Thomas T Perkins

Summary

Affiliation: University of Colorado
Country: USA

Publications

  1. doi request reprint Ångström-precision optical traps and applications
    Thomas T Perkins
    JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309 email
    Annu Rev Biophys 43:279-302. 2014
  2. pmc Sequence-dependent pausing of single lambda exonuclease molecules
    Thomas T Perkins
    Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
    Science 301:1914-8. 2003
  3. pmc Forward and reverse motion of single RecBCD molecules on DNA
    Thomas T Perkins
    Department of Biological Sciences, Stanford University, Stanford, California 94305 5020, USA
    Biophys J 86:1640-8. 2004
  4. ncbi request reprint Stabilization of an optical microscope to 0.1 nm in three dimensions
    Ashley R Carter
    JILA, University of Colorado and National Institute of Standards and Technology, Boulder, CO 80309, USA
    Appl Opt 46:421-7. 2007
  5. pmc Precision surface-coupled optical-trapping assay with one-basepair resolution
    Ashley R Carter
    JILA, National Institute of Standards and Technology, University of Colorado, Boulder, Colorado, USA
    Biophys J 96:2926-34. 2009
  6. pmc Atomic force microscopy with sub-picoNewton force stability for biological applications
    Ruby May A Sullan
    JILA, National Institute of Standards and Technology, University of Colorado, Boulder, CO 80309, USA
    Methods 60:131-41. 2013
  7. doi request reprint Single-molecule optical-trapping measurements with DNA anchored to an array of gold nanoposts
    D Hern Paik
    JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO, USA
    Methods Mol Biol 875:335-56. 2012
  8. doi request reprint Integrating a high-force optical trap with gold nanoposts and a robust gold-DNA bond
    D Hern Paik
    JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, USA
    Nano Lett 9:2978-83. 2009
  9. doi request reprint Optimizing bead size reduces errors in force measurements in optical traps
    Rebecca K Montange
    JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, USA
    Opt Express 21:39-48. 2013
  10. pmc Elasticity of short DNA molecules: theory and experiment for contour lengths of 0.6-7 microm
    Yeonee Seol
    JILA, National Institute of Standards and Technology and University of Colorado, USA
    Biophys J 93:4360-73. 2007

