Structure and dynamics of phosphate linkages and sugars in an abasic hexaloop RNA hairpin

¹ university Paris 13
² IBPC

^* To whom correspondence should be addressed. E-mail: fjoli{at}smbh.univ-paris13.fr.

Submitted on July 15, 2005
Revised on September 13, 2005
Accepted on 12 October 2005

	Abstract

Hairpins containing hexaloops are well represented among the diverse conformations adopted by the RNA molecules. In order to investigate the intrinsic properties of a backbone submitted to a hexaloop fold, we present here a molecular dynamics study of an abasic hexaloop closed by an A-form 6bp stem. The analysis of the 23ns trajectory made in explicit solvent shows that both the sugars and the torsion angles in the loop undergo numerous conformational transitions. The South sugars, although not in majority, are the major actors of the loop stretching. The five torsion angles , , , and are unequally variable and only and exhibit trimodal distributions. The analysis of the phosphate linkages in terms of ----combinations allows to define five conformational families, each one composed of one major sub-state in equilibrium with several less populated ones. The transitions between the sub-states within a family follow specific pathways involving the angles , and . Thus, this work reveals that the backbone conformational space is both reduced and ordered even in a hexaloop devoid of bases.

Key Words: RNA hexaloop structure, backbone structure and dynamics, molecular dynamics

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