Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments.

Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments. Research Abstract Details 

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Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments. Abstract Text:

M Manosas,J-D Wen,P T X Li,S B Smith,C Bustamante,I Tinoco,F Ritort,

By exerting mechanical force, it is possible to unfold/refold RNA molecules one at a time. In a small range of forces, an RNA molecule can hop between the folded and the unfolded state with force-dependent kinetic rates. Here, we introduce a mesoscopic model to analyze the hopping kinetics of RNA hairpins in an optical tweezers setup. The model includes different elements of the experimental setup (beads, handles, and RNA sequence) and limitations of the instrument (time lag of the force-feedback mechanism and finite bandwidth of data acquisition). We investigated the influence of the instrument on the measured hopping rates. Results from the model are in good agreement with the experiments reported in the companion article. The comparison between theory and experiments allowed us to infer the values of the intrinsic molecular rates of the RNA hairpin alone and to search for the optimal experimental conditions to do the measurements. We conclude that the longest handles and softest traps that allow detection of the folding/unfolding signal (handles approximately 5-10 Kbp and traps approximately 0.03 pN/nm) represent the best conditions to obtain the intrinsic molecular rates. The methodology and rationale presented here can be applied to other experimental setups and other molecules.

Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments. Publishing Authors By Initials

M Manosas,JD Wen,PT Li,SB Smith,C Bustamante,I Tinoco,F Ritort,

For similar biomechanics: stress, mechanical research abstracts see: biomechanics: stress, mechanical research

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Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: Biophysical journal

VOLUME: 92

Page Numbers: 3010-21

Journal Abbreviation:

ISSN: 0006-3495

DAY: 9

MONTH: 02

YEAR: 2007

Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 370626

Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments. Keywords Mesh Terms:

KEYWORDS: Stress, Mechanical

MESH TERMS: ultrastructure

Chemical & Substance for Abstract: Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments. Information

Substance Name: RNA

Registry Number: 63231-63-0

Grant and Affiliation Information for Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments.

AFFILIATION: Department of Chemistry, University of California at Berkeley, Berkeley, California, USA.

Country: United States

AGENCY: United States NIGMS

GRANT: GM-32543

ACRONYM: GM

MEDLINETA: Biophys J

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