Taekjip Ha

Taekjip Ha

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Taekjip Ha

Publications by authors named "Taekjip Ha"

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Single-Molecule Analysis and Engineering of DNA Motors.

Chem Rev 2020 Jan 29;120(1):36-78. Epub 2019 Oct 29.

Howard Hughes Medical Institute , Baltimore , Maryland 21205 , United States.

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http://dx.doi.org/10.1021/acs.chemrev.9b00361DOI Listing
January 2020

Streamlining effects of extra telomeric repeat on telomeric DNA folding revealed by fluorescence-force spectroscopy.

Nucleic Acids Res 2019 Dec;47(21):11044-11056

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1093/nar/gkz906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6868435PMC
December 2019

Single molecule analysis of effects of non-canonical guide RNAs and specificity-enhancing mutations on Cas9-induced DNA unwinding.

Nucleic Acids Res 2019 Dec;47(22):11880-11888

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1093/nar/gkz1058DOI Listing
December 2019

Structural basis for DNA unwinding at forked dsDNA by two coordinating Pif1 helicases.

Nat Commun 2019 Nov 26;10(1):5375. Epub 2019 Nov 26.

Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou, 310058, China.

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http://dx.doi.org/10.1038/s41467-019-13414-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879534PMC
November 2019

Determinants of target prioritization and regulatory hierarchy for the bacterial small RNA SgrS.

Mol Microbiol 2019 10 6;112(4):1199-1218. Epub 2019 Aug 6.

Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave., Urbana, IL, 61801, USA.

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http://dx.doi.org/10.1111/mmi.14355DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6800775PMC
October 2019

Nanomechanics and co-transcriptional folding of Spinach and Mango.

Nat Commun 2019 09 20;10(1):4318. Epub 2019 Sep 20.

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, 21205, USA.

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http://dx.doi.org/10.1038/s41467-019-12299-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6754394PMC
September 2019

Fight against background noise in stimulated emission depletion nanoscopy.

Authors:
Ye Ma Taekjip Ha

Phys Biol 2019 07 5;16(5):051002. Epub 2019 Jul 5.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America.

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http://dx.doi.org/10.1088/1478-3975/ab255cDOI Listing
July 2019

Nuclear speckle fusion via long-range directional motion regulates speckle morphology after transcriptional inhibition.

J Cell Sci 2019 Apr 17;132(8). Epub 2019 Apr 17.

Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

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http://dx.doi.org/10.1242/jcs.226563DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6503955PMC
April 2019

Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy.

Proc Natl Acad Sci U S A 2019 Apr 3;116(17):8350-8359. Epub 2019 Apr 3.

Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801;

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http://dx.doi.org/10.1073/pnas.1815162116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6486787PMC
April 2019

Single-Molecule Studies of ssDNA-Binding Proteins Exchange.

Methods Enzymol 2018 1;600:463-477. Epub 2018 Feb 1.

Johns Hopkins School of Medicine, Baltimore, MD, United States; Howard Hughes Medical Institute, Baltimore, MD, United States; Johns Hopkins University, Baltimore, MD, United States. Electronic address:

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http://dx.doi.org/10.1016/bs.mie.2017.11.017DOI Listing
March 2019

Single-Molecule FRET Analysis of Replicative Helicases.

Methods Mol Biol 2018 ;1805:233-250

Department of Biophysics and Biophysical Chemistry, Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, MD, USA.

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http://link.springer.com/10.1007/978-1-4939-8556-2_12
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http://dx.doi.org/10.1007/978-1-4939-8556-2_12DOI Listing
March 2019

Junction resolving enzymes use multivalency to keep the Holliday junction dynamic.

Nat Chem Biol 2019 03 21;15(3):269-275. Epub 2019 Jan 21.

Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Champaign, IL, USA.

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http://dx.doi.org/10.1038/s41589-018-0209-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377835PMC
March 2019

Functional instability allows access to DNA in longer transcription Activator-Like effector (TALE) arrays.

