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Physics Colloquium
Friday, April 27th, 2007, 4:00 P.M.

E300 Math/Science Center; Refreshments at 3:30 P.M. in Room E200

Udayan Mohanty

Department of Chemistry,
Boston College,
Chestnut Hill, MA 02467

Polyelectrolyte behavior of RNA

The polyelectrolyte behavior of a three-way junction from 16S rRNA is studied in the presence of monovalent and divalent cations. We predict the salt dependence of folding and opening rates of the RNA three-helix junction as a function of Mg2+ and Na+ concentrations (1). A coarse-grained description of the ribosome with activated rate processes is formulated to describe the rotational motion of the ternary complex EF-Tu(GTP)aa-tRNA towards the peptidyl-tRNA after matching of mRNA codon with anticodon of cognate ternary complex (1). We employ grand Monte Carlo simulations to predict the magnesium binding sites in the sarcin ricin loop in Escherichia coli ribosome. We will discuss the nature of interaction of magnesium with RNA bases (1). Finally, if time permits, we will present our work on conformation order of random RNA sequences. We have employed physical and chemical methods to probe structural properties of RNAs having randomly generated oligonucleotide sequences that were of sufficient length and information content to encode complex, functional folds, yet were unbiased by either genealogical or functional constraints (2). These unevolved RNAs acquired magnesium-dependent folding states as compact as those of evolved RNA isolates, but unlike evolved sequences, were prone to having multiple competing conformations (2).
(1) in collaboration with Steve Chu, Stanford and Berkeley; Clifford H Taubes, Harvard
(2) in collaboration with David P Bartel and Erik A Schultes, MIT

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