Literature DB >> 15252203

From the Cover: The dynamics of genomic-length DNA molecules in 100-nm channels.

Jonas O Tegenfeldt1, Christelle Prinz, Han Cao, Steven Chou, Walter W Reisner, Robert Riehn, Yan Mei Wang, Edward C Cox, James C Sturm, Pascal Silberzan, Robert H Austin.   

Abstract

We show that genomic-length DNA molecules imaged in nanochannels have an extension along the channel that scales linearly with the contour length of the polymer, in agreement with the scaling arguments developed by de Gennes for self-avoiding confined polymers. This fundamental relationship allows us to measure directly the contour length of single DNA molecules confined in the channels, and the statistical analysis of the dynamics of the polymer in the nanochannel allows us to compute the SD of the mean of the extension. This statistical analysis allows us to measure the extension of lambda DNA multimers with a 130-nm SD in 1 min.

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Year:  2004        PMID: 15252203      PMCID: PMC503729          DOI: 10.1073/pnas.0403849101

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  10 in total

1.  Whole-genome shotgun optical mapping of Deinococcus radiodurans.

Authors:  J Lin; R Qi; C Aston; J Jing; T S Anantharaman; B Mishra; O White; M J Daly; K W Minton; J C Venter; D C Schwartz
Journal:  Science       Date:  1999-09-03       Impact factor: 47.728

2.  Separation of long DNA molecules in a microfabricated entropic trap array.

Authors:  J Han; H G Craighead
Journal:  Science       Date:  2000-05-12       Impact factor: 47.728

Review 3.  Theory of DNA electrophoresis: a look at some current challenges.

Authors:  G W Slater; C Desruisseaux; S J Hubert; J F Mercier; J Labrie; J Boileau; F Tessier; M P Pépin
Journal:  Electrophoresis       Date:  2000-12       Impact factor: 3.535

4.  Precise nanometer localization analysis for individual fluorescent probes.

Authors:  Russell E Thompson; Daniel R Larson; Watt W Webb
Journal:  Biophys J       Date:  2002-05       Impact factor: 4.033

5.  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

6.  Kinks, rings, and rackets in filamentous structures.

Authors:  Adam E Cohen; L Mahadevan
Journal:  Proc Natl Acad Sci U S A       Date:  2003-10-06       Impact factor: 11.205

7.  Estimating the persistence length of a worm-like chain molecule from force-extension measurements.

Authors:  C Bouchiat; M D Wang; J Allemand; T Strick; S M Block; V Croquette
Journal:  Biophys J       Date:  1999-01       Impact factor: 4.033

8.  Stretching of a single tethered polymer in a uniform flow.

Authors:  T T Perkins; D E Smith; R G Larson; S Chu
Journal:  Science       Date:  1995-04-07       Impact factor: 47.728

9.  Nucleotide sequence of bacteriophage lambda DNA.

Authors:  F Sanger; A R Coulson; G F Hong; D F Hill; G B Petersen
Journal:  J Mol Biol       Date:  1982-12-25       Impact factor: 5.469

10.  Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization.

Authors:  Ahmet Yildiz; Joseph N Forkey; Sean A McKinney; Taekjip Ha; Yale E Goldman; Paul R Selvin
Journal:  Science       Date:  2003-06-05       Impact factor: 47.728

  10 in total
  104 in total

1.  Surface charge, electroosmotic flow and DNA extension in chemically modified thermoplastic nanoslits and nanochannels.

Authors:  Franklin I Uba; Swathi R Pullagurla; Nichanun Sirasunthorn; Jiahao Wu; Sunggook Park; Rattikan Chantiwas; Yoon-Kyoung Cho; Heungjoo Shin; Steven A Soper
Journal:  Analyst       Date:  2015-01-07       Impact factor: 4.616

2.  Fluctuation modes of nanoconfined DNA.

Authors:  Alena Karpusenko; Joshua H Carpenter; Chunda Zhou; Shuang Fang Lim; Junhan Pan; Robert Riehn
Journal:  J Appl Phys       Date:  2012-01-17       Impact factor: 2.546

3.  Simulation of conformational preconditioning strategies for electrophoretic stretching of DNA in a microcontraction.

Authors:  Chih-Chen Hsieh; Tsung-Hsien Lin
Journal:  Biomicrofluidics       Date:  2011-11-10       Impact factor: 2.800

4.  Shape transition of semi-flexible macromolecules confined in channel and cavity.

Authors:  P Cifra; T Bleha
Journal:  Eur Phys J E Soft Matter       Date:  2010-07-27       Impact factor: 1.890

5.  Single-molecule denaturation mapping of DNA in nanofluidic channels.

Authors:  Walter Reisner; Niels B Larsen; Asli Silahtaroglu; Anders Kristensen; Niels Tommerup; Jonas O Tegenfeldt; Henrik Flyvbjerg
Journal:  Proc Natl Acad Sci U S A       Date:  2010-07-07       Impact factor: 11.205

6.  Visualizing the entire DNA from a chromosome in a single frame.

Authors:  C Freitag; C Noble; J Fritzsche; F Persson; M Reiter-Schad; A N Nilsson; A Granéli; T Ambjörnsson; K U Mir; J O Tegenfeldt
Journal:  Biomicrofluidics       Date:  2015-08-05       Impact factor: 2.800

7.  Presentation of large DNA molecules for analysis as nanoconfined dumbbells.

Authors:  Kristy L Kounovsky-Shafer; Juan P Hernández-Ortiz; Kyubong Jo; Theo Odijk; Juan J de Pablo; David C Schwartz
Journal:  Macromolecules       Date:  2013-10-22       Impact factor: 5.985

8.  Exact curvilinear diffusion coefficients in the repton model.

Authors:  A Buhot
Journal:  Eur Phys J E Soft Matter       Date:  2005-10-19       Impact factor: 1.890

9.  Restriction mapping in nanofluidic devices.

Authors:  Robert Riehn; Manchun Lu; Yan-Mei Wang; Shuang Fang Lim; Edward C Cox; Robert H Austin
Journal:  Proc Natl Acad Sci U S A       Date:  2005-07-06       Impact factor: 11.205

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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