Elife 2019 02 27;8. Epub 2019 Feb 27.

T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States.

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https://elifesciences.org/articles/38298
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http://dx.doi.org/10.7554/eLife.38298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6461438PMC
February 2019

Structural Mechanisms of Cooperative DNA Binding by Bacterial Single-Stranded DNA-Binding Proteins.

J Mol Biol 2019 Jan 22;431(2):178-195. Epub 2018 Nov 22.

Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00222836183104
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http://dx.doi.org/10.1016/j.jmb.2018.11.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6331220PMC
January 2019

Contractility kits promote assembly of the mechanoresponsive cytoskeletal network.

J Cell Sci 2019 01 16;132(2). Epub 2019 Jan 16.

Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA

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http://dx.doi.org/10.1242/jcs.226704DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6362397PMC
January 2019

Hexameric helicase G40P unwinds DNA in single base pair steps.

Elife 2019 01 28;8. Epub 2019 Jan 28.

Physics Department and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Illinois, United States.

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http://dx.doi.org/10.7554/eLife.42001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6370340PMC
January 2019

Mimicking Co-Transcriptional RNA Folding Using a Superhelicase.

J Am Chem Soc 2018 08 3;140(32):10067-10070. Epub 2018 Aug 3.

Department of Biophysics and Biophysical Chemistry , Johns Hopkins School of Medicine , Baltimore , Maryland 21205 , United States.

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http://dx.doi.org/10.1021/jacs.8b03784DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6169520PMC
August 2018

Toward Single-Cell Single-Molecule Pull-Down.

Biophys J 2018 07 25;115(2):283-288. Epub 2018 May 25.

Department of Physics, Center for the Physics of Living Cells and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Howard Hughes Medical Institute, Baltimore, Maryland; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, Maryland; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2018.05.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6050716PMC
July 2018

Cdc42-dependent modulation of rigidity sensing and cell spreading in tumor repopulating cells.

Biochem Biophys Res Commun 2018 06 23;500(3):557-563. Epub 2018 Apr 23.

Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1016/j.bbrc.2018.04.085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6133653PMC
June 2018

Real-time observation of DNA target interrogation and product release by the RNA-guided endonuclease CRISPR Cpf1 (Cas12a).

Proc Natl Acad Sci U S A 2018 05 7;115(21):5444-5449. Epub 2018 May 7.

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205;

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http://www.pnas.org/lookup/doi/10.1073/pnas.1718686115
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http://dx.doi.org/10.1073/pnas.1718686115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6003496PMC
May 2018

Correlating Transcription Initiation and Conformational Changes by a Single-Subunit RNA Polymerase with Near Base-Pair Resolution.

Mol Cell 2018 05;70(4):695-706.e5

Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA; Departments of Biophysics and Biophysical Chemistry, Biophysics, and Biomedical Engineering, Johns Hopkins University, MD 21205, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.04.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5983381PMC
May 2018

Mechanisms of improved specificity of engineered Cas9s revealed by single-molecule FRET analysis.

Nat Struct Mol Biol 2018 04 5;25(4):347-354. Epub 2018 Apr 5.

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

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http://dx.doi.org/10.1038/s41594-018-0051-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6195204PMC
April 2018

Understanding the Molecular Mechanisms of the CRISPR Toolbox Using Single Molecule Approaches.

ACS Chem Biol 2018 03 9;13(3):516-526. Epub 2018 Feb 9.

Department of Biophysics and Biophysical Chemistry , Johns Hopkins University School of Medicine , Baltimore , Maryland 21205 , United States.

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http://dx.doi.org/10.1021/acschembio.7b00905DOI Listing
March 2018

The Single-Molecule Centroid Localization Algorithm Improves the Accuracy of Fluorescence Binding Assays.

Biochemistry 2018 03 28;57(10):1572-1576. Epub 2018 Feb 28.

