Hyper-mobile Water and Raman 2900 cm-1 Peak Band of Water Observed around Backbone Phosphates of Double Stranded DNA by High-Resolution Spectroscopies and MD Structural Feature Analysis of Water

High-resolution measurements of microwave dielectric relaxation and Raman spectroscopies for waters in double stranded (ds) 10-mer DNA solution revealed the presence of hyper mobile water (HMW) and a marked OH stretching band appearing in the range from 2500 to 3100 cm-1, here called the LA band, at the low wavenumber tail of the major OH stretching band of water. Quantitation of the Raman scattering intensity for ds 10-mer DNA in phosphate or tris(hydroxymethyl)aminomethane (TRIS) buffers showed that the LA band was formed by 2000-3000 water molecules per ds 10-mer DNA, indicating collective OH stretching vibrations of water molecules around the backbone phosphate oxygen atoms. The LA band intensity of ds 10-mer DNA in 10 mM TRIS increased and decreased by 30% with the addition of 2 mM MgCl2 and 2 mM CaCl2, respectively. The LA band intensity and the effect of adding Mg(II) or Ca(II) ions to the band intensity were maintained in the presence of 0.14 M KCl; however, the changes induced by the divalent cations were reduced by half. Molecular dynamics calculations of water molecules around the backbone phosphate groups of ds 10-mer DNA indicate the presence of high-density water and broad regions of fluctuating water density, suggesting that they correspond to HMW and the LA band, respectively.

Automated summary

High-resolution measurements of microwave dielectric relaxation and Raman spectroscopies revealed the presence of hyper mobile water and a marked OH stretching band in ds 10-mer DNA solution. The LA band, observed at the low wavenumber tail of water's major OH stretching band, is formed by collective OH stretching vibrations of water molecules around the backbone phosphate oxygen atoms. The LA band intensity is affected by the addition of Mg(II) or Ca(II) ions, and this effect is reduced in the presence of 0.14 M KCl.