Dynamics and stability of individual base pairs in two homologous RNA-DNA hybrids.

ABSTRACT: Nuclear magnetic resonance spectroscopy and proton exchange have been used to characterize two RNA-DNA hybrids from the tR2 intrinsic transcription terminator site of phage lambda. The hybrids have the same base sequence [5'-GGCGCAGGCC(T/U)(T/U)CC-3'/5'-GGAAGGCC(T/U)GCGCC-3'] but differ from each other by an interchange of DNA and RNA strands. The opening of single base pairs in the two hybrids is characterized by measuring the rates of exchange of imino protons with solvent protons as a function of the concentration of a proton acceptor (ammonia base) at 10 degrees C. The free energy change in the opening reaction provides a measure of the stability of the base pair, while the rates of opening and closing define the base pair dynamics. The results demonstrate that, within the same base se

SUBMITTER: Huang Y 

PROVIDER: S-EPMC2758270 | biostudies-literature | 2009 May

REPOSITORIES: biostudies-literature