Literature DB >> 17328679

High-resolution, single-molecule measurements of biomolecular motion.

William J Greenleaf1, Michael T Woodside, Steven M Block.   

Abstract

Many biologically important macromolecules undergo motions that are essential to their function. Biophysical techniques can now resolve the motions of single molecules down to the nanometer scale or even below, providing new insights into the mechanisms that drive molecular movements. This review outlines the principal approaches that have been used for high-resolution measurements of single-molecule motion, including centroid tracking, fluorescence resonance energy transfer, magnetic tweezers, atomic force microscopy, and optical traps. For each technique, the principles of operation are outlined, the capabilities and typical applications are examined, and various practical issues for implementation are considered. Extensions to these methods are also discussed, with an eye toward future application to outstanding biological problems.

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Year:  2007        PMID: 17328679      PMCID: PMC1945240          DOI: 10.1146/annurev.biophys.36.101106.101451

Source DB:  PubMed          Journal:  Annu Rev Biophys Biomol Struct        ISSN: 1056-8700


  108 in total

1.  Can non-mechanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation.

Authors:  R B Best; B Li; A Steward; V Daggett; J Clarke
Journal:  Biophys J       Date:  2001-10       Impact factor: 4.033

2.  Reverse engineering of the giant muscle protein titin.

Authors:  Hongbin Li; Wolfgang A Linke; Andres F Oberhauser; Mariano Carrion-Vazquez; Jason G Kerkvliet; Hui Lu; Piotr E Marszalek; Julio M Fernandez
Journal:  Nature       Date:  2002-08-29       Impact factor: 49.962

3.  Elastic properties of a single-stranded charged homopolymeric ribonucleotide.

Authors:  Yeonee Seol; Gary M Skinner; Koen Visscher
Journal:  Phys Rev Lett       Date:  2004-09-10       Impact factor: 9.161

4.  Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB.

Authors:  Daniel A Koster; Vincent Croquette; Cees Dekker; Stewart Shuman; Nynke H Dekker
Journal:  Nature       Date:  2005-03-31       Impact factor: 49.962

5.  Direct observation of steps in rotation of the bacterial flagellar motor.

Authors:  Yoshiyuki Sowa; Alexander D Rowe; Mark C Leake; Toshiharu Yakushi; Michio Homma; Akihiko Ishijima; Richard M Berry
Journal:  Nature       Date:  2005-10-06       Impact factor: 49.962

6.  Mechanism of force generation of a viral DNA packaging motor.

Authors:  Yann R Chemla; K Aathavan; Jens Michaelis; Shelley Grimes; Paul J Jardine; Dwight L Anderson; Carlos Bustamante
Journal:  Cell       Date:  2005-09-09       Impact factor: 41.582

7.  Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins.

Authors:  Michael T Woodside; William M Behnke-Parks; Kevan Larizadeh; Kevin Travers; Daniel Herschlag; Steven M Block
Journal:  Proc Natl Acad Sci U S A       Date:  2006-04-10       Impact factor: 11.205

8.  DNA primase acts as a molecular brake in DNA replication.

Authors:  Jong-Bong Lee; Richard K Hite; Samir M Hamdan; X Sunney Xie; Charles C Richardson; Antoine M van Oijen
Journal:  Nature       Date:  2006-02-02       Impact factor: 49.962

9.  Tracking kinesin-driven movements with nanometre-scale precision.

Authors:  J Gelles; B J Schnapp; M P Sheetz
Journal:  Nature       Date:  1988-02-04       Impact factor: 49.962

10.  Direct observation of kinesin stepping by optical trapping interferometry.

Authors:  K Svoboda; C F Schmidt; B J Schnapp; S M Block
Journal:  Nature       Date:  1993-10-21       Impact factor: 49.962

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  137 in total

Review 1.  Single-molecule views of protein movement on single-stranded DNA.

Authors:  Taekjip Ha; Alexander G Kozlov; Timothy M Lohman
Journal:  Annu Rev Biophys       Date:  2012-02-23       Impact factor: 12.981

2.  Colored noise in the fluctuations of an extended DNA molecule detected by optical trapping.

Authors:  Ignacio A Martínez; Saurabh Raj; Dmitri Petrov
Journal:  Eur Biophys J       Date:  2011-11-02       Impact factor: 1.733

Review 3.  Physics of bacterial morphogenesis.

Authors:  Sean X Sun; Hongyuan Jiang
Journal:  Microbiol Mol Biol Rev       Date:  2011-12       Impact factor: 11.056

4.  A structural perspective on the dynamics of kinesin motors.

Authors:  Changbong Hyeon; José N Onuchic
Journal:  Biophys J       Date:  2011-12-07       Impact factor: 4.033

5.  Anti-Arrhenius cleavage of covalent bonds in bottlebrush macromolecules on substrate.

Authors:  Natalia V Lebedeva; Alper Nese; Frank C Sun; Krzysztof Matyjaszewski; Sergei S Sheiko
Journal:  Proc Natl Acad Sci U S A       Date:  2012-05-29       Impact factor: 11.205

6.  Routine and timely sub-picoNewton force stability and precision for biological applications of atomic force microscopy.

Authors:  Allison B Churnside; Ruby May A Sullan; Duc M Nguyen; Sara O Case; Matthew S Bull; Gavin M King; Thomas T Perkins
Journal:  Nano Lett       Date:  2012-06-15       Impact factor: 11.189

7.  Mechanistic constraints from the substrate concentration dependence of enzymatic fluctuations.

Authors:  Jeffrey R Moffitt; Yann R Chemla; Carlos Bustamante
Journal:  Proc Natl Acad Sci U S A       Date:  2010-08-20       Impact factor: 11.205

8.  Simple dark-field microscopy with nanometer spatial precision and microsecond temporal resolution.

Authors:  Hiroshi Ueno; So Nishikawa; Ryota Iino; Kazuhito V Tabata; Shouichi Sakakihara; Toshio Yanagida; Hiroyuki Noji
Journal:  Biophys J       Date:  2010-05-19       Impact factor: 4.033

Review 9.  Single-molecule fluorescence studies of intrinsically disordered proteins and liquid phase separation.

Authors:  Irem Nasir; Paulo L Onuchic; Sergio R Labra; Ashok A Deniz
Journal:  Biochim Biophys Acta Proteins Proteom       Date:  2019-05-02       Impact factor: 3.036

10.  Differentiating amino acid residues and side chain orientations in peptides using scanning tunneling microscopy.

Authors:  Shelley A Claridge; John C Thomas; Miles A Silverman; Jeffrey J Schwartz; Yanlian Yang; Chen Wang; Paul S Weiss
Journal:  J Am Chem Soc       Date:  2013-12-02       Impact factor: 15.419

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