Thomas T Perkins

Thomas T Perkins

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Thomas T Perkins

Thomas T Perkins

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Quantifying the Initial Unfolding of Bacteriorhodopsin Reveals Retinal Stabilization.

Angew Chem Int Ed Engl 2019 Feb 9;58(6):1710-1713. Epub 2019 Jan 9.

JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO, 80309, USA.

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http://doi.wiley.com/10.1002/anie.201812072
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http://dx.doi.org/10.1002/anie.201812072DOI Listing
February 2019

High-Precision Single-Molecule Characterization of the Folding of an HIV RNA Hairpin by Atomic Force Microscopy.

Nano Lett 2018 10 24;18(10):6318-6325. Epub 2018 Sep 24.

JILA, National Institute of Standards and Technology, and University of Colorado , Boulder , Colorado 80309 , United States.

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http://dx.doi.org/10.1021/acs.nanolett.8b02597DOI Listing
October 2018

FEATHER: Automated Analysis of Force Spectroscopy Unbinding and Unfolding Data via a Bayesian Algorithm.

Biophys J 2018 Sep 7;115(5):757-762. Epub 2018 Aug 7.

JILA, National Institute of Standards and Technology, University of Colorado, Boulder, Colorado; Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2018.07.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6127848PMC
September 2018

Improved free-energy landscape reconstruction of bacteriorhodopsin highlights local variations in unfolding energy.

J Chem Phys 2018 Mar;148(12):123313

JILA, National Institute of Standard and Technology and University of Colorado, Boulder, Colorado 80309, USA.

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http://dx.doi.org/10.1063/1.5009108DOI Listing
March 2018

A Surface-Coupled Optical Trap with 1-bp Precision via Active Stabilization.

Methods Mol Biol 2017 ;1486:77-107

JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, CO, 80309, USA.

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http://dx.doi.org/10.1007/978-1-4939-6421-5_4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5510953PMC
January 2018

Improved Free-Energy Landscape Quantification Illustrated with a Computationally Designed Protein-Ligand Interaction.

Chemphyschem 2018 01 4;19(1):19-23. Epub 2017 Dec 4.

JILA, National Institute of Standards and Technology and the University of Colorado, Department of Physics and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, 440 UCB, Boulder, CO, 80309-0440, USA.

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http://dx.doi.org/10.1002/cphc.201701147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5760306PMC
January 2018

Going Vertical To Improve the Accuracy of Atomic Force Microscopy Based Single-Molecule Force Spectroscopy.

ACS Nano 2018 Jan 22;12(1):198-207. Epub 2017 Dec 22.

JILA, National Institute of Standards and Technology , and University of Colorado, Boulder, Colorado 80309, United States.

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http://dx.doi.org/10.1021/acsnano.7b05721DOI Listing
January 2018

Force Spectroscopy with 9-μs Resolution and Sub-pN Stability by Tailoring AFM Cantilever Geometry.

Biophys J 2017 Dec 11;113(12):2595-2600. Epub 2017 Nov 11.

JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado; Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2017.10.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5770970PMC
December 2017

Force-activated DNA substrates for probing individual proteins interacting with single-stranded DNA.

Nucleic Acids Res 2017 Oct;45(18):10775-10782

JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309-0440, USA.

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http://dx.doi.org/10.1093/nar/gkx761DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737210PMC
October 2017

Hidden dynamics in the unfolding of individual bacteriorhodopsin proteins.

Science 2017 Mar;355(6328):945-950

JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA.

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http://dx.doi.org/10.1126/science.aah7124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5436802PMC
March 2017

Optimizing force spectroscopy by modifying commercial cantilevers: Improved stability, precision, and temporal resolution.

J Struct Biol 2017 01 1;197(1):13-25. Epub 2016 Feb 1.

JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA; Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jsb.2016.01.009DOI Listing
January 2017

Sequence-dependent nanometer-scale conformational dynamics of individual RecBCD-DNA complexes.