Department of Biophysics and Biophysical Chemistry , Johns Hopkins School of Medicine , Baltimore , Maryland 21205 , United States.

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http://dx.doi.org/10.1021/acs.biochem.7b01293DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6149537PMC
March 2018

Editorial Overview: Single-Molecule Approaches up to Difficult Challenges in Folding and Dynamics.

J Mol Biol 2018 02 27;430(4):405-408. Epub 2017 Dec 27.

Department of Molecular & Cell Biology, Institute for Quantitative Biosciences (QB3)-Berkeley, University of California, Berkeley, Berkeley, CA 94720, United States. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2017.12.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5858691PMC
February 2018

TGFβ1 reinforces arterial aging in the vascular smooth muscle cell through a long-range regulation of the cytoskeletal stiffness.

Sci Rep 2018 02 8;8(1):2668. Epub 2018 Feb 8.

Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.

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http://dx.doi.org/10.1038/s41598-018-20763-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5805716PMC
February 2018

Probing Single Helicase Dynamics on Long Nucleic Acids Through Fluorescence-Force Measurement.

Methods Mol Biol 2017 ;1486:295-316

Department of Biophysics and Biophysical Chemistry, Thomas C. Jenkins Department of Biophysics and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.

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http://dx.doi.org/10.1007/978-1-4939-6421-5_11DOI Listing
January 2018

Mechanism of polypurine tract primer generation by HIV-1 reverse transcriptase.

J Biol Chem 2018 01 9;293(1):191-202. Epub 2017 Nov 9.

Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland

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http://dx.doi.org/10.1074/jbc.M117.798256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5766924PMC
January 2018

Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution.

J Cell Sci 2017 Dec 13;130(24):4180-4192. Epub 2017 Nov 13.

Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1242/jcs.206854DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769577PMC
December 2017

Voltage-gated sodium channels assemble and gate as dimers.

Nat Commun 2017 12 12;8(1):2077. Epub 2017 Dec 12.

Heart and Vascular Research Center, MetroHealth Campus, Case Western Reserve University, Cleveland, 44109, USA.

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http://dx.doi.org/10.1038/s41467-017-02262-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5727259PMC
December 2017

Single-cell analysis of early antiviral gene expression reveals a determinant of stochastic IFNB1 expression.

Integr Biol (Camb) 2017 Nov;9(11):857-867

Center for Computational Biology and Biophysics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1039/c7ib00146kDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6201300PMC
November 2017

Sphingolipids facilitate age asymmetry of membrane proteins in dividing yeast cells.

Mol Biol Cell 2017 Oct 2;28(20):2712-2722. Epub 2017 Aug 2.

Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205

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http://dx.doi.org/10.1091/mbc.E17-05-0335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5620378PMC
October 2017

Metals induce transient folding and activation of the twister ribozyme.

Nat Chem Biol 2017 Oct 21;13(10):1109-1114. Epub 2017 Aug 21.

T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA.

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http://www.nature.com/doifinder/10.1038/nchembio.2459
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http://dx.doi.org/10.1038/nchembio.2459DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5605428PMC
October 2017

Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes.

Nat Commun 2017 09 8;8(1):492. Epub 2017 Sep 8.

T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA.

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http://dx.doi.org/10.1038/s41467-017-00536-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5591316PMC
September 2017

Single-molecule imaging reveals the translocation and DNA looping dynamics of hepatitis C virus NS3 helicase.

Protein Sci 2017 Jul 6;26(7):1391-1403. Epub 2017 Mar 6.

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, Maryland.

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http://dx.doi.org/10.1002/pro.3136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5477530PMC
July 2017

A genetically encoded fluorescent tRNA is active in live-cell protein synthesis.

Nucleic Acids Res 2017 04;45(7):4081-4093

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1093/nar/gkw1229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5397188PMC
April 2017

Notch-Jagged complex structure implicates a catch bond in tuning ligand sensitivity.

