Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results.

Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results. Research Abstract Details 

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Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results. Abstract Text:

Jin-Der Wen,Maria Manosas,Pan T X Li,Steven B Smith,Carlos Bustamante,Felix Ritort,Ignacio Tinoco,

Experimental variables of optical tweezers instrumentation that affect RNA folding/unfolding kinetics were investigated. A model RNA hairpin, P5ab, was attached to two micron-sized beads through hybrid RNA/DNA handles; one bead was trapped by dual-beam lasers and the other was held by a micropipette. Several experimental variables were changed while measuring the unfolding/refolding kinetics, including handle lengths, trap stiffness, and modes of force applied to the molecule. In constant-force mode where the tension applied to the RNA was maintained through feedback control, the measured rate coefficients varied within 40% when the handle lengths were changed by 10-fold (1.1-10.2 Kbp); they increased by two- to threefold when the trap stiffness was lowered to one-third (from 0.1 to 0.035 pN/nm). In the passive mode, without feedback control and where the force applied to the RNA varied in response to the end-to-end distance change of the tether, the RNA hopped between a high-force folded-state and a low-force unfolded-state. In this mode, the rates increased up to twofold with longer handles or softer traps. Overall, the measured rates remained with the same order-of-magnitude over the wide range of conditions studied. In the companion article on pages 3010-3021, we analyze how the measured kinetics parameters differ from the intrinsic molecular rates of the RNA, and thus how to obtain the molecular rates.

Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results. Publishing Authors By Initials

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

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

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MEDLINE DATE:

Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results. Journal Published:

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

Journal: Biophysical journal

VOLUME: 92

Page Numbers: 2996-3009

Journal Abbreviation:

ISSN: 0006-3495

DAY: 9

MONTH: 02

YEAR: 2007

Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 370626

Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results. Keywords Mesh Terms:

KEYWORDS: Stress, Mechanical

MESH TERMS: ultrastructure

Chemical & Substance for Abstract: Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results. Information

Substance Name: RNA

Registry Number: 63231-63-0

Grant and Affiliation Information for Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results.

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

Country: United States

AGENCY: United States NIGMS

GRANT: GM-32543

ACRONYM: GM

MEDLINETA: Biophys J

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