Does water play a structural role in the folding of small nucleic acids?

¹ Stanford University

^* To whom correspondence should be addressed. E-mail: pande{at}stanford.edu.

Submitted on November 2, 2004
Revised on January 2, 2005
Accepted on 21 January 2005

	Abstract

Nucleic acid structure and dynamics are known to be closely coupled to local environmental conditions and, in particular, to the ionic character of the solvent. Here we consider what role the discrete properties of water and ions play in the collapse and folding of small nucleic acids. We study the folding of an experimentally well-characterized RNA hairpin-loop motif (sequence 5'-GGGC[GCAA]GCCU-3') via ensemble molecular dynamics simulation and, with nearly 500 µs of aggregate simulation time using an explicit representation of the ionic solvent, report successful ensemble folding simulations, with a predicted folding time of 8.8(±2.0) µs, in agreement with experimental measurements of ~10 µs. Comparing our results to previous folding simulations using the GB/SA continuum solvent model shows that accounting for water-mediated interactions is necessary to accurately characterize the free energy surface and stochastic nature of folding. The formation of secondary structure appears to be more rapid than the fastest ionic degrees of freedom, and counterions do not participate discretely in observed folding events. We find that hydrophobic collapse follows a predominantly expulsive mechanism in which a diffusion-search of early structural compaction is followed by final formation of native structure that occurs in tandem with solvent evacuation.

Key Words: RNA folding, distributed computing, ensemble dynamics, explicit solvent, implicit solvent, tetraloop

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