Structural Energetics of a RNA Transcription Switch

Wesleyan University, Middletown CT

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Abstract

[unreadable] DESCRIPTION (provided by applicant): The genetic information necessary to produce proteins in living cells is stored in DNA as genes. When genes are expressed, this information is first copied into a complementary messenger RNA molecule in a process called transcription. Living cells use various mechanisms to insure that the transmission of information from DNA to messenger RNA is accurate. One mechanism provides the exact definition of the point where transcription should stop. This point must coincide with the end of the gene. The cells make this definition by using specific terminator sites, strategically located at the ends of genes. In bacteria, about half of all terminator sites perform their function without the assistance of proteins. Instead, in these intrinsic terminators, the signal for transcription termination is encoded in the base sequences of the DNA template and of the nascent RNA. The research proposed in this application will use 1H and 15N nuclear magnetic resonance (NMR) spectroscopy to elucidate the molecular mechanism of transcription termination at an intrinsic terminator site. The nucleic acid molecules targeted for investigation reproduce key modules of the terminator. They include the double helical structure that forms in the newly synthesized RNA when transcription stops, DNA double helical structures from the transcription template, and RNA-DNA hybrid structures that copy the sequence of bases from DNA into messenger RNA. The stability of each base pair in these structures will be defined by NMR measurements of protium-deuterium fractionation factors and rates of exchange of imino protons. The results will provide high-resolution energetic maps for each structure. These maps will reveal how different modules of intrinsic terminators work in concert to achieve the functional states necessary for termination of transcription. This information will contribute to the broader understanding of the conformational transitions that occur in RNA and DNA when the genetic information is expressed, in normal and diseased cells. [unreadable] [unreadable] [unreadable]