JILA Science Publications
Displaying 1 - 62 of 62
2024
Quantifying a light-induced energetic change in bacteriorhodopsin by force spectroscopy
David Jacobson, Thomas Perkins, Proceedings of the National Academy of Sciences 121, e2313818121 (2024).
View Record | DOI
David Jacobson, Thomas Perkins, Proceedings of the National Academy of Sciences 121, e2313818121 (2024).
View Record | DOI
2022
Force-Activated DNA Substrates for In Situ Generation of ssDNA and Designed ssDNA/dsDNA Structures in an Optical-Trapping Assay
Arnulf Taylor, Stephen Okoniewski, Lyle Uyetake, Thomas Perkins, Methods in Biology , 273-312 (2022).
View Record | DOI | PDF
Arnulf Taylor, Stephen Okoniewski, Lyle Uyetake, Thomas Perkins, Methods in Biology , 273-312 (2022).
View Record | DOI | PDF
2021
Free-energy changes of bacteriorhodopsin point mutants measured by single-molecule force spectroscopy
David Jacobson, Thomas Perkins, Proceedings of the National Academy of Sciences 118, e2020083118 (2021).
View Record | DOI | URL/Arxiv Link
David Jacobson, Thomas Perkins, Proceedings of the National Academy of Sciences 118, e2020083118 (2021).
View Record | DOI | URL/Arxiv Link
Modulation of a protein-folding landscape revealed by AFM-based force spectroscopy notwithstanding instrumental limitations
Devin Edwards, Marc-Andre LeBlanc, Thomas Perkins, Proceedings of the National Academy of Sciences 118, e2015728118 (2021).
View Record | DOI
Devin Edwards, Marc-Andre LeBlanc, Thomas Perkins, Proceedings of the National Academy of Sciences 118, e2015728118 (2021).
View Record | DOI
Type III secretion system effector proteins are mechanically labile
Marc-Andre LeBlanc, Morgan Fink, Thomas Perkins, Marcelo Sousa, Proceedings of the National Academy of Sciences 118, e2019566118 (2021).
View Record | DOI
Marc-Andre LeBlanc, Morgan Fink, Thomas Perkins, Marcelo Sousa, Proceedings of the National Academy of Sciences 118, e2019566118 (2021).
View Record | DOI
2020
Correcting molecular transition rates measured by single-molecule force spectroscopy for limited temporal resolution
David Jacobson, Thomas Perkins, Physical Review E 102, 022402 (2020).
View Record | DOI | URL/Arxiv Link
David Jacobson, Thomas Perkins, Physical Review E 102, 022402 (2020).
View Record | DOI | URL/Arxiv Link
Quantifying the native energetics stabilizing bacteriorhodopsin by single-molecule force spectroscopy
Hao Yu, David Jacobson, Hao Luo, Thomas Perkins, Physical Review Letters 125, 068102 (2020).
View Record | DOI | URL/Arxiv Link
Hao Yu, David Jacobson, Hao Luo, Thomas Perkins, Physical Review Letters 125, 068102 (2020).
View Record | DOI | URL/Arxiv Link
Bending and looping of long DNA by polycomb repressive complex 2 revealed by AFM imaging in liquid
Patrick Heenan, Xueyin Wang, Anne Gooding, Thomas Cech, Thomas Perkins, Nucleic Acids Research 48, 2969-2981 (2020).
View Record | DOI | URL/Arxiv Link
Patrick Heenan, Xueyin Wang, Anne Gooding, Thomas Cech, Thomas Perkins, Nucleic Acids Research 48, 2969-2981 (2020).
View Record | DOI | URL/Arxiv Link
Membrane-protein unfolding intermediates detected with enhanced precision using a zigzag force ramp
David Jacobson, Lyle Uyetake, Thomas Perkins, Biophysical Journal 118, 667-675 (2020).
View Record | DOI
David Jacobson, Lyle Uyetake, Thomas Perkins, Biophysical Journal 118, 667-675 (2020).
View Record | DOI
2019
Imaging DNA equilibrated onto mica in liquid using biochemically relevant deposition conditions
Patrick Heenan, Thomas Perkins, ACS Nano 13, 4220-4229 (2019).
View Record | DOI | URL/Arxiv Link
Patrick Heenan, Thomas Perkins, ACS Nano 13, 4220-4229 (2019).
