

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Six figures showing 1/TM vs ln CT plots for the 20 sequences presented in Table 1 which are not shown in Figure 1 (3 pages). Ordering information is given on any current masthead page.

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