| Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes. | |
| | |
MedLine Citation:
|
PMID: 18621721 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
|
The sequence-dependent folding landscapes of nucleic acid hairpins reflect much of the complexity of biomolecular folding. Folding trajectories, generated by using single-molecule force-clamp experiments by attaching semiflexible polymers to the ends of hairpins, have been used to infer their folding landscapes. Using simulations and theory, we study the effect of the dynamics of the attached handles on the handle-free RNA free-energy profile F(o)(eq)(z(m)), where z(m) is the molecular extension of the hairpin. Accurate measurements of F(o)(eq)(z(m)) requires stiff polymers with small L/l(p), where L is the contour length of the handle, and l(p) is the persistence length. Paradoxically, reliable estimates of the hopping rates can only be made by using flexible handles. Nevertheless, we show that the equilibrium free-energy profile F(o)(eq)(z(m)) at an external tension f(m), the force (f) at which the folded and unfolded states are equally populated, in conjunction with Kramers' theory, can provide accurate estimates of the force-dependent hopping rates in the absence of handles at arbitrary values of f. Our theoretical framework shows that z(m) is a good reaction coordinate for nucleic acid hairpins under tension. |
| | |
Authors:
|
Changbong Hyeon; Greg Morrison; D Thirumalai |
Publication Detail:
|
Type: Journal Article; Research Support, Non-U.S. Gov't Date: 2008-07-10 |
Journal Detail:
|
Title: Proceedings of the National Academy of Sciences of the United States of America Volume: 105 ISSN: 1091-6490 ISO Abbreviation: Proc. Natl. Acad. Sci. U.S.A. Publication Date: 2008 Jul |
Date Detail:
|
Created Date: 2008-07-17 Completed Date: 2008-09-03 Revised Date: 2009-11-18 |
Medline Journal Info:
|
Nlm Unique ID: 7505876 Medline TA: Proc Natl Acad Sci U S A Country: United States |
Other Details:
|
Languages: eng Pagination: 9604-9 Citation Subset: IM |
Affiliation:
|
Department of Chemistry, Chung-Ang University, Seoul 156-756, Republic of Korea. |
Export Citation:
|
APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
|
Kinetics Models, Theoretical* Nucleic Acid Conformation RNA / chemistry* Thermodynamics |
| Chemical | |
Reg. No./Substance:
|
63231-63-0/RNA |
| Comments/Corrections | |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
Previous Document: A protein from the salivary glands of the pea aphid, Acyrthosiphon pisum, is essential in feeding on...
Next Document: Class 1A PI3K regulates vessel integrity during development and tumorigenesis.