View Record | DOI | URL/Arxiv Link
Quantifying the initial unfolding of bacteriorhodopsin reveals retinal stabilization
Hao Yu, Patrick Heenan, Devin Edwards, Lyle Uyetake, Thomas Perkins, Angewandte Chemie 131, 1724-1727 (2019).
View Record | DOI | URL/Arxiv Link
Hao Yu, Patrick Heenan, Devin Edwards, Lyle Uyetake, Thomas Perkins, Angewandte Chemie 131, 1724-1727 (2019).
View Record | DOI | URL/Arxiv Link
2018
High-precision single-molecule characterization of the folding of an HIV RNA hairpin by atomic force microscopy
Robert Walder, William Van Patten, Dustin Ritchie, Rebecca Montange, Ty Miller, Michael Woodside, Thomas Perkins, Nano Letters 18, 6318-6325 (2018).
View Record | DOI
Robert Walder, William Van Patten, Dustin Ritchie, Rebecca Montange, Ty Miller, Michael Woodside, Thomas Perkins, Nano Letters 18, 6318-6325 (2018).
View Record | DOI
FEATHER: Automated Analysis of Force Spectroscopy Unbinding and Unfolding Data via a Bayesian Algorithm
Patrick Heenan, Thomas Perkins, Biophysical Journal 115, 757-762 (2018).
View Record | DOI | URL/Arxiv Link
Patrick Heenan, Thomas Perkins, Biophysical Journal 115, 757-762 (2018).
View Record | DOI | URL/Arxiv Link
Going vertical to improve accuracy in AFM-based single-molecule force spectroscopy
Robert Walder, William Van Patten, Ayush Adhikari, Thomas Perkins, ACS Nano 12, 198-207 (2018).
View Record | DOI
Robert Walder, William Van Patten, Ayush Adhikari, Thomas Perkins, ACS Nano 12, 198-207 (2018).
View Record | DOI
Improved free-energy landscape quantification illustrated with a computationally designed protein-ligand interactionWilliam Van Patten, Robert Walder, Ayush Adhikari, Stephen Okoniewski, Rashmi Ravichandran, Christine Tinberg, David Baker, Thomas Perkins, ChemPhysChem 19, 19-23 (2018).
View Record | DOI | URL/Arxiv Link
Improved free-energy landscape reconstruction of bacteriorhodopsin highlights local variations in unfolding energy
Patrick Heenan, Hao Yu, Matthew Siewny, Thomas Perkins, The Journal of Chemical Physics 148, 123313 (2018).
View Record | DOI | URL/Arxiv Link | PDF
Patrick Heenan, Hao Yu, Matthew Siewny, Thomas Perkins, The Journal of Chemical Physics 148, 123313 (2018).
View Record | DOI | URL/Arxiv Link | PDF
2017
Force spectroscopy with 9-μs resolution and sub-pN stability by tailoring AFM cantilever geometry
Devin Edwards, Jaevyn Faulk, Marc-Andre LeBlanc, Thomas Perkins, Biophysical Journal 113, 2595-2600 (2017).
View Record | DOI | URL/Arxiv Link
Devin Edwards, Jaevyn Faulk, Marc-Andre LeBlanc, Thomas Perkins, Biophysical Journal 113, 2595-2600 (2017).
View Record | DOI | URL/Arxiv Link
Force-activated DNA substrates for probing individual proteins interacting with single-stranded DNA
Stephen Okoniewski, Lyle Uyetake, Thomas Perkins, Nucleic Acids Research 45, 10775-10782 (2017).
View Record | DOI | URL/Arxiv Link
Stephen Okoniewski, Lyle Uyetake, Thomas Perkins, Nucleic Acids Research 45, 10775-10782 (2017).
View Record | DOI | URL/Arxiv Link
Rapid characterization of a mechanically labile α-helical protein enabled by efficient site-specific bioconjugation
Robert Walder, Marc-Andre LeBlanc, William Van Patten, Devin Edwards, Jacob Greenberg, Ayush Adhikari, Stephen Okoniewski, Ruby Sullan, David Rabuka, Marcelo Sousa, Thomas Perkins, Journal of the American Chemical Society 139, 9867-9875 (2017).
