Literature DB >> 23150038

Studying genomic processes at the single-molecule level: introducing the tools and applications.

David Dulin1, Jan Lipfert, M Charl Moolman, Nynke H Dekker.   

Abstract

To understand genomic processes such as transcription, translation or splicing, we need to be able to study their spatial and temporal organization at the molecular level. Single-molecule approaches provide this opportunity, allowing researchers to monitor molecular conformations, interactions or diffusion quantitatively and in real time in purified systems and in the context of the living cell. This Review introduces the types of application of single-molecule approaches that can enhance our understanding of genome function.

Mesh:

Year:  2012        PMID: 23150038     DOI: 10.1038/nrg3316

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  133 in total

1.  Imaging of single-molecule translocation through nuclear pore complexes.

Authors:  Weidong Yang; Jeff Gelles; Siegfried M Musser
Journal:  Proc Natl Acad Sci U S A       Date:  2004-08-11       Impact factor: 11.205

2.  Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase.

Authors:  Daniel S Johnson; Lu Bai; Benjamin Y Smith; Smita S Patel; Michelle D Wang
Journal:  Cell       Date:  2007-06-29       Impact factor: 41.582

Review 3.  DNA replicases from a bacterial perspective.

Authors:  Charles S McHenry
Journal:  Annu Rev Biochem       Date:  2011       Impact factor: 23.643

4.  A unified model of transcription elongation: what have we learned from single-molecule experiments?

Authors:  Vasisht R Tadigotla; Evgeny Nudler; Andrei E Ruckenstein
Journal:  Biophys J       Date:  2011-03-02       Impact factor: 4.033

5.  Five challenges to bringing single-molecule force spectroscopy into living cells.

Authors:  Yves F Dufrêne; Evan Evans; Andreas Engel; Jonne Helenius; Hermann E Gaub; Daniel J Müller
Journal:  Nat Methods       Date:  2011-02       Impact factor: 28.547

Review 6.  Patch clamp techniques for studying ionic channels in excitable membranes.

Authors:  B Sakmann; E Neher
Journal:  Annu Rev Physiol       Date:  1984       Impact factor: 19.318

7.  Single molecule study of the intrinsically disordered FG-repeat nucleoporin 153.

Authors:  Sigrid Milles; Edward A Lemke
Journal:  Biophys J       Date:  2011-10-05       Impact factor: 4.033

8.  GTP hydrolysis by IF2 guides progression of the ribosome into elongation.

Authors:  R Andrew Marshall; Colin Echeverría Aitken; Joseph D Puglisi
Journal:  Mol Cell       Date:  2009-07-10       Impact factor: 17.970

9.  Measuring mechanical tension across vinculin reveals regulation of focal adhesion dynamics.

Authors:  Carsten Grashoff; Brenton D Hoffman; Michael D Brenner; Ruobo Zhou; Maddy Parsons; Michael T Yang; Mark A McLean; Stephen G Sligar; Christopher S Chen; Taekjip Ha; Martin A Schwartz
Journal:  Nature       Date:  2010-07-08       Impact factor: 49.962

10.  Probing cellular protein complexes using single-molecule pull-down.

Authors:  Ankur Jain; Ruijie Liu; Biswarathan Ramani; Edwin Arauz; Yuji Ishitsuka; Kaushik Ragunathan; Jeehae Park; Jie Chen; Yang K Xiang; Taekjip Ha
Journal:  Nature       Date:  2011-05-26       Impact factor: 49.962

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  33 in total

1.  High Spatiotemporal-Resolution Magnetic Tweezers: Calibration and Applications for DNA Dynamics.

Authors:  David Dulin; Tao Ju Cui; Jelmer Cnossen; Margreet W Docter; Jan Lipfert; Nynke H Dekker
Journal:  Biophys J       Date:  2015-11-17       Impact factor: 4.033

Review 2.  Modeling stochastic kinetics of molecular machines at multiple levels: from molecules to modules.

Authors:  Debashish Chowdhury
Journal:  Biophys J       Date:  2013-06-04       Impact factor: 4.033

Review 3.  Facilitated diffusion of Argonaute-mediated target search.

Authors:  Tao Ju Cui; Chirlmin Joo
Journal:  RNA Biol       Date:  2019-05-20       Impact factor: 4.652

Review 4.  Bacterial replication, transcription and translation: mechanistic insights from single-molecule biochemical studies.

Authors:  Andrew Robinson; Antoine M van Oijen
Journal:  Nat Rev Microbiol       Date:  2013-04-03       Impact factor: 60.633

5.  The dynamics of forming a triplex in an artificial telomere inferred by DNA mechanics.

Authors:  Ning Li; Junli Wang; Kangkang Ma; Lin Liang; Lipei Mi; Wei Huang; Xiaofeng Ma; Zeyu Wang; Wei Zheng; Linyan Xu; Jun-Hu Chen; Zhongbo Yu
Journal:  Nucleic Acids Res       Date:  2019-09-05       Impact factor: 16.971

6.  Tethered particle analysis of supercoiled circular DNA using peptide nucleic acid handles.

Authors:  Kamilla Norregaard; Magnus Andersson; Peter Eigil Nielsen; Stanley Brown; Lene B Oddershede
Journal:  Nat Protoc       Date:  2014-08-21       Impact factor: 13.491

7.  Invincible DNA tethers: covalent DNA anchoring for enhanced temporal and force stability in magnetic tweezers experiments.

Authors:  Richard Janissen; Bojk A Berghuis; David Dulin; Max Wink; Theo van Laar; Nynke H Dekker
Journal:  Nucleic Acids Res       Date:  2014-08-19       Impact factor: 16.971

8.  Integrated magnetic tweezers and single-molecule FRET for investigating the mechanical properties of nucleic acid.

Authors:  Xi Long; Joseph W Parks; Michael D Stone
Journal:  Methods       Date:  2016-06-15       Impact factor: 3.608

9.  Multimodal Measurements of Single-Molecule Dynamics Using FluoRBT.

Authors:  Ivan E Ivanov; Paul Lebel; Florian C Oberstrass; Charles H Starr; Angelica C Parente; Athena Ierokomos; Zev Bryant
Journal:  Biophys J       Date:  2017-12-13       Impact factor: 4.033

Review 10.  Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics.

Authors:  Carlos A Aguilar; Harold G Craighead
Journal:  Nat Nanotechnol       Date:  2013-10       Impact factor: 39.213

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