IMPROVED NEAREST-NEIGHBOR PARAMETERS FOR PREDICTING DNA DUPLEX STABILITY

Thermodynamic data were determined from UV absorbance vs temperature p rofiles of 23 oligonucleotides. These data were combined with data fro m the literature for 21 sequences to derive improved parameters for th e 10 Watson-Crick nearest neighbors. The observed trend in nearest-nei ghbor stabilities at 37 degrees C is GC > CG > GG > GA approximate to GT approximate to CA > CT > AA > AT > TA (where only the top strand is shown for each nearest neighbor). This trend suggests that both seque nce and base composition are important determinants of DNA duplex stab ility. On average, the improved parameters predict Delta G degrees(37) , Delta H degrees, Delta S degrees, and T-M within 4%, 7%, 8%, and 2 d egrees C, respectively. The parameters are optimized for the predictio n of oligonucleotides dissolved in 1 M NaCl.