View Record | DOI | URL/Arxiv Link | PDF
Robert Walder, Marc-Andre LeBlanc, William Van Patten, Devin Edwards, Jacob Greenberg, Ayush Adhikari, Stephen Okoniewski, Ruby Sullan, David Rabuka, Marcelo Sousa, Thomas Perkins, Journal of the American Chemical Society 139, 9867-9875 (2017).
View Record | DOI | URL/Arxiv Link | PDF
Hidden dynamics in the unfolding of individual bacteriorhodopsin proteins
Hao Yu, Matthew Siewny, Devin Edwards, Aric Sanders, Thomas Perkins, Science 355, 945-950 (2017).
View Record | DOI | URL/Arxiv Link
Hao Yu, Matthew Siewny, Devin Edwards, Aric Sanders, Thomas Perkins, Science 355, 945-950 (2017).
View Record | DOI | URL/Arxiv Link
A surface-coupled optical trap with 1-bp precision via active stabilization
Stephen Okoniewski, Ashley Carter, Thomas Perkins, Methods in Molecular Biology 1486, 77-107 (2017).
View Record | DOI | URL/Arxiv Link
Stephen Okoniewski, Ashley Carter, Thomas Perkins, Methods in Molecular Biology 1486, 77-107 (2017).
View Record | DOI | URL/Arxiv Link
Improved force spectroscopy using focused-ion-beam modified cantilevers
Jaevyn Faulk, Devin Edwards, Matthew Bull, Thomas Perkins, Methods in Enzymology 582, 321-351 (2017).
View Record | DOI | URL/Arxiv Link
Jaevyn Faulk, Devin Edwards, Matthew Bull, Thomas Perkins, Methods in Enzymology 582, 321-351 (2017).
View Record | DOI | URL/Arxiv Link
Optimizing force spectroscopy by modifying commercial cantilevers: Improved stability, precision, and temporal resolution
Devin Edwards, Thomas Perkins, Journal of Structural Biology 197, 13-25 (2017).
View Record | DOI | PDF
Devin Edwards, Thomas Perkins, Journal of Structural Biology 197, 13-25 (2017).
View Record | DOI | PDF
2016
Sequence-dependent nanometer-scale conformational dynamics of individual RecBCD-DNA complexes
Ashley Carter, Maasa Seaberg, Hsiu-Fang Fan, Gang Sun, Christopher Wilds, Hung-Wen Li, Thomas Perkins, Nucleic Acids Research 44, 5849-5860 (2016).
View Record | DOI | URL/Arxiv Link | PDF
Ashley Carter, Maasa Seaberg, Hsiu-Fang Fan, Gang Sun, Christopher Wilds, Hung-Wen Li, Thomas Perkins, Nucleic Acids Research 44, 5849-5860 (2016).
View Record | DOI | URL/Arxiv Link | PDF
2015
Optimizing 1-μs-resolution single-molecule force spectroscopy on a commercial AFMDevin Edwards, Jaevyn Faulk, Aric Sanders, Matthew Bull, Robert Walder, Marc-Andre LeBlanc, Marcelo Sousa, Thomas Perkins, Nano Letters , 151005120507003 (2015).
View Record | DOI | URL/Arxiv Link
Direct observation of the reversible two-state unfolding and refolding of an α/β protein by single-molecule atomic force microscopy
Chengzhi He, Chunguang Hu, Xiaodong Hu, Xiaotang Hu, Adam Xiao, Thomas Perkins, Hongbin Li, Angewandte Chemie International Edition 54, 9921-9925 (2015).
View Record | DOI | URL/Arxiv Link
Chengzhi He, Chunguang Hu, Xiaodong Hu, Xiaotang Hu, Adam Xiao, Thomas Perkins, Hongbin Li, Angewandte Chemie International Edition 54, 9921-9925 (2015).
View Record | DOI | URL/Arxiv Link
Ultrastable measurement platform: sub-nm drift over hours in 3D at room temperature
Robert Walder, Hern Paik, Matthew Bull, Carl Sauer, Thomas Perkins, Optics Express 23, 16554 (2015).
View Record | DOI | URL/Arxiv Link
Robert Walder, Hern Paik, Matthew Bull, Carl Sauer, Thomas Perkins, Optics Express 23, 16554 (2015).
