Hydration of the dT(n)·dA(n)xdT(n) parallel triple helix: A Fourier transform infrared and gravimetric study correlated with molecular dynamics simulations

Abstract

We present a comparative analysis of the water organization around the dT(n)·dA(n)xdT(n) triple helix and the Watson-Crick double helix dT(n)·dA(n) respectively by means of gravimetric measurements, infrared spectroscopy and molecular dynamics simulations. The hydration per nucleotide determined by gravimetric and spectroscopic methods correlated with the molecular dynamics simulations shows that at high relative humidity (98% RH) the triple helix is less solvated than the duplex (17 ± 2 water molecules per nucleotide instead of 21 ± 1). The experimental desorption curves are different for both structures and indicate that below 81% RH the triplex becomes more hydrated than the duplex. At this RH the FTIR spectra show the emergence of N-type sugars in the adenosine strand of the triplex. When the third strand is bound in the major groove of the Watson-Crick duplex molecular dynamics simulations show the formation of a spine of water molecules between the two thymidine strands.