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Thomas Perkins - Publications

Affiliations: 
University of Colorado / JILA, Boulder, CO, United States 
Area:
Single Molecule Biophysics
Website:
http://jilawww.colorado.edu/perkinsgroup/tom.html
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68 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Taylor AMK, Okoniewski SR, Uyetake L, Perkins TT. Force-Activated DNA Substrates for In Situ Generation of ssDNA and Designed ssDNA/dsDNA Structures in an Optical-Trapping Assay. Methods in Molecular Biology (Clifton, N.J.). 2478: 273-312. PMID 36063324 DOI: 10.1007/978-1-0716-2229-2_10  0.353
2021 Jacobson DR, Perkins TT. Free-energy changes of bacteriorhodopsin point mutants measured by single-molecule force spectroscopy. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33753487 DOI: 10.1073/pnas.2020083118  0.571
2021 Edwards DT, LeBlanc MA, Perkins TT. Modulation of a protein-folding landscape revealed by AFM-based force spectroscopy notwithstanding instrumental limitations. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33723041 DOI: 10.1073/pnas.2015728118  0.343
2020 Jacobson DR, Perkins TT. Correcting molecular transition rates measured by single-molecule force spectroscopy for limited temporal resolution. Physical Review. E. 102: 022402. PMID 32942397 DOI: 10.1103/Physreve.102.022402  0.544
2020 Yu H, Jacobson DR, Luo H, Perkins TT. Quantifying the Native Energetics Stabilizing Bacteriorhodopsin by Single-Molecule Force Spectroscopy. Physical Review Letters. 125: 068102. PMID 32845671 DOI: 10.1103/Physrevlett.125.068102  0.595
2019 Jacobson DR, Uyetake L, Perkins TT. Membrane-Protein Unfolding Intermediates Detected with Enhanced Precision Using a Zigzag Force Ramp. Biophysical Journal. PMID 31882249 DOI: 10.1016/J.Bpj.2019.12.003  0.576
2018 Walder R, Van Patten WJ, Ritchie DB, Montange RK, Miller TW, Woodside MT, Perkins TT. High-Precision Single-Molecule Characterization of the Folding of an HIV RNA Hairpin by Atomic Force Microscopy. Nano Letters. PMID 30234311 DOI: 10.1021/Acs.Nanolett.8B02597  0.794
2018 LeBlanc M, Walder R, Edwards D, Perkins T, Sousa M. High Precision AFM-Based SMFS of Mechanically Labile T3SS Effectors Biophysical Journal. 114: 355a. DOI: 10.1016/J.Bpj.2017.11.1975  0.329
2018 Walder R, Miller TW, Van Patten WJ, Perkins TT. New Obligate Folding Intermediate of an RNA Pseudoknot Observed Using Atomic Force Microscopy Based Force Spectroscopy with 10 μs Resolution Biophysical Journal. 114: 354a. DOI: 10.1016/J.BPJ.2017.11.1968  0.337
2017 Walder R, Van Patten WJ, Adhikari A, Perkins TT. Going Vertical to Improve the Accuracy of Atomic Force Microscopy Based Single-Molecule Force Spectroscopy. Acs Nano. PMID 29244486 DOI: 10.1021/acsnano.7b05721  0.436
2017 Edwards DT, Faulk JK, LeBlanc MA, Perkins TT. Force Spectroscopy with 9-μs Resolution and Sub-pN Stability by Tailoring AFM Cantilever Geometry. Biophysical Journal. PMID 29132641 DOI: 10.1016/J.Bpj.2017.10.023  0.401
2017 Okoniewski SR, Uyetake L, Perkins TT. Force-activated DNA substrates for probing individual proteins interacting with single-stranded DNA. Nucleic Acids Research. PMID 28977580 DOI: 10.1093/nar/gkx761  0.332
2017 Walder R, LeBlanc MA, Van Patten WJ, Edwards D, Greenberg JA, Adhikari A, Okoniewski SR, Sullan RMA, Rabuka D, Sousa MC, Perkins TT. Rapid Characterization of a Mechanically Labile α-helical Protein Enabled by Efficient Site-Specific Bioconjugation. Journal of the American Chemical Society. PMID 28677396 DOI: 10.1021/Jacs.7B02958  0.304
2017 Faulk JK, Edwards DT, Bull MS, Perkins TT. Improved Force Spectroscopy Using Focused-Ion-Beam-Modified Cantilevers. Methods in Enzymology. 582: 321-351. PMID 28062041 DOI: 10.1016/Bs.Mie.2016.08.007  0.379
