Thermodynamics of single strand DNA base stacking

Abstract

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 degrees 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 <or=60% self-complementarily in the reverse direction were independent of concentration with transition temperatures ranging from 15 to 70 degrees 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.

Single-Molecule Kinetics Reveal Cation-Promoted DNA Duplex Formation Through Ordering of Single-Stranded Helices

“…In support of this notion, Vesnaver and Breslauer (24) estimated from calorimetry and UV melting experiments that such SS structure could account for upwards of 40% of the total enthalpy release in duplex formation at room temperature. Subsequently, SS base stacking was characterized with a variety of experimental techniques (24)(25)(26)(27)(28)(29). These ideas were summarized in a mechanism proposed by Holbrook et al (25), whereby duplex formation proceeds via a docking type of reaction.…”

Influence of thermodynamically unfavorable secondary structures on DNA hybridization kinetics

“…Also, the δ seq values were compared with enthalpy and entropy change ( \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\Delta H^\circ_\mathrm{nuc}$\end{document} and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\Delta S^\circ_{\mathrm{nuc}}$\end{document} , respectively), for formation of a nucleus duplex, calculated from the NN parameters, however there was no strong correlation ( Supplementary Figure S11b-c ). Although the sequence dependence of ssDNA conformations, such as the single-strand base-stacking ( 38 ), can be related to the sequence dependence of δ seq , more detailed invesigations such as molecular dynamics simulations would be necessary to elucidate the underlying mechanisms.…”

Electrophoretic Mobility of DNA in Solutions of High Ionic Strength

“…The persistence length has been found to vary from 1.5 to 6 nm in solutions containing monovalent cations, depending on the size and sequence of the DNA (10,11) and the ionic strength of the solution (10)(11)(12)(13)(14)(15)(16). Some short ssDNA strands exhibit sequencedependent thermal transitions, suggesting that these oligomers have nonrandom conformations in solution (16)(17)(18)(19)(20)(21). Other ssDNA strands of the same size do not exhibit sequence-dependent thermal transitions, suggesting that their conformational ensembles primarily consist of unstructured molecules (20).…”

“…Some short ssDNA strands exhibit sequencedependent thermal transitions, suggesting that these oligomers have nonrandom conformations in solution (16)(17)(18)(19)(20)(21). Other ssDNA strands of the same size do not exhibit sequence-dependent thermal transitions, suggesting that their conformational ensembles primarily consist of unstructured molecules (20).…”