Publications Repository - Helmholtz-Zentrum Dresden-Rossendorf

Conformational substates of B-DNA have been reported to be involved in DNA recognition by proteins [1]. BI and BII substates, that co-exist in B-DNA, differ in the phosphate backbone conformation about the C3'-O3'-P segment related to the variability of the dihedral e and z angles (see figure left [2]). Typical IR marker bands have previously been identified which allow assessing the relative population of BI and BII conformers by FTIR spectroscopy for DNA from salmon testes, poly(dG-dC) and the d(CGCGAATTCGCG)2 dodecamer [3]. So far, BI/BII dynamics studies were restricted to static FTIR spectroscopy under isothermal relaxation at low temperatures . We have attempted to monitor the BI/BII transition under defined native-like conditions using rapid scan FTIR-difference-spectroscopy at a time resolution of 70 ms. An ATR-cell accessory was designed that allows both, the application of flashes to induce small temperature jumps and the adjustment of constant humidity of the sample. The latter is critical to address the role of backbone hydration in the dynamics of the BI/BII transition.