Literature DB >> 23186544

Nanoscale squeezing in elastomeric nanochannels for single chromatin linearization.

Toshiki Matsuoka1, Byoung Choul Kim, Jiexi Huang, Nicholas Joseph Douville, M D Thouless, Shuichi Takayama.   

Abstract

This paper describes a novel nanofluidic phenomenon where untethered DNA and chromatin are linearized by rapidly narrowing an elastomeric nanochannel filled with solutions of the biopolymers. This nanoscale squeezing procedure generates hydrodynamic flows while also confining the biopolymers into smaller and smaller volumes. The unique features of this technique enable full linearization then trapping of biopolymers such as DNA. The versatility of the method is also demonstrated by analysis of chromatin stretchability and mapping of histone states using single strands of chromatin.

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Year:  2012        PMID: 23186544      PMCID: PMC3522175          DOI: 10.1021/nl304063f

Source DB:  PubMed          Journal:  Nano Lett        ISSN: 1530-6984            Impact factor:   11.189


  27 in total

Review 1.  Chromatin higher-order structure and dynamics.

Authors:  Christopher L Woodcock; Rajarshi P Ghosh
Journal:  Cold Spring Harb Perspect Biol       Date:  2010-04-07       Impact factor: 10.005

2.  Instantaneous fabrication of arrays of normally closed, adjustable, and reversible nanochannels by tunnel cracking.

Authors:  K L Mills; Dongeun Huh; Shuichi Takayama; M D Thouless
Journal:  Lab Chip       Date:  2010-03-25       Impact factor: 6.799

3.  Statics and dynamics of single DNA molecules confined in nanochannels.

Authors:  Walter Reisner; Keith J Morton; Robert Riehn; Yan Mei Wang; Zhaoning Yu; Michael Rosen; James C Sturm; Stephen Y Chou; Erwin Frey; Robert H Austin
Journal:  Phys Rev Lett       Date:  2005-05-16       Impact factor: 9.161

4.  Tuneable elastomeric nanochannels for nanofluidic manipulation.

Authors:  Dongeun Huh; K L Mills; Xiaoyue Zhu; Mark A Burns; M D Thouless; Shuichi Takayama
Journal:  Nat Mater       Date:  2007-05-07       Impact factor: 43.841

5.  A device for extraction, manipulation and stretching of DNA from single human chromosomes.

Authors:  Kristian H Rasmussen; Rodolphe Marie; Jacob M Lange; Winnie E Svendsen; Anders Kristensen; Kalim U Mir
Journal:  Lab Chip       Date:  2011-02-25       Impact factor: 6.799

6.  Single molecule epigenetic analysis in a nanofluidic channel.

Authors:  Benjamin R Cipriany; Ruqian Zhao; Patrick J Murphy; Stephen L Levy; Christine P Tan; Harold G Craighead; Paul D Soloway
Journal:  Anal Chem       Date:  2010-03-15       Impact factor: 6.986

Review 7.  DNA in nanochannels--directly visualizing genomic information.

Authors:  Fredrik Persson; Jonas O Tegenfeldt
Journal:  Chem Soc Rev       Date:  2010-01-25       Impact factor: 54.564

8.  Nanochannel confinement: DNA stretch approaching full contour length.

Authors:  Yoori Kim; Ki Seok Kim; Kristy L Kounovsky; Rakwoo Chang; Gun Young Jung; Juan J dePablo; Kyubong Jo; David C Schwartz
Journal:  Lab Chip       Date:  2011-03-23       Impact factor: 6.799

Review 9.  Confining euchromatin/heterochromatin territory: jumonji crosses the line.

Authors:  Hisashi Tamaru
Journal:  Genes Dev       Date:  2010-07-15       Impact factor: 11.361

10.  Stretching chromatin through confinement.

Authors:  Diana E Streng; Shuang Fang Lim; Junhan Pan; Alena Karpusenka; Robert Riehn
Journal:  Lab Chip       Date:  2009-08-14       Impact factor: 6.799

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  20 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.  The Collapse and Expansion of Liquid-Filled Elastic Channels and Cracks.

Authors:  Fanbo Meng; Jiexi Huang; M D Thouless
Journal:  J Appl Mech       Date:  2015-07-22       Impact factor: 2.168

3.  Chromatin modification mapping in nanochannels.

Authors:  Shuang Fang Lim; Alena Karpusenko; Ansel L Blumers; Diana E Streng; Robert Riehn
Journal:  Biomicrofluidics       Date:  2013-11-21       Impact factor: 2.800

4.  Micro- and nanofluidic technologies for epigenetic profiling.

Authors:  Toshiki Matsuoka; Byoung Choul Kim; Christopher Moraes; Minsub Han; Shuichi Takayama
Journal:  Biomicrofluidics       Date:  2013-07-24       Impact factor: 2.800

5.  Electrophoretic stretching and imaging of single native chromatin fibers in nanoslits.

Authors:  Jia-Wei Yeh; Kylan Szeto
Journal:  Biomicrofluidics       Date:  2017-07-25       Impact factor: 2.800

6.  Defined topologically-complex protein matrices to manipulate cell shape via three-dimensional fiber-like patterns.

Authors:  Christopher Moraes; Byoung Choul Kim; Xiaoyue Zhu; Kristen L Mills; Angela R Dixon; M D Thouless; Shuichi Takayama
Journal:  Lab Chip       Date:  2014-03-14       Impact factor: 6.799

7.  Fracture fabrication of a multi-scale channel device that efficiently captures and linearizes DNA from dilute solutions.

Authors:  Byoung Choul Kim; Priyan Weerappuli; M D Thouless; Shuichi Takayama
Journal:  Lab Chip       Date:  2015-03-07       Impact factor: 6.799

8.  Dynamic simulations show repeated narrowing maximizes DNA linearization in elastomeric nanochannels.

Authors:  Minsub Han; Byoung Choul Kim; Toshiki Matsuoka; M D Thouless; Shuichi Takayama
Journal:  Biomicrofluidics       Date:  2016-11-23       Impact factor: 2.800

Review 9.  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

10.  Super-resolution imaging of PDMS nanochannels by single-molecule micelle-assisted blink microscopy.

Authors:  Mou-Chi Cheng; Austin T Leske; Toshiki Matsuoka; Byoung Choul Kim; Jaesung Lee; Mark A Burns; Shuichi Takayama; Julie S Biteen
Journal:  J Phys Chem B       Date:  2013-01-08       Impact factor: 2.991

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