eprintid: 1816
rev_number: 7
eprint_status: archive
userid: 6
dir: disk0/00/00/18/16
datestamp: 2013-10-04 09:15:39
lastmod: 2013-11-21 12:17:44
status_changed: 2013-10-04 09:15:39
type: article
metadata_visibility: show
creators_name: Hyeon, Changbong
creators_name: Morrison, Greg
creators_name: Thirumalai, D.
creators_id: 
creators_id: greg.morrison@imtlucca.it
creators_id: 
title: Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes
ispublished: pub
subjects: QC
divisions: EIC
full_text_status: none
abstract: 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 Foeq(zm), where zm is the molecular extension of the hairpin. Accurate measurements of Foeq(zm) requires stiff polymers with small L/lp, where L is the contour length of the handle, and lp 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 Foeq(zm) at an external tension fm, 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 zm is a good reaction coordinate for nucleic acid hairpins under tension.
date: 2008
date_type: published
publication: Proceedings of the National Academy of Sciences
volume: 105
number: 28
publisher: National Academy of Sciences
pagerange: 9604-9609
id_number: 10.1073/pnas.0802484105 
refereed: TRUE
issn: 1091-6490
official_url: http://www.pnas.org/content/105/28/9604.abstract
related_url_url: http://arxiv.org/abs/0808.0480
citation:   Hyeon, Changbong and Morrison, Greg and Thirumalai, D.  Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes.  Proceedings of the National Academy of Sciences, 105 (28).  pp. 9604-9609.  ISSN 1091-6490      (2008)