2017 Okoniewski SR, Carter AR, Perkins TT. A Surface-Coupled Optical Trap with 1-bp Precision via Active Stabilization. Methods in Molecular Biology (Clifton, N.J.). 1486: 77-107. PMID 27844426 DOI: 10.1007/978-1-4939-6421-5_4  0.671
2016 Carter AR, Seaberg MH, Fan HF, Sun G, Wilds CJ, Li HW, Perkins TT. Sequence-dependent nanometer-scale conformational dynamics of individual RecBCD-DNA complexes. Nucleic Acids Research. PMID 27220465 DOI: 10.1093/Nar/Gkw445  0.595
2016 Edwards DT, Perkins TT. Optimizing force spectroscopy by modifying commercial cantilevers: improved stability, precision, and temporal resolution. Journal of Structural Biology. PMID 26804584 DOI: 10.1016/J.Jsb.2016.01.009  0.387
2016 Walder R, Van Patten WJ, Adhikari A, LeBlanc M, Okoniewski SR, Sullan RMA, Sousa MC, Perkins TT. Enhanced Site-Specific Anchoring of Biomolecules for Single-Molecule Force Spectroscopy Biophysical Journal. 110: 499a-500a. DOI: 10.1016/J.Bpj.2015.11.2670  0.329
2016 Perkins TT. Probing Single Individual Proteins Unfold and Refold with 1-μs Resolution: Improved AFM-Based Single Molecule Force Spectroscopy Biophysical Journal. 110: 375a. DOI: 10.1016/J.BPJ.2015.11.2023  0.341
2015 Edwards DT, Faulk JK, Sanders AW, Bull MS, Walder R, LeBlanc MA, Sousa MC, Perkins TT. Optimizing 1-μs-Resolution Single-Molecule Force Spectroscopy on a Commercial Atomic Force Microscope. Nano Letters. 15: 7091-8. PMID 26421945 DOI: 10.1021/Acs.Nanolett.5B03166  0.422
2015 Walder R, Paik DH, Bull MS, Sauer C, Perkins TT. Ultrastable measurement platform: sub-nm drift over hours in 3D at room temperature. Optics Express. 23: 16554-64. PMID 26191667 DOI: 10.1364/OE.23.016554  0.669
2015 Sanders AW, Faulk JK, Edwards DT, Perkins TT. Custom Modification of AFM Tips for Fast, High Force Resolution Single-Molecule Force Spectroscopy Microscopy and Microanalysis. 21: 1617-1618. DOI: 10.1017/S1431927615008867  0.369
2014 Churnside AB, Perkins TT. Ultrastable atomic force microscopy: improved force and positional stability. Febs Letters. 588: 3621-30. PMID 24801176 DOI: 10.1016/J.Febslet.2014.04.033  0.82
2014 Perkins TT. Ångström-precision optical traps and applications. Annual Review of Biophysics. 43: 279-302. PMID 24773015 DOI: 10.1146/annurev-biophys-042910-155223  0.322
2014 Bull MS, Sullan RM, Li H, Perkins TT. Improved single molecule force spectroscopy using micromachined cantilevers. Acs Nano. 8: 4984-95. PMID 24670198 DOI: 10.1021/nn5010588  0.41
2014 Walder R, Paik DH, Bull MS, Perkins TT. An Ultrastable Measurement Platform for Single-Molecule Studies: Sub-NM Lateral Stability Over 1 hour using a Multiplexed Back-Scattered Detection Biophysical Journal. 106: 392a. DOI: 10.1016/J.Bpj.2013.11.2217  0.675
2013 Paik DH, Roskens VA, Perkins TT. Torsionally constrained DNA for single-molecule assays: an efficient, ligation-free method. Nucleic Acids Research. 41: e179. PMID 23935118 DOI: 10.1016/J.Bpj.2013.11.2234  0.616
2013 Sullan RM, Churnside AB, Nguyen DM, Bull MS, Perkins TT. Atomic force microscopy with sub-picoNewton force stability for biological applications. Methods (San Diego, Calif.). 60: 131-41. PMID 23562681 DOI: 10.1016/J.Ymeth.2013.03.029  0.808
2013 Montange RK, Bull MS, Shanblatt ER, Perkins TT. Optimizing bead size reduces errors in force measurements in optical traps. Optics Express. 21: 39-48. PMID 23388894 DOI: 10.1364/OE.21.000039  0.795
2013 King GM, Churnside AB, Perkins TT. A precision force microscope for biophysics Conference Proceedings of the Society For Experimental Mechanics Series. 6: 31-36. DOI: 10.1007/978-1-4614-4436-7_5  0.822
2012 Churnside AB, Sullan RM, Nguyen DM, Case SO, Bull MS, King GM, Perkins TT. Routine and timely sub-picoNewton force stability and precision for biological applications of atomic force microscopy. Nano Letters. 12: 3557-61. PMID 22694769 DOI: 10.1016/J.Bpj.2012.11.1191  0.818
