Literature DB >> 31251042

A Tour de Force on the Double Helix: Exploiting DNA Mechanics To Study DNA-Based Molecular Machines.

Michael R Wasserman1, Shixin Liu1.   

Abstract

DNA is both a fundamental building block of life and a fascinating natural polymer. The advent of single-molecule manipulation tools made it possible to exert controlled force on individual DNA molecules and measure their mechanical response. Such investigations elucidated the elastic properties of DNA and revealed its distinctive structural configurations across force regimes. In the meantime, a detailed understanding of DNA mechanics laid the groundwork for single-molecule studies of DNA-binding proteins and DNA-processing enzymes that bend, stretch, and twist DNA. These studies shed new light on the metabolism and transactions of nucleic acids, which constitute a major part of the cell's operating system. Furthermore, the marriage of single-molecule fluorescence visualization and force manipulation has enabled researchers to directly correlate the applied tension to changes in the DNA structure and the behavior of DNA-templated complexes. Overall, experimental exploitation of DNA mechanics has been and will continue to be a unique and powerful strategy for understanding how molecular machineries recognize and modify the physical state of DNA to accomplish their biological functions.

Entities:  

Year:  2019        PMID: 31251042      PMCID: PMC6879785          DOI: 10.1021/acs.biochem.9b00346

Source DB:  PubMed          Journal:  Biochemistry        ISSN: 0006-2960            Impact factor:   3.162


  114 in total

1.  Molecular structure of deoxypentose nucleic acids.

Authors:  M H F WILKINS; A R STOKES; H R WILSON
Journal:  Nature       Date:  1953-04-25       Impact factor: 49.962

2.  Forces during bacteriophage DNA packaging and ejection.

Authors:  Prashant K Purohit; Mandar M Inamdar; Paul D Grayson; Todd M Squires; Jané Kondev; Rob Phillips
Journal:  Biophys J       Date:  2004-11-19       Impact factor: 4.033

3.  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

Review 4.  Honey, I shrunk the DNA: DNA length as a probe for nucleic-acid enzyme activity.

Authors:  Antoine M van Oijen
Journal:  Biopolymers       Date:  2007-02-05       Impact factor: 2.505

5.  Single-molecule imaging of RNA polymerase-DNA interactions in real time.

Authors:  Y Harada; T Funatsu; K Murakami; Y Nonoyama; A Ishihama; T Yanagida
Journal:  Biophys J       Date:  1999-02       Impact factor: 4.033

6.  Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching by single-molecule calorimetry.

Authors:  Xinghua Zhang; Hu Chen; Shimin Le; Ioulia Rouzina; Patrick S Doyle; Jie Yan
Journal:  Proc Natl Acad Sci U S A       Date:  2013-02-19       Impact factor: 11.205

7.  Introduction to Optical Tweezers: Background, System Designs, and Commercial Solutions.

Authors:  Joost van Mameren; Gijs J L Wuite; Iddo Heller
Journal:  Methods Mol Biol       Date:  2018

8.  SSB functions as a sliding platform that migrates on DNA via reptation.

Authors:  Ruobo Zhou; Alexander G Kozlov; Rahul Roy; Jichuan Zhang; Sergey Korolev; Timothy M Lohman; Taekjip Ha
Journal:  Cell       Date:  2011-07-22       Impact factor: 41.582

Review 9.  Revisiting the central dogma one molecule at a time.

Authors:  Carlos Bustamante; Wei Cheng; Yara X Mejia; Yara X Meija
Journal:  Cell       Date:  2011-02-18       Impact factor: 41.582

10.  The mechanism of DNA unwinding by the eukaryotic replicative helicase.

Authors:  Daniel R Burnham; Hazal B Kose; Rebecca B Hoyle; Hasan Yardimci
Journal:  Nat Commun       Date:  2019-05-14       Impact factor: 14.919

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