Science 2017 03 2;355(6331):1320-1324. Epub 2017 Mar 2.

Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1126/science.aaf9739DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5459593PMC
March 2017

Mapping cell surface adhesion by rotation tracking and adhesion footprinting.

Sci Rep 2017 03 14;7:44502. Epub 2017 Mar 14.

Department of Physics and Center for Physics of Living Cells, University of Illinois at Urbana-Champaign, 1110 W Green St., Urbana, IL, 61801, USA.

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http://dx.doi.org/10.1038/srep44502DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5349612PMC
March 2017

Structural biology: Growth factor rattled out of its cage.

Authors:
Taekjip Ha

Nature 2017 02 25;542(7639):40-41. Epub 2017 Jan 25.

Departments of Biophysics, Biomedical Engineering and Biophysics and Biochemistry, Johns Hopkins University, Howard Hughes Medical Institute, Baltimore, Maryland 21205, USA.

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http://dx.doi.org/10.1038/nature21119DOI Listing
February 2017

Flipping nanoscopy on its head.

Authors:
Jie Xiao Taekjip Ha

Science 2017 02;355(6325):582-584

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1126/science.aam5409DOI Listing
February 2017

Single-molecule fluorescence microscopy of native macromolecular complexes.

Curr Opin Struct Biol 2016 12 21;41:225-232. Epub 2016 Sep 21.

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, USA; Department of Biophysics, Johns Hopkins University, USA; Department of Biomedical Engineering, Johns Hopkins University, USA; Howard Hughes Medical Institute, Baltimore, MD, USA.

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http://dx.doi.org/10.1016/j.sbi.2016.09.006DOI Listing
December 2016

Nanoscale mechanics guides cellular decision making.

Integr Biol (Camb) 2016 09 1;8(9):929-35. Epub 2016 Aug 1.

Department of Bioengineering, University of Illinois, Urbana, IL, USA.

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http://dx.doi.org/10.1039/c6ib00113kDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5021613PMC
September 2016

Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9.

Nat Commun 2016 09 14;7:12778. Epub 2016 Sep 14.

Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.

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http://dx.doi.org/10.1038/ncomms12778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5027287PMC
September 2016

Correction: Nanoscale mechanics guides cellular decision making.

Integr Biol (Camb) 2016 09;8(9):1002

Department of Bioengineering, University of Illinois, Urbana, IL, USA and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA. and Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, IL, USA.

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http://dx.doi.org/10.1039/c6ib90035fDOI Listing
September 2016

In Planta Single-Molecule Pull-Down Reveals Tetrameric Stoichiometry of HD-ZIPIII:LITTLE ZIPPER Complexes.

Plant Cell 2016 08 6;28(8):1783-94. Epub 2016 Jul 6.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany

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http://dx.doi.org/10.1105/tpc.16.00289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5006705PMC
August 2016

Defining Single Molecular Forces Required for Notch Activation Using Nano Yoyo.

Nano Lett 2016 06 12;16(6):3892-7. Epub 2016 May 12.

Department of Physics and Center for Physics of Living Cells, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.

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http://dx.doi.org/10.1021/acs.nanolett.6b01403DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4899123PMC
June 2016

Natural antisense RNA promotes 3' end processing and maturation of MALAT1 lncRNA.

Nucleic Acids Res 2016 Apr 29;44(6):2898-908. Epub 2016 Jan 29.

Department of Cell and Developmental Biology, University of Illinois Urbana, IL 61801, USA

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http://dx.doi.org/10.1093/nar/gkw047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824109PMC
April 2016

Rupture force of cell adhesion ligand tethers modulates biological activities of a cell-laden hydrogel.

Chem Commun (Camb) 2016 Apr 25;52(26):4757-60. Epub 2016 Feb 25.

