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