Literature DB >> 16963512

DNA as a metrology standard for length and force measurements with optical tweezers.

John Peter Rickgauer1, Derek N Fuller, Douglas E Smith.   

Abstract

Optical tweezers have broad applications in studies of structures and processes in molecular and cellular biophysics. Use of optical tweezers for quantitative molecular-scale measurement requires careful calibration in physical units. Here we show that DNA molecules may be used as metrology standards for force and length measurements. Analysis of DNA molecules of two specific lengths allows simultaneous determination of all essential measurement parameters. We validate this biological-calibration method experimentally and with simulated data, and show that precisions in determining length scale factor ( approximately 0.2%), length offset ( approximately 0.03%), force scale factor ( approximately 2%), and compliance of the traps ( approximately 3%) are limited only by current measurement variation, much of which arises from polydispersity of the microspheres ( approximately 2%). We find this procedure to be simpler and more convenient than previous methods, and suggest that it provides an easily replicated standard that can insure uniformity of measurements made in different laboratories.

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Year:  2006        PMID: 16963512      PMCID: PMC1635671          DOI: 10.1529/biophysj.106.089524

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  27 in total

1.  Reversible unfolding of single RNA molecules by mechanical force.

Authors:  J Liphardt; B Onoa; S B Smith; I Tinoco; C Bustamante
Journal:  Science       Date:  2001-04-27       Impact factor: 47.728

2.  Three-dimensional high-resolution particle tracking for optical tweezers by forward scattered light.

Authors:  A Pralle; M Prummer; E L Florin; E H Stelzer; J K Hörber
Journal:  Microsc Res Tech       Date:  1999-03-01       Impact factor: 2.769

3.  Optical-trap force transducer that operates by direct measurement of light momentum.

Authors:  Steven B Smith; Yujia Cui; Carlos Bustamante
Journal:  Methods Enzymol       Date:  2003       Impact factor: 1.600

4.  Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads.

Authors:  S B Smith; L Finzi; C Bustamante
Journal:  Science       Date:  1992-11-13       Impact factor: 47.728

5.  Control of relative radiation pressure in optical traps: application to phagocytic membrane binding studies.

Authors:  Holger Kress; Ernst H K Stelzer; Gareth Griffiths; Alexander Rohrbach
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2005-06-29

6.  Resource Letter: LBOT-1: Laser-based optical tweezers.

Authors:  Matthew J Lang; Steven M Block
Journal:  Am J Phys       Date:  2003-03       Impact factor: 1.022

7.  Multiple- and single-molecule analysis of the actomyosin motor by nanometer-piconewton manipulation with a microneedle: unitary steps and forces.

Authors:  A Ishijima; H Kojima; H Higuchi; Y Harada; T Funatsu; T Yanagida
Journal:  Biophys J       Date:  1996-01       Impact factor: 4.033

8.  Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules.

Authors:  S B Smith; Y Cui; C Bustamante
Journal:  Science       Date:  1996-02-09       Impact factor: 47.728

9.  Quantitative measurements of force and displacement using an optical trap.

Authors:  R M Simmons; J T Finer; S Chu; J A Spudich
Journal:  Biophys J       Date:  1996-04       Impact factor: 4.033

10.  Optical trapping and manipulation of viruses and bacteria.

Authors:  A Ashkin; J M Dziedzic
Journal:  Science       Date:  1987-03-20       Impact factor: 47.728

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  18 in total

1.  Measurements of single DNA molecule packaging dynamics in bacteriophage lambda reveal high forces, high motor processivity, and capsid transformations.

Authors:  Derek N Fuller; Dorian M Raymer; John Peter Rickgauer; Rae M Robertson; Carlos E Catalano; Dwight L Anderson; Shelley Grimes; Douglas E Smith
Journal:  J Mol Biol       Date:  2007-09-11       Impact factor: 5.469

2.  Single phage T4 DNA packaging motors exhibit large force generation, high velocity, and dynamic variability.

Authors:  Derek N Fuller; Dorian M Raymer; Vishal I Kottadiel; Venigalla B Rao; Douglas E Smith
Journal:  Proc Natl Acad Sci U S A       Date:  2007-10-17       Impact factor: 11.205

3.  Portal motor velocity and internal force resisting viral DNA packaging in bacteriophage phi29.

Authors:  John Peter Rickgauer; Derek N Fuller; Shelley Grimes; Paul J Jardine; Dwight L Anderson; Douglas E Smith
Journal:  Biophys J       Date:  2007-09-07       Impact factor: 4.033

4.  Precision steering of an optical trap by electro-optic deflection.

Authors:  Megan T Valentine; Nicholas R Guydosh; Braulio Gutiérrez-Medina; Adrian N Fehr; Johan O Andreasson; Steven M Block
Journal:  Opt Lett       Date:  2008-03-15       Impact factor: 3.776

5.  Elasticity of short DNA molecules: theory and experiment for contour lengths of 0.6-7 microm.

Authors:  Yeonee Seol; Jinyu Li; Philip C Nelson; Thomas T Perkins; M D Betterton
Journal:  Biophys J       Date:  2007-08-31       Impact factor: 4.033

6.  Accurate measurement of force and displacement with optical tweezers using DNA molecules as metrology standards.

Authors:  Damian delToro; Douglas E Smith
Journal:  Appl Phys Lett       Date:  2014-04-08       Impact factor: 3.791

7.  Continuous allosteric regulation of a viral packaging motor by a sensor that detects the density and conformation of packaged DNA.

Authors:  Zachary T Berndsen; Nicholas Keller; Douglas E Smith
Journal:  Biophys J       Date:  2015-01-20       Impact factor: 4.033

8.  Repulsive DNA-DNA interactions accelerate viral DNA packaging in phage Phi29.

Authors:  Nicholas Keller; Damian delToro; Shelley Grimes; Paul J Jardine; Douglas E Smith
Journal:  Phys Rev Lett       Date:  2014-06-17       Impact factor: 9.161

9.  Walker-A Motif Acts to Coordinate ATP Hydrolysis with Motor Output in Viral DNA Packaging.

Authors:  Damian delToro; David Ortiz; Mariam Ordyan; Jean Sippy; Choon-Seok Oh; Nicholas Keller; Michael Feiss; Carlos E Catalano; Douglas E Smith
Journal:  J Mol Biol       Date:  2016-04-30       Impact factor: 5.469

10.  Functional Dissection of a Viral DNA Packaging Machine's Walker B Motif.

Authors:  Damian delToro; David Ortiz; Mariam Ordyan; Joshua Pajak; Jean Sippy; Alexis Catala; Choon-Seok Oh; Amber Vu; Gaurav Arya; Douglas E Smith; Carlos E Catalano; Michael Feiss
Journal:  J Mol Biol       Date:  2019-08-30       Impact factor: 5.469

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