ArticleBiophysical journal2006
Structure and dynamics of phosphate linkages and sugars in an abasic hexaloop RNA hairpin.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- RNA duplexes with abasic substitutions are potent and allele-selective inhibitors of huntingtin and ataxin-3 expression.Nucleic acids research · 2013Article
- The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation.Journal of chemical theory and computation · 2012Article
- Review
- The electrostatic characteristics of G.U wobble base pairs.Nucleic acids research · 2007Article
- Solution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides.Nucleic acids research · 2006Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hairpins containing hexaloops are well represented among the diverse conformations adopted by the RNA molecules. 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 6 basepair stem. The analysis of the 23 ns 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 a majority, are the major actors of the loop stretching. The five torsion angles, epsilon, zeta, alpha, beta, and gamma, are unequally variable, and only zeta and alpha exhibit trimodal distributions. The analysis of the phosphate linkages in terms of epsilonzeta'-alpha'-beta'-gamma-combinations allows us to define five conformational families, each one composed of one major substate in equilibrium with several less populated ones. The transitions between the substates within a family follow specific pathways involving the angles epsilon, zeta, and alpha. Thus, this work reveals that the backbone conformational space is both reduced and ordered even in a hexaloop devoid of bases.
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