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Nucleic Acids Research Advance Access originally published online on October 16, 2007
Nucleic Acids Research 2007 35(20):6995-7002; doi:10.1093/nar/gkm719
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Nucleic Acids Research, 2007, Vol. 35, No. 20 6995-7002
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin

Zhuoyun Zhuang1, Luc Jaeger1,2 and Joan-Emma Shea1,*

1Department of Chemistry and Biochemistry and 2Bio-molecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA

*To whom correspondence should be addressed. Tel: +1 805 893 5604; Fax: +1 805 893 4120; Email: shea{at}chem.ucsb.edu

Correspondence may also be addressed to Luc Jaeger. Email: jaeger{at}chem.ucsb.edu

Received July 10, 2007. Revised August 29, 2007. Accepted August 29, 2007.

The T-loop motif is an important recurrent RNA structural building block consisting of a U-turn sub-motif and a UA trans Watson–Crick/Hoogsteen base pair. In the presence of a hairpin stem, the UA non-canonical base pair becomes part of the UA-handle motif. To probe the hierarchical organization and energy landscape of the T-loop, we performed replica exchange molecular dynamics (REMD) simulations of the T-loop in isolation and as part of a hairpin. Our simulations reveal that the isolated T-loop adopts coil conformers stabilized by base stacking. The T-loop hairpin shows a highly rugged energy landscape featuring multiple local minima with a transition state for folding consisting of partially zipped states. The U-turn displays a high conformational flexibility both when the T-loop is in isolation and as part of a hairpin. On the other hand, the stability of the UA non-canonical base pair is enhanced in the presence of the UA-handle. This motif is apparently a key component for stabilizing the T-loop, while the U-turn is mostly involved in long-range interaction. Our results suggest that the stability and folding of small RNA motifs are highly dependent on local context.


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