Thermodynamics of single strand DNA base stacking

The thermodynamics of the stacking to unstacking transitions of 24 single‐stranded DNA sequences (ssDNA), 10–12 bases in length, in sodium phosphate buffer were determined from 10 to 95°C, using differential scanning calorimetry (DSC). An additional 22 ssDNA sequences did not exhibit an S⇔︁U transition in this temperature range. The transition properties of the ssDNA sequences with ≤60% self‐complementarily in the reverse direction were independent of concentration with transition temperatures ranging from 15 to 70°C, van't Hoff transition enthalpies from 92 to 201 kJ mol−1 and transition enthalpies from 5 to 75% of the corresponding van't Hoff transition enthalpies. Since all the 16 doublets and 60 of the 64 triplets are present in both the transition and the non‐transition ssDNA sequences, it is unlikely that the nucleation subset initiating stacking of the sequence is a specific doublet or triplet subset. Of the 141 quadruplet subsets of the 46 sequences, each transition ssDNA sequence contained at least one or more quadruplets not found in the non‐transition ssDNA sequences. It could be concluded that the thermal stability of the stacked conformation was dependent on the presence of a possible nucleation quadruplet and the length of the ssDNA sequence and not on the G or C content of the ssDNA sequence, nor on the number of purine bases in the sequence. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 969–979, 2008. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com