Dresden 2009 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 20: DNA, RNA and Chromatin

BP 20.4: Vortrag

Donnerstag, 26. März 2009, 15:00–15:15, HÜL 186

Promoter proximal transcript secondary structure — •Abigail Klopper and Stephan Grill — Max Planck Institute for the Physics of Complex Systems, Dresden

RNA polymerase transcribes selected parts of the DNA genome into RNA transcripts by advancing processively along a double-stranded DNA template. It melts the DNA into a single-stranded bubble and catalyzes bond formation, which effectively polymerizes the complementary RNA strand. There is evidence to suggest that the nascent RNA forms self-interacting secondary structure elements. These are thought to serve as barriers to an inactive backtracked state, aiding recovery to an active conformation and ensuring the timely production of a functional transcript. We investigate the role of conformational characteristics of the RNA strand in the context of the early stages of transcription, during which the polymerase is prone to premature and irreversible stalling. Specifically, we examine the hypothesis that the absence of long transcripts is the primary cause of stalling in the vicinity of the promoter. Despite prolific attention paid to the conformational statistics of long RNA strands, little is understood about the implications of finite size in shorter strands. With a recursive formulation of the partition function for homogeneous and disordered RNA molecules, we utilize numerical and analytical approaches to calculate the average number of unpaired bases adjacent to the polymerase. We find that the length-dependent equilibrium fold attributed to the nascent strand poses a marked barrier to a backtracking polymerase within length scales commensurate with early stalling events.