2012 Paik DH, Perkins TT. Single-molecule optical-trapping measurements with DNA anchored to an array of gold nanoposts. Methods in Molecular Biology (Clifton, N.J.). 875: 335-56. PMID 22573450 DOI: 10.1007/978-1-61779-806-1_18  0.649
2012 Paik DH, Perkins TT. Dynamics and multiple stable binding modes of DNA intercalators revealed by single-molecule force spectroscopy. Angewandte Chemie (International Ed. in English). 51: 1811-5. PMID 22162006 DOI: 10.1002/anie.201105540  0.639
2012 Paik DH, Perkins TT. Force spectroscopy of DNA: There is still a lot to learn Proceedings of Spie - the International Society For Optical Engineering. 8458. DOI: 10.1117/12.945812  0.661
2012 Montange RK, Bull MS, Shanblatt ER, Perkins TT. Optimizing Bead Size Improves Force Precision in Optical Traps Biophysical Journal. 102: 577a. DOI: 10.1016/j.bpj.2011.11.3142  0.787
2011 Paik DH, Perkins TT. Overstretching DNA at 65 pN does not require peeling from free ends or nicks. Journal of the American Chemical Society. 133: 3219-21. PMID 21207940 DOI: 10.1021/ja108952v  0.611
2011 Emanuel GA, Kuriabova T, Carpenter AE, Betterton M, Perkins TT. Accommodating Drift in Hidden Markov Analysis of Single-Molecule Data Biophysical Journal. 100: 154a. DOI: 10.1016/J.Bpj.2010.12.1055  0.623
2011 Paik DH, Perkins TT. Cover Picture: Dynamics and Multiple Stable Binding Modes of DNA Intercalators Revealed by Single-Molecule Force Spectroscopy (Angew. Chem. Int. Ed. 8/2012) Angewandte Chemie International Edition. 51: 1731-1731. DOI: 10.1002/Anie.201108162  0.638
2011 Paik DH, Perkins TT. Titelbild: Dynamics and Multiple Stable Binding Modes of DNA Intercalators Revealed by Single-Molecule Force Spectroscopy (Angew. Chem. 8/2012) Angewandte Chemie. 124: 1765-1765. DOI: 10.1002/Ange.201108162  0.639
2010 Churnside AB, King GM, Perkins TT. Label-free optical imaging of membrane patches for atomic force microscopy. Optics Express. 18: 23924-32. PMID 21164738 DOI: 10.1364/Oe.18.023924  0.81
2010 King GM, Churnside AB, Perkins TT. Optical trapping meets atomic force microscopy: A precision force microscope for biophysics Proceedings of Spie - the International Society For Optical Engineering. 7762. DOI: 10.1117/12.862745  0.828
2010 Churnside AB, King GM, Perkins TT. Tip-Free Method Used to Locate Single Purple Membrane Patches for Atomic Force Microscopy Biophysical Journal. 98: 192a. DOI: 10.1016/J.Bpj.2009.12.4244  0.81
2010 Hosotani M, Carter AR, Fan H, Li H, Perkins TT. Conformational Dynamics of Single RecBCD Molecules Biophysical Journal. 98: 65a. DOI: 10.1016/J.Bpj.2009.12.371  0.761
2010 King GM, Churnside AB, Perkins TT. Precision Force Spectroscopy of Bacteriorhodopsin Biophysical Journal. 98: 588a. DOI: 10.1016/J.Bpj.2009.12.3196  0.811
2010 Perkins TT, King GM, Churnside AB, Carter AR. Ultrastable atomic force microscopy using laser-based, active noise cancelation Optics Infobase Conference Papers.  0.798
2010 Perkins TT, King GM, Churnside AB, Carter AR. Ultrastable atomic force microscopy using laser-based, active noise cancelation Optics Infobase Conference Papers.  0.798
2009 Paik DH, Seol Y, Halsey WA, Perkins TT. Integrating a high-force optical trap with gold nanoposts and a robust gold-DNA bond. Nano Letters. 9: 2978-83. PMID 19492836 DOI: 10.1021/Nl901404S  0.746
2009 King GM, Carter AR, Churnside AB, Eberle LS, Perkins TT. Ultrastable atomic force microscopy: atomic-scale stability and registration in ambient conditions. Nano Letters. 9: 1451-6. PMID 19351191 DOI: 10.1021/Nl803298Q  0.809
2009 Carter AR, Seol Y, Perkins TT. Precision surface-coupled optical-trapping assay with one-basepair resolution. Biophysical Journal. 96: 2926-34. PMID 19348774 DOI: 10.1016/J.Bpj.2008.12.3933  0.759
2009 Churnside AB, King GM, Perkins TT. Independent measurements of force and position in atomic force microscopy Proceedings of Spie - the International Society For Optical Engineering. 7405. DOI: 10.1117/12.826567  0.829
