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The conformational substates BI and BII of the phosphodiester backbone in B-DNA are thought to contribute to DNA flexibility and protein recognition. We have studied by rapid scan FTIR spectroscopy the isothermal BI-BII transition on its intrinsic time scale. Correlation analysis of IR absorption changes occurring within seconds after a reversible incremental growth of the DNA hydration shell identifies water populations w1 (PO2--bound) and w2 (non-PO2--bound) exhibiting weaker and stronger H-bonds, respectively, than those dominating in bulk water. The BII substate is stabilized by w2. The water H-bond imbalance of 3-4 kJ mol-1 is equalized at little enthalpic cost upon formation of a contiguous water network (at 12-14 H2O molecules per DNA phosphate) of reduced n(OH) band width. In this state, hydration water cooperatively stabilizes the BI conformer via the entropically favored replacement of w2-DNA interactions by additional w2-water contacts, rather than binding to BI-specific hydration sites. Such water rearrangements contribute to the recognition of DNA by indolicidin, an antimicrobial 13-mer peptide from bovine neutrophils which, despite little intrinsic structure, preferentially binds to the BI conformer in a water-mediated induced fit. The FTIR spectra resolve sequential steps leading from PO2--solvation to substate transition and eventually to base stacking changes in the complex. In combination with CD-spectral titrations, the data indicate that in the absence of a bulk aqueous phase, as in molecular crowded environments, water relocation within the DNA hydration shell allows for entropic contributions similar to those assigned to water upon DNA ligand recognition in solution.

Herein, we study the nanomechanical characteristics of single DNA molecules in the presence of DNA binders, including intercalating agents (ethidium bromide and doxorubicin), a minor groove binder (netropsin) and a typical alkylating damaging agent (cisplatin). We have used magnetic tweezers manipulation techniques, which allow us to measure the contour and persistence lengths together with the bending and torsional properties of DNA. For each drug, the specific variations of the nanomechanical properties induced in the DNA have been compared. We observed that the presence of drugs causes a specific variation in the DNA extension, a shift in the natural twist and a modification of bending dependence on the imposed twist. By introducing a naive model, we have justified an anomalous correlation of torsion data observed in the presence of intercalators. Finally, a data analysis criterion for discriminating between different molecular interactions among DNA and drugs has been suggested.