Collaborators

Detail Information

Publications26

  1. doi request reprint Ångström-precision optical traps and applications
    Thomas T Perkins
    JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309 email
    Annu Rev Biophys 43:279-302. 2014
    ..This information in turn is providing mechanistic insight into kinetic pathways that are difficult to probe by traditional assays. I conclude with a brief discussion of emerging techniques and future directions. ..
  2. pmc Sequence-dependent pausing of single lambda exonuclease molecules
    Thomas T Perkins
    Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
    Science 301:1914-8. 2003
    ..This sequence is found in the left lambda cohesive end, where exonuclease inhibition may contribute to the reduced recombination efficiency at that end...
  3. pmc Forward and reverse motion of single RecBCD molecules on DNA
    Thomas T Perkins
    Department of Biological Sciences, Stanford University, Stanford, California 94305 5020, USA
    Biophys J 86:1640-8. 2004
    ..Our observations show that RecBCD-DNA complexes can exist in multiple, functionally distinct states that persist for many catalytic turnovers: such states may help tune enzyme activity for various biological functions...
  4. ncbi request reprint Stabilization of an optical microscope to 0.1 nm in three dimensions
    Ashley R Carter
    JILA, University of Colorado and National Institute of Standards and Technology, Boulder, CO 80309, USA
    Appl Opt 46:421-7. 2007
    ..11, 0.10, and 0.09 nm (rms) and long-term (100 s) stabilities of 0.17, 0.12, and 0.35 nm (rms) in x, y, and z, respectively, as measured by an independent detection laser...
  5. pmc Precision surface-coupled optical-trapping assay with one-basepair resolution
    Ashley R Carter
    JILA, National Institute of Standards and Technology, University of Colorado, Boulder, Colorado, USA
    Biophys J 96:2926-34. 2009
    ..This work brings the benefit of atomic-scale resolution, currently limited to dual-beam trapping assays, along with enhanced force precision to the widely used, surface-coupled optical-trapping assay...
  6. pmc Atomic force microscopy with sub-picoNewton force stability for biological applications
    Ruby May A Sullan
    JILA, National Institute of Standards and Technology, University of Colorado, Boulder, CO 80309, USA
    Methods 60:131-41. 2013
    ..Thus, we conclude by briefly reviewing site-specific covalent-immobilization protocols for linking a biomolecule to the substrate and to the AFM tip...
  7. doi request reprint Single-molecule optical-trapping measurements with DNA anchored to an array of gold nanoposts
    D Hern Paik
    JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO, USA
    Methods Mol Biol 875:335-56. 2012
    ....
  8. doi request reprint Integrating a high-force optical trap with gold nanoposts and a robust gold-DNA bond
    D Hern Paik
    JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, USA
    Nano Lett 9:2978-83. 2009
    ..Thus, surface conjugation of biomolecules onto an array of gold nanostructures by chemically and mechanically robust bonds provides a unique way to carry out spatially controlled, repeatable measurements of single molecules...
  9. doi request reprint Optimizing bead size reduces errors in force measurements in optical traps
    Rebecca K Montange
    JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, USA
    Opt Express 21:39-48. 2013
    ..This improvement in force precision was verified by pulling on a canonical DNA hairpin. Thus, by using an optimum bead size, one can simultaneously maximize k(trap) while minimizing errors in F...
  10. pmc Elasticity of short DNA molecules: theory and experiment for contour lengths of 0.6-7 microm
    Yeonee Seol
    JILA, National Institute of Standards and Technology and University of Colorado, USA
    Biophys J 93:4360-73. 2007
    ....
  11. pmc Routine and timely sub-picoNewton force stability and precision for biological applications of atomic force microscopy
    Allison B Churnside
    JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, United States
    Nano Lett 12:3557-61. 2012
    ..We expect that many current and future applications of AFM can immediately benefit from these improvements in force stability and precision...
  12. pmc Torsionally constrained DNA for single-molecule assays: an efficient, ligation-free method
    D Hern Paik
    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
    Nucleic Acids Res 41:e179. 2013
    ..This protocol significantly simplifies the application and adoption of torsionally constrained assays to a wide range of single-molecule systems. ..
  13. ncbi request reprint TFIIA changes the conformation of the DNA in TBP/TATA complexes and increases their kinetic stability
    Aaron R Hieb
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, 215 UCB, Boulder, CO 80309 0215, USA
    J Mol Biol 372:619-32. 2007
    ..Furthermore, we present a refined model for the effect that TFIIA has on DNA conformation that takes into account potential changes in bend angle as well as twist angle...
  14. doi request reprint Overstretching DNA at 65 pN does not require peeling from free ends or nicks
    D Hern Paik
    JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, Colorado 80309, USA
    J Am Chem Soc 133:3219-21. 2011