View Record | DOI | URL/Arxiv Link
2014
Ångström-precision optical traps and applications
Thomas Perkins, Annual Review of Biophysics 43, 279-302 (2014).
View Record | DOI | URL/Arxiv Link | PDF
Thomas Perkins, Annual Review of Biophysics 43, 279-302 (2014).
View Record | DOI | URL/Arxiv Link | PDF
Ultrastable atomic force microscopy: Improved force and positional stability
A. Churnside, Thomas Perkins, FEBS Letters 588, 3621-3630 (2014).
View Record | DOI | URL/Arxiv Link | PDF
A. Churnside, Thomas Perkins, FEBS Letters 588, 3621-3630 (2014).
View Record | DOI | URL/Arxiv Link | PDF
Improved single-molecule force spectroscopy using micromachined cantileversMatthew Bull, Ruby Sullan, Hongbin Li, Thomas Perkins, ACS Nano 8, 4984-4995 (2014).
View Record | DOI | URL/Arxiv Link | PDF
2013
Nano-chemical infrared imaging of membrane proteins in lipid bilayers
Samuel Berweger, D. Nguyen, Eric Muller, Hans Bechtel, Thomas Perkins, Markus Raschke, Journal of the American Chemical Society 135, 18292-18295 (2013).
View Record | DOI | URL/Arxiv Link | PDF
Samuel Berweger, D. Nguyen, Eric Muller, Hans Bechtel, Thomas Perkins, Markus Raschke, Journal of the American Chemical Society 135, 18292-18295 (2013).
View Record | DOI | URL/Arxiv Link | PDF
Torsionally constrained DNA for single-molecule assays: an efficient, ligation-free method
Hern Paik, V. Roskens, Thomas Perkins, Nucleic Acids Research 41, e179 - e179 (2013).
View Record | DOI | URL/Arxiv Link | PDF
Hern Paik, V. Roskens, Thomas Perkins, Nucleic Acids Research 41, e179 - e179 (2013).
View Record | DOI | URL/Arxiv Link | PDF
Atomic force microscopy with sub-picoNewton force stability for biological applications
Ruby Sullan, A. Churnside, D. Nguyen, Matthew Bull, Thomas Perkins, Methods 60, 131-141 (2013).
View Record | DOI | URL/Arxiv Link | PDF
Ruby Sullan, A. Churnside, D. Nguyen, Matthew Bull, Thomas Perkins, Methods 60, 131-141 (2013).
View Record | DOI | URL/Arxiv Link | PDF
Optimizing bead size reduces errors in force measurements in optical traps
Rebecca Montange, Matthew Bull, Elisabeth Shanblatt, Thomas Perkins, Optics Express 21, 39 (2013).
View Record | DOI | PDF
Rebecca Montange, Matthew Bull, Elisabeth Shanblatt, Thomas Perkins, Optics Express 21, 39 (2013).
View Record | DOI | PDF
2012
Dynamics and multiple stable binding modes of DNA intercalators revealed by single molecule force spectroscopyHern Paik, Thomas Perkins, Angewandte Chemie International Edition 51, 1731-1731 (2012).
View Record | DOI | URL/Arxiv Link | PDF
Routine and timely sub-picoNewton force stability and precision for biological applications of atomic force microscopy
A. Churnside, Ruby Sullan, D. Nguyen, Sara Case, Matthew Bull, G. King, Thomas Perkins, Nano Letters 12, 3557-3561 (2012).
View Record | DOI | URL/Arxiv Link | PDF
A. Churnside, Ruby Sullan, D. Nguyen, Sara Case, Matthew Bull, G. King, Thomas Perkins, Nano Letters 12, 3557-3561 (2012).
View Record | DOI | URL/Arxiv Link | PDF
Single-molecule optical-trapping measurements with DNA anchored to an array of gold nanoposts
Hern Paik, Thomas Perkins, Methods in Molecular Biology 875, 335-356 (2012).
View Record | DOI
Hern Paik, Thomas Perkins, Methods in Molecular Biology 875, 335-356 (2012).
View Record | DOI
2011
Overstretching DNA at 65 pN does not require peeling from free ends or nicksHern Paik, Thomas Perkins, Journal of the American Chemical Society 133, 3219-3221 (2011).