Department of Chemical and Biomolecular Engineering, Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1039/c6cc00036cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4803541PMC
April 2016

A Chemical Controller of SNARE-Driven Membrane Fusion That Primes Vesicles for Ca(2+)-Triggered Millisecond Exocytosis.

J Am Chem Soc 2016 Apr 25;138(13):4512-21. Epub 2016 Mar 25.

Department of Genetic Engineering, College of Biotechnology and Bioengineering, and Center for Human Interface Nano Technology, Sungkyunkwan University , Suwon, Gyeonggi-do 440-746, South Korea.

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http://dx.doi.org/10.1021/jacs.5b13449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4852477PMC
April 2016

Single-Molecule Analysis of Lipid-Protein Interactions in Crude Cell Lysates.

Anal Chem 2016 Apr 1;88(8):4269-76. Epub 2016 Apr 1.

Howard Hughes Medical Institute, Baltimore, Maryland 21205, United States.

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http://dx.doi.org/10.1021/acs.analchem.5b04127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863138PMC
April 2016

Spider Silk Peptide Is a Compact, Linear Nanospring Ideal for Intracellular Tension Sensing.

Nano Lett 2016 Mar 3;16(3):2096-102. Epub 2016 Feb 3.

Institute for Genomic Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.

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http://dx.doi.org/10.1021/acs.nanolett.6b00305DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4851340PMC
March 2016

Probing Nature's Nanomachines One Molecule at a Time.

Authors:
Taekjip Ha

Biophys J 2016 Mar;110(5):1004-7

Departments of Biophysics and Biophysical Chemistry, Biophysics, and Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland; Howard Hughes Medical Institute, Baltimore, Maryland. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2016.02.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4788748PMC
March 2016

Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation.

Nat Commun 2016 Mar 22;7:11045. Epub 2016 Mar 22.

Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.

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http://dx.doi.org/10.1038/ncomms11045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4804163PMC
March 2016

Plantazolicin is an ultra-narrow spectrum antibiotic that targets the membrane.

ACS Infect Dis 2016 Mar 23;2(3):207-220. Epub 2015 Dec 23.

Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801.

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http://dx.doi.org/10.1021/acsinfecdis.5b00115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4852872PMC
March 2016

Constructing modular and universal single molecule tension sensor using protein G to study mechano-sensitive receptors.

Sci Rep 2016 Feb 15;6:21584. Epub 2016 Feb 15.

Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.

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http://dx.doi.org/10.1038/srep21584DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4753514PMC
February 2016

The light side of the force.

Elife 2016 Feb 23;5. Epub 2016 Feb 23.

Department of Biophysics and Biophysical Chemistry, the Department of Biomedical Engineering and the Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, United States.

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http://dx.doi.org/10.7554/eLife.14274DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4775208PMC
February 2016

Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability.

Nat Commun 2016 Feb 24;7:10813. Epub 2016 Feb 24.

Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.

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http://dx.doi.org/10.1038/ncomms10813DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4770088PMC
February 2016

Kaposi's Sarcoma-Associated Herpesvirus Viral Interferon Regulatory Factor 4 (vIRF4) Perturbs the G1-S Cell Cycle Progression via Deregulation of the cyclin D1 Gene.

J Virol 2016 01 21;90(2):1139-43. Epub 2015 Oct 21.

Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California, USA

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http://dx.doi.org/10.1128/JVI.01897-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702683PMC
January 2016

Structural dynamics of potassium-channel gating revealed by single-molecule FRET.

Nat Struct Mol Biol 2016 Jan 7;23(1):31-36. Epub 2015 Dec 7.

Center for Investigation of Membrane Excitability Diseases, Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis MO.

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http://dx.doi.org/10.1038/nsmb.3138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833211PMC
January 2016

Dynamic growth and shrinkage govern the pH dependence of RecA filament stability.

PLoS One 2015 21;10(1):e0115611. Epub 2015 Jan 21.

Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America; Howard Hughes Medical Institute, Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4301630PMC
December 2015

Integrin Molecular Tension within Motile Focal Adhesions.

Biophys J 2015 Dec;109(11):2259-67

Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, Maryland; Department of Biophysics & Biophysical Chemistry, Department of Biophysics, and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland.

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http://dx.doi.org/10.1016/j.bpj.2015.10.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4675889PMC
December 2015

Effects of DNA replication on mRNA noise.

Proc Natl Acad Sci U S A 2015 Dec 15;112(52):15886-91. Epub 2015 Dec 15.

Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801;

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http://dx.doi.org/10.1073/pnas.1516246112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702981PMC
December 2015

Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells.

Sci Rep 2015 Nov 27;5:17295. Epub 2015 Nov 27.

Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA.

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http://dx.doi.org/10.1038/srep17295DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4661537PMC
November 2015

Single molecular force across single integrins dictates cell spreading.

Integr Biol (Camb) 2015 Oct 6;7(10):1265-1271. Epub 2015 Jul 6.

Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA.

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http://dx.doi.org/10.1039/c5ib00080gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4593737PMC
October 2015

Allosteric Regulation of E-Cadherin Adhesion.

J Biol Chem 2015 Aug 14;290(35):21749-61. Epub 2015 Jul 14.

From the Departments of Biochemistry, Chemical and Biomolecular Engineering, University of Illinois, Urbana-Champaign, Illinois 61801,

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http://dx.doi.org/10.1074/jbc.M115.657098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4571897PMC
August 2015

BEND3 represses rDNA transcription by stabilizing a NoRC component via USP21 deubiquitinase.

Proc Natl Acad Sci U S A 2015 Jul 22;112(27):8338-43. Epub 2015 Jun 22.

Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801;

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http://dx.doi.org/10.1073/pnas.1424705112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4500215PMC
July 2015

RNA fluorescence in situ hybridization in cultured mammalian cells.

Methods Mol Biol 2015 ;1206:123-36

Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Avenue, Urbana, IL, 61801, USA.

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http://dx.doi.org/10.1007/978-1-4939-1369-5_11DOI Listing
June 2015

A parameter estimation method for fluorescence lifetime data.

BMC Res Notes 2015 Jun 9;8:230. Epub 2015 Jun 9.

Department of Statistics, University of Georgia, 101 Cedar Street, Athens, GA, 30602, USA.

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http://dx.doi.org/10.1186/s13104-015-1176-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4467687PMC
June 2015

Nucleosomes undergo slow spontaneous gaping.

Nucleic Acids Res 2015 Apr 30;43(8):3964-71. Epub 2015 Mar 30.

Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA Department of Physics, Center for Physics in Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA Howard Hughes Medical Institute, University of Illinois, Urbana, IL 61801-2902, USA

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http://dx.doi.org/10.1093/nar/gkv276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417179PMC
April 2015

Protein structure. Engineering of a superhelicase through conformational control.

Science 2015 Apr;348(6232):344-7

Physics Department and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Howard Hughes Medical Institute, University of Illinois, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1126/science.aaa0445DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417355PMC
April 2015

Protein structure. Direct observation of structure-function relationship in a nucleic acid-processing enzyme.

Science 2015 Apr 16;348(6232):352-4. Epub 2015 Apr 16.

Department of Physics, Center for the Physics of Living Cells, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1126/science.aaa0130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4424897PMC
April 2015

Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility.

Cell 2015 Mar;160(6):1135-44

Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA; Department of Physics, Center for Physics in Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA; Howard Hughes Medical Institute, University of Illinois, Urbana, IL 61801-2902, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.02.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4409768PMC
March 2015

RNA biochemistry. Determination of in vivo target search kinetics of regulatory noncoding RNA.

Science 2015 Mar;347(6228):1371-4

Center for the Physics of Living Cells, Department of Physics, University of Illinois, Urbana, IL, USA. Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL, USA. Carl R. Woese Institute for Genomic Biology, Howard Hughes Medical Institute, Urbana, IL, USA. Howard Hughes Medical Institute, Urbana, IL, USA.