2009 Carpenter AE, Hieb AR, Betterton MD, Goodrich JA, Perkins TT. Human TBP Bending of DNA Measured at the Single Molecule Level Biophysical Journal. 96: 57a. DOI: 10.1016/J.Bpj.2008.12.190  0.665
2009 Seol Y, Perkins T. Sensitivity Of Dna-hairpins Dynamics To The Mechanism Of Force Feedback Probed Using A Surface-coupled Passive Force Clamp Biophysical Journal. 96: 291a. DOI: 10.1016/J.Bpj.2008.12.1441  0.686
2008 Churnside AB, King GM, Carter AR, Perkins TT. Improved performance of an ultrastable measurement platform using a field-programmable gate array for real-time deterministic control Proceedings of Spie - the International Society For Optical Engineering. 7042. DOI: 10.1117/12.795700  0.737
2007 Carter AR, King GM, Perkins TT. Back-scattered detection provides atomic-scale localization precision, stability, and registration in 3D. Optics Express. 15: 13434-45. PMID 19550612 DOI: 10.1364/Oe.15.013434  0.712
2007 Seol Y, Li J, Nelson PC, Perkins TT, Betterton MD. Elasticity of short DNA molecules: theory and experiment for contour lengths of 0.6-7 microm. Biophysical Journal. 93: 4360-73. PMID 17766363 DOI: 10.1529/Biophysj.107.112995  0.524
2007 Carter AR, King GM, Ulrich TA, Halsey W, Alchenberger D, Perkins TT. Stabilization of an optical microscope to 0.1 nm in three dimensions. Applied Optics. 46: 421-7. PMID 17228390 DOI: 10.1364/Ao.46.000421  0.704
2006 Seol Y, Carpenter AE, Perkins TT. Gold nanoparticles: enhanced optical trapping and sensitivity coupled with significant heating. Optics Letters. 31: 2429-31. PMID 16880845 DOI: 10.1364/Ol.31.002429  0.675
2005 Carter AR, King GM, Ulrich TA, Halsey WA, Perkins TT. 3D stabilization of an optical microscope to 0.1 nm at 1 Hz using an array of nano-posts Optics Infobase Conference Papers. DOI: 10.1364/Ls.2005.Ltue5  0.671
2004 Nugent-Glandorf L, Perkins TT. Measuring 0.1-nm motion in 1 ms in an optical microscope with differential back-focal-plane detection. Optics Letters. 29: 2611-3. PMID 15552661 DOI: 10.1364/Ol.29.002611  0.752
2004 Perkins TT, Li HW, Dalal RV, Gelles J, Block SM. Forward and reverse motion of single RecBCD molecules on DNA. Biophysical Journal. 86: 1640-8. PMID 14990491 DOI: 10.1016/S0006-3495(04)74232-0  0.803
2003 Perkins TT, Dalal RV, Mitsis PG, Block SM. Sequence-dependent pausing of single lambda exonuclease molecules. Science (New York, N.Y.). 301: 1914-8. PMID 12947034 DOI: 10.1126/Science.1088047  0.773
1997 Perkins TT, Smith DE, Chu S. Single polymer dynamics in an elongational flow. Science (New York, N.Y.). 276: 2016-21. PMID 9197259 DOI: 10.1126/Science.276.5321.2016  0.564
1997 Larson RG, Perkins TT, Smith DE, Chu S. Hydrodynamics of a DNA molecule in a flow field Physical Review E. 55: 1794-1797. DOI: 10.1103/Physreve.55.1794  0.591
1996 Smith DE, Perkins TT, Chu S. Dynamical Scaling of DNA Diffusion Coefficients Macromolecules. 29: 1372-1373. DOI: 10.1021/Ma951455P  0.576
1995 Smith DE, Perkins TT, Chu S. Self-diffusion of an entangled DNA molecule by reptation. Physical Review Letters. 75: 4146-4149. PMID 10059826 DOI: 10.1103/Physrevlett.75.4146  0.555
1995 Perkins TT, Smith DE, Larson RG, Chu S. Stretching of a single tethered polymer in a uniform flow. Science (New York, N.Y.). 268: 83-7. PMID 7701345 DOI: 10.1126/Science.7701345  0.597
1994 Perkins TT, Quake SR, Smith DE, Chu S. Relaxation of a single DNA molecule observed by optical microscopy. Science (New York, N.Y.). 264: 822-6. PMID 8171336 DOI: 10.1126/Science.8171336  0.7
1994 Perkins TT, Smith DE, Chu S. Direct observation of tube-like motion of a single polymer chain. Science (New York, N.Y.). 264: 819-22. PMID 8171335 DOI: 10.1126/Science.8171335  0.61
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