View Record | DOI | PDF
2010
Label-free optical imaging of membrane patches for atomic force microscopy
A. Churnside, G. King, Thomas Perkins, Optics Express 18, 23924 (2010).
View Record | DOI | PDF
A. Churnside, G. King, Thomas Perkins, Optics Express 18, 23924 (2010).
View Record | DOI | PDF
2009
Single-molecule studies of RecBCD
Thomas Perkins, Hung-Wen Li, Methods in Molecular Biology 587, 155-172 (2009).
View Record | DOI
Thomas Perkins, Hung-Wen Li, Methods in Molecular Biology 587, 155-172 (2009).
View Record | DOI
Integrating a high-force optical trap with gold nanoposts and a robust gold-DNA bond
Hern Paik, Y. Seol, W. Halsey, Thomas Perkins, Nano Letters 9, 2978-2983 (2009).
View Record | DOI | PDF
Hern Paik, Y. Seol, W. Halsey, Thomas Perkins, Nano Letters 9, 2978-2983 (2009).
View Record | DOI | PDF
Precision surface-coupled optical-trapping assay with 1 base-pair resolution
Ashley Carter, Yeonee Seol, Thomas Perkins, Biophysical Journal 96, 2926-2934 (2009).
View Record | DOI | PDF
Ashley Carter, Yeonee Seol, Thomas Perkins, Biophysical Journal 96, 2926-2934 (2009).
View Record | DOI | PDF
Ultrastable atomic force microscopy: atomic-scale stability and registration in ambient conditions
G. King, A. Carter, A. Churnside, L. Eberle, Thomas Perkins, Nano Letters 9, 1451-1456 (2009).
View Record | DOI | PDF
G. King, A. Carter, A. Churnside, L. Eberle, Thomas Perkins, Nano Letters 9, 1451-1456 (2009).
View Record | DOI | PDF
Optical traps for single molecule biophysics: a primerThomas Perkins, Laser & Photonics Review 3, 203-220 (2009).
View Record | DOI | PDF
2007
Elasticity of short DNA molecules: theory and experiment for contour lengths of 0.6–7 μm
Yeonee Seol, Jinyu Li, Philip Nelson, Thomas Perkins, M. Betterton, Biophysical Journal 93, 4360-4373 (2007).
View Record | DOI | PDF
Yeonee Seol, Jinyu Li, Philip Nelson, Thomas Perkins, M. Betterton, Biophysical Journal 93, 4360-4373 (2007).
View Record | DOI | PDF
Back-scattered detection provides atomic-scale localization precision, stability, and registration in 3D
A. Carter, G. King, Thomas Perkins, Optics Express 15, 13434 (2007).
View Record | DOI | PDF
A. Carter, G. King, Thomas Perkins, Optics Express 15, 13434 (2007).
View Record | DOI | PDF
TFIIA changes the conformation of the DNA in TBP/TATA complexes and increases their kinetic stability
A. Hieb, W. Halsey, M. Betterton, Thomas Perkins, Jennifer Kugel, James Goodrich, Journal of Molecular Biology 372, 619-632 (2007).
View Record | DOI | PDF
A. Hieb, W. Halsey, M. Betterton, Thomas Perkins, Jennifer Kugel, James Goodrich, Journal of Molecular Biology 372, 619-632 (2007).
View Record | DOI | PDF
Stabilization of an optical microscope to 0.1 nm in three dimensions
A. Carter, G. King, T. Ulrich, W. Halsey, David Alchenberger, Thomas Perkins, Applied Optics 46, 421 (2007).
View Record | DOI | PDF
A. Carter, G. King, T. Ulrich, W. Halsey, David Alchenberger, Thomas Perkins, Applied Optics 46, 421 (2007).
View Record | DOI | PDF
2006
Gold nanoparticles: enhanced optical trapping and sensitivity coupled with significant heating
Y. Seol, A. Carpenter, Thomas Perkins, Optics Letters 31, 2429 (2006).
View Record | DOI | PDF
Y. Seol, A. Carpenter, Thomas Perkins, Optics Letters 31, 2429 (2006).
View Record | DOI | PDF
2004
Measuring 0.1-nm motion in 1 ms in an optical microscope with differential back-focal-plane detection
L. Nugent-Glandorf, Thomas Perkins, Optics Letters 29, 2611 (2004).
View Record | DOI | PDF
L. Nugent-Glandorf, Thomas Perkins, Optics Letters 29, 2611 (2004).
View Record | DOI | PDF
Forward and reverse motion of single RecBCD molecules on DNA
Thomas Perkins, Hung-Wen Li, Ravindra Dalal, Jeff Gelles, Steven Block, Biophysical Journal 86, 1640-1648 (2004).
