Literature DB >> 25316922

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

Damian delToro1, Douglas E Smith1.   

Abstract

Optical tweezers facilitate measurement of piconewton-level forces and nanometer-level displacements and have broad applications in biophysics and soft matter physics research. We have shown previously that DNA molecules can be used as metrology standards to define such measurements. Force-extension measurements on two DNA molecules of different lengths can be used to determine four necessary measurement parameters. Here, we show that the accuracy of determining these parameters can be improved by more than 7-fold by incorporating measurements of the DNA overstretching transition and using a multi-step data analysis procedure. This method results in very robust and precise fitting of DNA force-extension measurements to the worm-like chain model. We verify the accuracy through independent measurements of DNA stretching, DNA unzipping, and microsphere contact forces.

Year:  2014        PMID: 25316922      PMCID: PMC4169375          DOI: 10.1063/1.4871005

Source DB:  PubMed          Journal:  Appl Phys Lett        ISSN: 0003-6951            Impact factor:   3.791


  24 in total

Review 1.  Grabbing the cat by the tail: manipulating molecules one by one.

Authors:  C Bustamante; J C Macosko; G J Wuite
Journal:  Nat Rev Mol Cell Biol       Date:  2000-11       Impact factor: 94.444

2.  Single-molecule studies of DNA mechanics.

Authors:  C Bustamante; S B Smith; J Liphardt; D Smith
Journal:  Curr Opin Struct Biol       Date:  2000-06       Impact factor: 6.809

3.  An integrated laser trap/flow control video microscope for the study of single biomolecules.

Authors:  G J Wuite; R J Davenport; A Rappaport; C Bustamante
Journal:  Biophys J       Date:  2000-08       Impact factor: 4.033

4.  Optical trapping.

Authors:  Keir C Neuman; Steven M Block
Journal:  Rev Sci Instrum       Date:  2004-09       Impact factor: 1.523

5.  Observation of a single-beam gradient force optical trap for dielectric particles.

Authors:  A Ashkin; J M Dziedzic; J E Bjorkholm; S Chu
Journal:  Opt Lett       Date:  1986-05-01       Impact factor: 3.776

6.  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

7.  Behavior of supercoiled DNA.

Authors:  T R Strick; J F Allemand; D Bensimon; V Croquette
Journal:  Biophys J       Date:  1998-04       Impact factor: 4.033

Review 8.  Single-molecule studies of viral DNA packaging.

Authors:  Douglas E Smith
Journal:  Curr Opin Virol       Date:  2011-07-01       Impact factor: 7.090

9.  Direct measurement of the intermolecular forces confining a single molecule in an entangled polymer solution.

Authors:  Rae M Robertson; Douglas E Smith
Journal:  Phys Rev Lett       Date:  2007-09-21       Impact factor: 9.161

10.  A general method for manipulating DNA sequences from any organism with optical tweezers.

Authors:  Derek N Fuller; Gregory J Gemmen; John Peter Rickgauer; Aurelie Dupont; Rachel Millin; Pierre Recouvreux; Douglas E Smith
Journal:  Nucleic Acids Res       Date:  2006-02-01       Impact factor: 16.971

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  9 in total

1.  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

2.  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

3.  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

4.  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

5.  Nonequilibrium dynamics and ultraslow relaxation of confined DNA during viral packaging.

Authors:  Zachary T Berndsen; Nicholas Keller; Shelley Grimes; Paul J Jardine; Douglas E Smith
Journal:  Proc Natl Acad Sci U S A       Date:  2014-05-27       Impact factor: 11.205

6.  Nucleotide-dependent DNA gripping and an end-clamp mechanism regulate the bacteriophage T4 viral packaging motor.

Authors:  Mariam Ordyan; Istiaq Alam; Marthandan Mahalingam; Venigalla B Rao; Douglas E Smith
Journal:  Nat Commun       Date:  2018-12-21       Impact factor: 14.919

7.  Determining Trap Compliances, Microsphere Size Variations, and Response Linearities in Single DNA Molecule Elasticity Measurements with Optical Tweezers.

Authors:  Youbin Mo; Mounir Fizari; Kristina Koharchik; Douglas E Smith
Journal:  Front Mol Biosci       Date:  2021-03-22

8.  Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor.

Authors:  Amy D Migliori; Nicholas Keller; Tanfis I Alam; Marthandan Mahalingam; Venigalla B Rao; Gaurav Arya; Douglas E Smith
Journal:  Nat Commun       Date:  2014-06-17       Impact factor: 14.919

9.  Function of a viral genome packaging motor from bacteriophage T4 is insensitive to DNA sequence.

Authors:  Youbin Mo; Nicholas Keller; Damian delToro; Neeti Ananthaswamy; Stephen C Harvey; Venigalla B Rao; Douglas E Smith
Journal:  Nucleic Acids Res       Date:  2020-11-18       Impact factor: 19.160

  9 in total

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