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http://dx.doi.org/10.1126/science.1258849DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410144PMC
March 2015

Relaxed rotational and scrunching changes in P266L mutant of T7 RNA polymerase reduce short abortive RNAs while delaying transition into elongation.

PLoS One 2014 20;9(3):e91859. Epub 2014 Mar 20.

Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3961267PMC
December 2014

An improved surface passivation method for single-molecule studies.

Nat Methods 2014 Dec 12;11(12):1233-6. Epub 2014 Oct 12.

1] Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [2] Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [3] Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [4] Howard Hughes Medical Institute, Urbana, Illinois, USA. [5] Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.

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http://dx.doi.org/10.1038/nmeth.3143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4245390PMC
December 2014

A price to pay for relaxed substrate specificity: a comparative kinetic analysis of the class II lanthipeptide synthetases ProcM and HalM2.

J Am Chem Soc 2014 Dec 4;136(50):17513-29. Epub 2014 Dec 4.

Institute for Genomic Biology, ‡Department of Physics, §Department of Chemistry University of Illinois , Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States.

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http://dx.doi.org/10.1021/ja5089452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4277782PMC
December 2014

Stoichiometry and assembly of mTOR complexes revealed by single-molecule pulldown.

Proc Natl Acad Sci U S A 2014 Dec 1;111(50):17833-8. Epub 2014 Dec 1.

Center for Biophysics and Computational Biology, Institute for Genomic Biology, Department of Physics, and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801

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http://www.pnas.org/lookup/doi/10.1073/pnas.1419425111
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http://dx.doi.org/10.1073/pnas.1419425111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4273350PMC
December 2014

Towards a computational model of a methane producing archaeum.

Archaea 2014 4;2014:898453. Epub 2014 Mar 4.

Department of Chemistry, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA ; Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA ; Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA.

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http://www.hindawi.com/journals/archaea/2014/898453/
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http://dx.doi.org/10.1155/2014/898453DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3960522PMC
November 2014

Single-molecule pull-down (SiMPull) for new-age biochemistry: methodology and biochemical applications of single-molecule pull-down (SiMPull) for probing biomolecular interactions in crude cell extracts.

Bioessays 2014 Nov 29;36(11):1109-19. Epub 2014 Aug 29.

Center for Biophysics and Computational Biology, University of Illinois Urbana Champaign, Urbana, IL, USA.

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http://dx.doi.org/10.1002/bies.201400090DOI Listing
November 2014

Targeting DNA G-quadruplexes with helical small molecules.

Chembiochem 2014 Nov 26;15(17):2563-70. Epub 2014 Sep 26.

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (UK); Cambridge Institute, Cancer Research UK, Li Ka Shing Center, Cambridge CB2 0RE (UK).

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http://dx.doi.org/10.1002/cbic.201402439DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4284101PMC
November 2014

Designing a nine cysteine-less DNA packaging motor from bacteriophage T4 reveals new insights into ATPase structure and function.

Virology 2014 Nov 16;468-470:660-668. Epub 2014 Oct 16.

Department of Biology, The Catholic University of America, 620 Michigan Avenue NE, Washington, DC, USA. Electronic address:

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http://dx.doi.org/10.1016/j.virol.2014.08.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4438746PMC
November 2014

Cooperative conformational transitions keep RecA filament active during ATPase cycle.

J Am Chem Soc 2014 Oct 7;136(42):14796-800. Epub 2014 Oct 7.

Department of Physics and Interdisciplinary Program of Integrated Biotechnology, Sogang University , Seoul 121-742, Korea.

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http://pubs.acs.org/doi/10.1021/ja506363y
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4210115PMC
October 2014

Single-molecule methods leap ahead.

