Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability

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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.