Literature DB >> 26156085

DNA Brushing Shoulders: Targeted Looping and Scanning of Large DNA Strands.

Zubair Azad1, Maedeh Roushan1, Robert Riehn1.   

Abstract

We present a nanofluidic device for targeted manipulations in the quarternary structure of single DNA molecules. We demonstrate the folding and unfolding of hairpin-shaped regions, similar to chromatin loops. These loops are stable for minutes at nanochannel junctions. We demonstrate continuous scanning of two DNA segments that occupy a common nanovolume. We present a model governing the stability of loop folds and discuss how the system achieves specific DNA configurations without operator intervention.

Entities:  

Keywords:  DNA; DNA loops; Nanofluidics; fluorescence microscopy; nanoconfinement; single-molecule

Mesh：

Substances：

Year:  2015        PMID： 26156085      PMCID： PMC4684187          DOI： 10.1021/acs.nanolett.5b02476

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


  29 in total

1.  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

2.  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

Review 3.  Facilitated target location in biological systems.

Authors:  P H von Hippel; O G Berg
Journal:  J Biol Chem       Date:  1989-01-15       Impact factor: 5.157

4.  Protein-mediated DNA loops: effects of protein bridge size and kinks.

Authors:  Nicolas Douarche; Simona Cocco
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2005-12-02

5.  Modeling the relaxation time of DNA confined in a nanochannel.

Authors:  Douglas R Tree; Yanwei Wang; Kevin D Dorfman
Journal:  Biomicrofluidics       Date:  2013-10-22       Impact factor: 2.800

6.  Abrupt buckling transition observed during the plectoneme formation of individual DNA molecules.

Authors:  Scott Forth; Christopher Deufel; Maxim Y Sheinin; Bryan Daniels; James P Sethna; Michelle D Wang
Journal:  Phys Rev Lett       Date:  2008-04-08       Impact factor: 9.161

Review 7.  DNA confinement in nanochannels: physics and biological applications.

Authors:  Walter Reisner; Jonas N Pedersen; Robert H Austin
Journal:  Rep Prog Phys       Date:  2012-09-13

8.  Simulation of DNA Extension in Nanochannels.

Authors:  Yanwei Wang; Douglas R Tree; Kevin D Dorfman
Journal:  Macromolecules       Date:  2011-08-23       Impact factor: 5.985

9.  DNA flexibility studied by covalent closure of short fragments into circles.

Authors:  D Shore; J Langowski; R L Baldwin
Journal:  Proc Natl Acad Sci U S A       Date:  1981-08       Impact factor: 11.205

10.  Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation.

Authors:  Remus T Dame; Maarten C Noom; Gijs J L Wuite
Journal:  Nature       Date:  2006-11-16       Impact factor: 49.962
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  4 in total

1.  Nanoplumbing with 2D Metamaterials.

Authors:  Saroj Dangi; Robert Riehn
Journal:  Small       Date:  2018-12-11       Impact factor: 13.281

2.  Optofluidic chips with nanochannels for dynamic molecular detection using enhanced fluorescence.

Authors:  P A Postigo; R Alvaro; A Juarros; S Merino
Journal:  Biomed Opt Express       Date:  2016-08-09       Impact factor: 3.732

Review 3.  Analysis of single nucleic acid molecules in micro- and nano-fluidics.

Authors:  Sarah M Friedrich; Helena C Zec; Tza-Huei Wang
Journal:  Lab Chip       Date:  2016-03-07       Impact factor: 6.799

4.  A nanofluidic knot factory based on compression of single DNA in nanochannels.

Authors:  Susan Amin; Ahmed Khorshid; Lili Zeng; Philip Zimny; Walter Reisner
Journal:  Nat Commun       Date:  2018-04-17       Impact factor: 14.919
  4 in total

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