Nucleic Acids Res 2016 07 24;44(12):5849-60. Epub 2016 May 24.

JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA

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http://dx.doi.org/10.1093/nar/gkw445DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937329PMC
July 2016

Optimizing 1-μs-Resolution Single-Molecule Force Spectroscopy on a Commercial Atomic Force Microscope.

Nano Lett 2015 Oct 5;15(10):7091-8. Epub 2015 Oct 5.

JILA, National Institute of Standards and Technology and University of Colorado , Boulder, Colorado 80309, United States.

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http://dx.doi.org/10.1021/acs.nanolett.5b03166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4663051PMC
October 2015

Direct Observation of the Reversible Two-State Unfolding and Refolding of an α/β Protein by Single-Molecule Atomic Force Microscopy.

Angew Chem Int Ed Engl 2015 Aug 1;54(34):9921-5. Epub 2015 Jul 1.

Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 (Canada).

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http://doi.wiley.com/10.1002/anie.201502938
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http://dx.doi.org/10.1002/anie.201502938DOI Listing
August 2015

Ultrastable atomic force microscopy: improved force and positional stability.

FEBS Lett 2014 Oct 4;588(19):3621-30. Epub 2014 May 4.

JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA; Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA. Electronic address:

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http://dx.doi.org/10.1016/j.febslet.2014.04.033DOI Listing
October 2014

Ångström-precision optical traps and applications.

Authors:
Thomas T Perkins

Annu Rev Biophys 2014 ;43:279-302

JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309; email:

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http://dx.doi.org/10.1146/annurev-biophys-042910-155223DOI Listing
August 2014

Improved single molecule force spectroscopy using micromachined cantilevers.

ACS Nano 2014 May 1;8(5):4984-95. Epub 2014 Apr 1.

JILA, National Institute of Standards and Technology and University of Colorado , Boulder, Colorado 80309, United States.

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http://dx.doi.org/10.1021/nn5010588DOI Listing
May 2014

Nano-chemical infrared imaging of membrane proteins in lipid bilayers.

J Am Chem Soc 2013 Dec 2;135(49):18292-5. Epub 2013 Dec 2.

Department of Physics and Department of Chemistry, ‡Department of Chemical and Biological Engineering, and §Department of Molecular, Cellular, and Developmental Biology, University of Colorado , Boulder, Colorado, 80309, United States.

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http://dx.doi.org/10.1021/ja409815gDOI Listing
December 2013

Torsionally constrained DNA for single-molecule assays: an efficient, ligation-free method.

Nucleic Acids Res 2013 Oct 9;41(19):e179. Epub 2013 Aug 9.

JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA.

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http://dx.doi.org/10.1093/nar/gkt699DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799452PMC
October 2013

Atomic force microscopy with sub-picoNewton force stability for biological applications.

Methods 2013 Apr 4;60(2):131-41. Epub 2013 Apr 4.

JILA, National Institute of Standards and Technology, University of Colorado, Boulder, CO 80309, USA.

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http://dx.doi.org/10.1016/j.ymeth.2013.03.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3669665PMC
April 2013

Optimizing bead size reduces errors in force measurements in optical traps.

Opt Express 2013 Jan;21(1):39-48

JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, USA.

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http://dx.doi.org/10.1364/OE.21.000039DOI Listing
January 2013

Single-molecule optical-trapping measurements with DNA anchored to an array of gold nanoposts.

Methods Mol Biol 2012 ;875:335-56

JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO, USA.

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http://dx.doi.org/10.1007/978-1-61779-806-1_18DOI Listing
September 2012

Dynamics and multiple stable binding modes of DNA intercalators revealed by single-molecule force spectroscopy.

Angew Chem Int Ed Engl 2012 Feb 9;51(8):1811-5. Epub 2011 Dec 9.

JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309-0440, USA.

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http://dx.doi.org/10.1002/anie.201105540DOI Listing
February 2012

Overstretching DNA at 65 pN does not require peeling from free ends or nicks.