Authors:
Taekjip Ha

Nat Methods 2014 Oct;11(10):1015-8

Department of Physics, Center for the Physics of Living Cells and Center for Biophysics and Quantitative Biology, Institute for Genomic Biology, University of Illinois at Urbana-Champaign and at the Howard Hughes Medical Institute, Urbana, Illinois, USA.

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http://dx.doi.org/10.1038/nmeth.3107DOI Listing
October 2014

Single-molecule packaging initiation in real time by a viral DNA packaging machine from bacteriophage T4.

Proc Natl Acad Sci U S A 2014 Oct 6;111(42):15096-101. Epub 2014 Oct 6.

Department of Physics, University of Illinois at Urbana-Champaign, Howard Hughes Medical Institute, Urbana, IL 61801; and

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http://dx.doi.org/10.1073/pnas.1407235111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4210281PMC
October 2014

Matrix softness regulates plasticity of tumour-repopulating cells via H3K9 demethylation and Sox2 expression.

Nat Commun 2014 Aug 6;5:4619. Epub 2014 Aug 6.

1] Laboratory for Cell Biomechanics and Regenerative Medicine, Department of Biomedical Engineering, School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China [2] Department of Mechanical Science and Engineering, College of Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.

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http://dx.doi.org/10.1038/ncomms5619DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4133791PMC
August 2014

A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment.

J Chem Theory Comput 2014 Aug 3;10(8):2891-2896. Epub 2014 Jun 3.

Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois, United States ; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois, United States.

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http://dx.doi.org/10.1021/ct500193uDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132850PMC
August 2014

Biophysics. Ultraslow relaxation of confined DNA.

Science 2014 Jul;345(6195):380-1

Department of Physics, Center for the Physics of Living Cells, and Center for Biophysics and Computational Biology, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA. Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA.

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http://dx.doi.org/10.1126/science.1256359DOI Listing
July 2014

Ultrafast redistribution of E. coli SSB along long single-stranded DNA via intersegment transfer.

J Mol Biol 2014 Jun 2;426(13):2413-21. Epub 2014 May 2.

Department of Physics, Center for Physics in Living Cells and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, IL 61801, USA; Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2014.04.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4096553PMC
June 2014

Periodic DNA patrolling underlies diverse functions of Pif1 on R-loops and G-rich DNA.

Elife 2014 Apr 29;3:e02190. Epub 2014 Apr 29.

Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, United States

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https://elifesciences.org/articles/02190
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3999857PMC
http://dx.doi.org/10.7554/eLife.02190DOI Listing
April 2014

Dynamic look at DNA unwinding by a replicative helicase.

Proc Natl Acad Sci U S A 2014 Mar 18;111(9):E827-35. Epub 2014 Feb 18.

W. M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, and Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724.

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http://dx.doi.org/10.1073/pnas.1322254111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3948270PMC
March 2014

Single-molecule fluorescence reveals the unwinding stepping mechanism of replicative helicase.

Cell Rep 2014 Mar 13;6(6):1037-1045. Epub 2014 Mar 13.

Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Howard Hughes Medical Institute, Urbana, IL 61801, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.02.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3988844PMC
March 2014

Single-molecule optical spectroscopy.

Chem Soc Rev 2014 Feb;43(4):973-6

MoNOS, Huygens Laboratory, Leiden University, 2300 RA Leiden, The Netherlands.

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http://dx.doi.org/10.1039/c4cs90001dDOI Listing
February 2014

Protein-guided RNA dynamics during early ribosome assembly.

Nature 2014 Feb 12;506(7488):334-8. Epub 2014 Feb 12.

1] T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA [2] CMDB Program, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA.

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http://dx.doi.org/10.1038/nature13039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3968076PMC
February 2014

Crosstalk between the cGAS DNA sensor and Beclin-1 autophagy protein shapes innate antimicrobial immune responses.

Cell Host Microbe 2014 Feb;15(2):228-38

Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2014.01.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3950946PMC
February 2014