Book of Abstracts: Albany 2009
June 16-20 2009
© Adenine Press (2008)
Structural Energetics of a DNA-RNA Hybrid Containing a Tract of dA-rU Base Pairs
The presence of tracts of A-T/U base pairs has a profound effect on the structural and functional properties of nucleic acid duplexes. For the DNA-RNA hybrid duplexes formed in transcription, the presence of a tract of dA-rU base pairs often provides a signal for the release of messenger RNA. The structural and dynamic properties of the tract, which are responsible for termination of transcription at these sites, are not yet known. To address this question, in the present work, we investigated a DNA-RNA hybrid from the intrinsic transcription terminator site tR2 of phage &lamda;. The hybrid contains a tract of five dA-rU base pairs in the following base sequence: 5?-dGCGATAAAAAGGCC-3?/5?-rGGCCUUUUUAUCGC-3?. The stability of individual base pairs in the DNA-RNA hybrid was characterized from the exchange of the hybrid?s imino protons with solvent protons using nuclear magnetic resonance (NMR) spectroscopy. The NMR resonances of the imino protons were assigned in 1H-1H NOESY and 15N-editing experiments on samples of the DNA-RNA hybrid in which the imino group of single uracil bases was labeled with 15N. The rates of exchange of imino protons were measured as a function of the concentration of a proton acceptor (ammonia base) to obtain the free energy change in the opening reaction for each base pair in the hybrid duplex. The results demonstrate that the stabilities of dA-rU base pairs in the tract are lower than that of an isolated dA-rU base pair. Furthermore, the stability depends on the location of the dA-rU base pair within the tract. The relationship between these findings and the energetic properties of other nucleic acid duplexes of similar base sequence will be discussed. (Supported by a grant from the NIH).
Department of Chemistry and Molecular Biophysics Program