J Am Chem Soc 2011 Mar 5;133(10):3219-21. Epub 2011 Jan 5.

JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, Colorado 80309, USA.

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http://dx.doi.org/10.1021/ja108952vDOI Listing
March 2011

Label-free optical imaging of membrane patches for atomic force microscopy.

Opt Express 2010 Nov;18(23):23924-32

JILA, National Institute of Standards and Technology and Department of Physics, University of Colorado, Boulder, Colorado 80309, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158999PMC
http://dx.doi.org/10.1364/OE.18.023924DOI Listing
November 2010

Single-molecule studies of RecBCD.

Methods Mol Biol 2010 ;587:155-72

MCD Biology, JILA, NIST & CU, University of Colorado at Boulder, Boulder, CO, USA.

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http://dx.doi.org/10.1007/978-1-60327-355-8_11DOI Listing
May 2010

Integrating a high-force optical trap with gold nanoposts and a robust gold-DNA bond.

Nano Lett 2009 Aug;9(8):2978-83

JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, USA.

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http://dx.doi.org/10.1021/nl901404sDOI Listing
August 2009

Precision surface-coupled optical-trapping assay with one-basepair resolution.

Biophys J 2009 Apr;96(7):2926-34

JILA, National Institute of Standards and Technology, University of Colorado, Boulder, Colorado, USA.

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http://dx.doi.org/10.1016/j.bpj.2008.12.3933DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2711297PMC
April 2009

Ultrastable atomic force microscopy: atomic-scale stability and registration in ambient conditions.

Nano Lett 2009 Apr;9(4):1451-6

JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, Colorado 80309, USA.

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http://dx.doi.org/10.1021/nl803298qDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2953871PMC
April 2009

Elasticity of short DNA molecules: theory and experiment for contour lengths of 0.6-7 microm.

Biophys J 2007 Dec 31;93(12):4360-73. Epub 2007 Aug 31.

JILA, National Institute of Standards and Technology and University of Colorado, USA.

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http://dx.doi.org/10.1529/biophysj.107.112995DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2098713PMC
December 2007

TFIIA changes the conformation of the DNA in TBP/TATA complexes and increases their kinetic stability.

J Mol Biol 2007 Sep 29;372(3):619-32. Epub 2007 Jun 29.

Department of Chemistry and Biochemistry, University of Colorado at Boulder, 215 UCB, Boulder, CO 80309-0215, USA.

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http://dx.doi.org/10.1016/j.jmb.2007.06.061DOI Listing
September 2007

Stabilization of an optical microscope to 0.1 nm in three dimensions.

Appl Opt 2007 Jan;46(3):421-7

JILA, University of Colorado and National Institute of Standards and Technology, Boulder, CO 80309, USA.

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January 2007

Gold nanoparticles: enhanced optical trapping and sensitivity coupled with significant heating.

Opt Lett 2006 Aug;31(16):2429-31

JILA, University of Colorado, and National Institute of Standards and Technology, Boulder, CO 80309, USA.

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https://jila.colorado.edu/perkins/sites/default/files/pdf/Se
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August 2006

Measuring 0.1-nm motion in 1 ms in an optical microscope with differential back-focal-plane detection.

Opt Lett 2004 Nov;29(22):2611-3

JILA, National Institute of Standards and Technology, Boulder, Colorado 80309-0440, USA.

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November 2004

Forward and reverse motion of single RecBCD molecules on DNA.

Biophys J 2004 Mar;86(3):1640-8

Department of Biological Sciences, Stanford University, Stanford, California 94305-5020, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1303999PMC
http://dx.doi.org/10.1016/S0006-3495(04)74232-0DOI Listing
March 2004

Sequence-dependent pausing of single lambda exonuclease molecules.

Science 2003 Sep 28;301(5641):1914-8. Epub 2003 Aug 28.

Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1126/science.1088047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1539570PMC
September 2003