Thermodynamic analysis of 3 -> 2 transition in oligonucleotide triple-helix complexes dAn-2dTm

Abstract

The work considers a possibility for thermodynamically describing the transition in oligomeric complexes dA₁₅-2dT₁₀ and dA₁₉-2dT₁₉ from the triplex form to the duplex+single strand (3—»2 transition), using the "Staggering Zipper" model and assuming the transition to be bimolecular reaction A 2B<=>AB+B. It was shown that upon physically grounded values of the transition thermodynamic parameters (ΔH₂₃, ΔS_:23, nucleation parameter β_23, and others) the model describes adequately the experimental melting curves for triplexes with various lengths of oligonucleotide chains and different ionic conditions. As well, the work considers the effects of the dye covalently attached to dT₁₀, intercalating between   A·T pairs of the duplex on the transition parameters. Possible causes of great dispersion of the experimental data obtained for ΔH₃₂ by different methods (DSC, ITC, van't Hoff analysis, and so on) are analyzed. It is shown that the disordering of the triplex and duplex ends (the so-called "end fraying") has a significant influence on the form of melting curves and on thermodynamic transition parameters.