A UNIFIED VIEW OF POLYMER, DUMBBELL, AND OLIGONUCLEOTIDE DNA NEAREST-NEIGHBOR THERMODYNAMICS

A unified view of polymer, dumbbell, and oligonucleotide nearest-neigh bor (NN) thermodynamics is presented, DNA NN Delta G(37)degrees parame ters from seven laboratories are presented in the same format so that careful comparisons can be made, The seven studies used data from natu ral polymers, synthetic polymers, oligonucleotide dumbbells, and oligo nucleotide duplexes to derive NN parameters; used different methods of data analysis; used different salt concentrations: and presented the NN thermodynamics in different formats, As a result of these differenc es, there has been much confusion regarding the NN thermodynamics of D NA polymers and oligomers, Herein I show that six of the studies are a ctually in remarkable agreement with one another and explanations are provided in cases where discrepancies remain, Further, a single set of parameters, derived from 108 oligonucleotide duplexes, adequately des cribes polymer and oligomer thermodynamics, Empirical salt dependencie s are also derived for oligonucleotides and polymers.