    ..Moreover, the degree of hysteresis increased with the number of nicks. Hence, the generation of single-stranded DNA from free ends or nicks is not an obligatory step in overstretching DNA, but rather a consequence...
  15. doi request reprint Single-molecule studies of RecBCD
    Thomas T Perkins
    MCD Biology, JILA, NIST and CU, University of Colorado at Boulder, Boulder, CO, USA
    Methods Mol Biol 587:155-72. 2010
    ..This technically demanding, high-resolution optical-trapping assay is complemented by a simpler single-molecule assay-the tethered particle motion assay...
  16. pmc Label-free optical imaging of membrane patches for atomic force microscopy
    Allison B Churnside
    JILA, National Institute of Standards and Technology and Department of Physics, University of Colorado, Boulder, Colorado 80309, USA
    Opt Express 18:23924-32. 2010
    ..Thus, this label-free imaging efficiently locates sparsely distributed protein assemblies for subsequent AFM study while simultaneously minimizing degradation of the tip and the sample...
  17. pmc Ultrastable atomic force microscopy: atomic-scale stability and registration in ambient conditions
    Gavin M King
    JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, Colorado 80309, USA
    Nano Lett 9:1451-6. 2009
    ..This work extends atomic-scale tip-sample control, previously restricted to cryogenic temperatures and ultrahigh vacuum, to a wide range of perturbative operating environments...
  18. doi request reprint Nano-chemical infrared imaging of membrane proteins in lipid bilayers
    Samuel Berweger
    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
    J Am Chem Soc 135:18292-5. 2013
    ..This demonstrates the general applicability of s-SNOM vibrational nanospectroscopy, with potential extension to a wide range of biomolecular systems. ..
  19. ncbi request reprint Gold nanoparticles: enhanced optical trapping and sensitivity coupled with significant heating
    Yeonee Seol
    JILA, University of Colorado, and National Institute of Standards and Technology, Boulder, CO 80309, USA
    Opt Lett 31:2429-31. 2006
    ..Also, such particles, with their increased detection sensitivity, make excellent probes for certain zero-force biophysical assays...
  20. doi request reprint Improved single molecule force spectroscopy using micromachined cantilevers
    Matthew S Bull
    JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, United States
    ACS Nano 8:4984-95. 2014
    ..Finally, these cantilevers were robust and were reused for SFMS over multiple days. Hence, we expect these responsive, yet stable, cantilevers to broadly benefit diverse AFM-based studies. ..
  21. doi request reprint Optimizing force spectroscopy by modifying commercial cantilevers: Improved stability, precision, and temporal resolution
    Devin T Edwards
    JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA
    J Struct Biol . 2016
    ..Currently, there is no perfect cantilever for all applications. Optimizing AFM-based SMFS requires understanding the tradeoffs inherent to using a specific cantilever and choosing the one best suited to a particular application...
  22. ncbi request reprint A Surface-Coupled Optical Trap with 1-bp Precision via Active Stabilization
    Stephen R Okoniewski
    JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, CO, 80309, USA
    Methods Mol Biol 1486:77-107. 2017
    ..These active stabilization techniques can also aid other biophysical assays that would benefit from improved laser stability and/or Å-scale sample stability, such as atomic force microscopy and super-resolution imaging...
  23. pmc Optimizing 1-μs-Resolution Single-Molecule Force Spectroscopy on a Commercial Atomic Force Microscope
    Devin T Edwards
    JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, United States
    Nano Lett 15:7091-8. 2015
    ..5). We therefore expect such cantilevers, along with the instrumentational improvements to detect them on a commercial AFM, to accelerate high-precision AFM-based SMFS studies. ..
  24. doi request reprint Ultrastable atomic force microscopy: improved force and positional stability
    Allison B Churnside
    JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA
    FEBS Lett 588:3621-30. 2014
    ..Finally, sub-pN force stability over 100 s was achieved by removing the gold coating from soft cantilevers. These enhancements to AFM instrumentation can immediately benefit research in biophysics and nanoscience...
  25. ncbi request reprint Measuring 0.1-nm motion in 1 ms in an optical microscope with differential back-focal-plane detection
    Lora Nugent-Glandorf
    JILA, National Institute of Standards and Technology, Boulder, Colorado 80309 0440, USA
    Opt Lett 29:2611-3. 2004
    ..1 nm in 1 ms and stability of 0.5 nm over 60 s. Repeated steps of 0.4 nm at 1 Hz are resolved with a signal-to-noise ratio of 25...
  26. ncbi request reprint Dynamics and multiple stable binding modes of DNA intercalators revealed by single-molecule force spectroscopy
    D Hern Paik
    JILA, National Institute of Standards and Technology and University of Colorado, Boulder Department of Molecular, Cellular, and Developmental Biology, University of Colorado, 440 UCB, Boulder, CO 80309 0440 USA http jila colorado edu perkinsgroup
    Angew Chem Int Ed Engl 51:1811-5. 2012
    ..The results show that binding/unbinding and intercalation/deintercalation are distinct processes that occur on very different time scales...