View Record | DOI | PDF
Thomas Perkins, Hung-Wen Li, Ravindra Dalal, Jeff Gelles, Steven Block, Biophysical Journal 86, 1640-1648 (2004).
View Record | DOI | PDF
2003
Sequence-dependent pausing of single lambda exonuclease molecules
Thomas Perkins, Ravindra Dalal, Paul Mitsis, Steven Block, Science 301, 1914-1918 (2003).
View Record | DOI | PDF
Thomas Perkins, Ravindra Dalal, Paul Mitsis, Steven Block, Science 301, 1914-1918 (2003).
View Record | DOI | PDF
1999
Single polymers in elongational flows: dynamic, steady-state, and population-averaged properties
Thomas Perkins, D. Smith, S. Chu, Flexible Polymer Chains in Elongational Flow , 283-334 (1999).
View Record | DOI
Thomas Perkins, D. Smith, S. Chu, Flexible Polymer Chains in Elongational Flow , 283-334 (1999).
View Record | DOI
The hydrodynamics of a DNA molecule in a flow field
R. Larson, Thomas Perkins, D. Smith, S. Chu, Flexible Polymer Chains in Elongational Flow , 259-282 (1999).
View Record | DOI
R. Larson, Thomas Perkins, D. Smith, S. Chu, Flexible Polymer Chains in Elongational Flow , 259-282 (1999).
View Record | DOI
1997
Single polymer dynamics in an elongational flow
Thomas Perkins, Douglas Smith, Steven Chu, Science 276, 2016-2021 (1997).
View Record | DOI | PDF
Thomas Perkins, Douglas Smith, Steven Chu, Science 276, 2016-2021 (1997).
View Record | DOI | PDF
Hydrodynamics of a DNA molecule in a flow field
R. Larson, Thomas Perkins, D. Smith, S. Chu, Physical Review E 55, 1794-1797 (1997).
View Record | DOI | URL/Arxiv Link
R. Larson, Thomas Perkins, D. Smith, S. Chu, Physical Review E 55, 1794-1797 (1997).
View Record | DOI | URL/Arxiv Link
1996
Dynamical scaling of DNA diffusion coefficients
Douglas Smith, Thomas Perkins, Steven Chu, Macromolecules 29, 1372-1373 (1996).
View Record | DOI
Douglas Smith, Thomas Perkins, Steven Chu, Macromolecules 29, 1372-1373 (1996).
View Record | DOI
1995
Self-diffusion of an entangled DNA molecule by reptation
Douglas Smith, Thomas Perkins, Steven Chu, Physical Review Letters 75, 4146-4149 (1995).
View Record | DOI
Douglas Smith, Thomas Perkins, Steven Chu, Physical Review Letters 75, 4146-4149 (1995).
View Record | DOI
Stretching of a single tethered polymer in a uniform flow
Thomas Perkins, Douglas Smith, Ronald Larson, Steven Chu, Science 268, 83-87 (1995).
View Record | DOI
Thomas Perkins, Douglas Smith, Ronald Larson, Steven Chu, Science 268, 83-87 (1995).
View Record | DOI
1994
Direct observation of tube-like motion of a single polymer chain
Thomas Perkins, Douglas Smith, Steven Chu, Science 264, 819-822 (1994).
View Record | DOI
Thomas Perkins, Douglas Smith, Steven Chu, Science 264, 819-822 (1994).
View Record | DOI
Relaxation of a single DNA molecule observed by optical microscopyThomas Perkins, Stephen Quake, Douglas Smith, Steven Chu, Science 264, 822-826 (1994).
View Record | DOI
1993
Steady‐state gain and saturation flux measurements in a high efficiency, electron‐beam‐pumped, Ar‐Xe laser
Thomas Perkins, Journal of Applied Physics 74, 4860-4866 (1993).
View Record | DOI
Thomas Perkins, Journal of Applied Physics 74, 4860-4866 (1993).
View Record | DOI