Taekjip Ha

Summary

Affiliation: University of Illinois
Country: USA

Publications

  1. pmc Probing cellular protein complexes using single-molecule pull-down
    Ankur Jain
    Center for Biophysics and Computational Biology and Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Nature 473:484-8. 2011
  2. pmc Quantitative fluorescence labeling of aldehyde-tagged proteins for single-molecule imaging
    Xinghua Shi
    Howard Hughes Medical Institute, Urbana, Illinois, USA
    Nat Methods 9:499-503. 2012
  3. pmc G-quadruplex DNA bound by a synthetic ligand is highly dynamic
    Prakrit V Jena
    Department of Physics, Howard Hughes Medical Institute, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    J Am Chem Soc 131:12522-3. 2009
  4. pmc Fluorescent lifetime trajectories of a single fluorophore reveal reaction intermediates during transcription initiation
    Maria Sorokina
    Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    J Am Chem Soc 131:9630-1. 2009
  5. pmc Single molecule analysis of Thermus thermophilus SSB protein dynamics on single-stranded DNA
    Jichuan Zhang
    Department of Physics and Center for the Physics of Living Cells, University of Illinois, Urbana, IL 61801, USA, Department of Materials Science and Engineering, University of Illinois, Urbana, IL 61801, USA, RIKEN, Cellular and Molecular Biology Unit, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan and Howard Hughes Medical Institute, University of Illinois, Urbana, IL 61801, USA
    Nucleic Acids Res 42:3821-32. 2014
  6. pmc Single-molecule fluorescence reveals the unwinding stepping mechanism of replicative helicase
    Salman Syed
    Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Cell Rep 6:1037-45. 2014
  7. pmc RecA filament sliding on DNA facilitates homology search
    Kaushik Ragunathan
    Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, United States corrected
    elife 1:e00067. 2012
  8. pmc Single-molecule approaches embrace molecular cohorts
    Taekjip Ha
    Department of Physics, Center for the Physics of Living Cells and Institute for Genomic Biology, University of Illinois at Urbana Champaign, Howard Hughes Medical Institute, Urbana, IL 61801, USA
    Cell 154:723-6. 2013
  9. pmc Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging
    Taekjip Ha
    Department of Physics, University of Illinois at Urbana Champaign, 61801, USA
    Annu Rev Phys Chem 63:595-617. 2012
  10. ncbi request reprint The euryarchaeota, nature's medium for engineering of single-stranded DNA-binding proteins
    Justin B Robbins
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    J Biol Chem 280:15325-39. 2005

Collaborators

Detail Information

Publications96

  1. pmc Probing cellular protein complexes using single-molecule pull-down
    Ankur Jain
    Center for Biophysics and Computational Biology and Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Nature 473:484-8. 2011
    ..SiMPull should provide a rapid, sensitive and robust platform for analysing protein assemblies in biological pathways...
  2. pmc Quantitative fluorescence labeling of aldehyde-tagged proteins for single-molecule imaging
    Xinghua Shi
    Howard Hughes Medical Institute, Urbana, Illinois, USA
    Nat Methods 9:499-503. 2012
    ..We also show the unique power of our method in single-molecule studies on the transient interactions and switching between two quantitatively labeled DNA polymerases on their processivity factor...
  3. pmc G-quadruplex DNA bound by a synthetic ligand is highly dynamic
    Prakrit V Jena
    Department of Physics, Howard Hughes Medical Institute, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    J Am Chem Soc 131:12522-3. 2009
    ..We report that the G-quadruplex can be stabilized without preventing the intrinsic intramolecular dynamics of telomeric DNA...
  4. pmc Fluorescent lifetime trajectories of a single fluorophore reveal reaction intermediates during transcription initiation
    Maria Sorokina
    Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    J Am Chem Soc 131:9630-1. 2009
    ..This work represents the first demonstration of real-time biochemical reactions observed via single molecule fluorescence lifetime trajectories of immobilized molecules...
  5. pmc Single molecule analysis of Thermus thermophilus SSB protein dynamics on single-stranded DNA
    Jichuan Zhang
    Department of Physics and Center for the Physics of Living Cells, University of Illinois, Urbana, IL 61801, USA, Department of Materials Science and Engineering, University of Illinois, Urbana, IL 61801, USA, RIKEN, Cellular and Molecular Biology Unit, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan and Howard Hughes Medical Institute, University of Illinois, Urbana, IL 61801, USA
    Nucleic Acids Res 42:3821-32. 2014
    ..These dynamic features of SSBs may facilitate SSB redistribution and removal on/from ssDNA, and help recruit other SSB-interacting proteins onto ssDNA for subsequent DNA processing in DNA replication, recombination and repair. ..
  6. pmc Single-molecule fluorescence reveals the unwinding stepping mechanism of replicative helicase
    Salman Syed
    Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Cell Rep 6:1037-45. 2014
    ....
  7. pmc RecA filament sliding on DNA facilitates homology search
    Kaushik Ragunathan
    Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, United States corrected
    elife 1:e00067. 2012
    ..Our data represents the first example of a DNA bound multi-protein complex which can slide along another DNA to facilitate target search.DOI:http://dx.doi.org/10.7554/eLife.00067.001...
  8. pmc Single-molecule approaches embrace molecular cohorts
    Taekjip Ha
    Department of Physics, Center for the Physics of Living Cells and Institute for Genomic Biology, University of Illinois at Urbana Champaign, Howard Hughes Medical Institute, Urbana, IL 61801, USA
    Cell 154:723-6. 2013
    ..The same approaches used to study proteins in isolation are now being leveraged to examine the changes in functional behavior that emerge when single molecules have company...
  9. pmc Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging
    Taekjip Ha
    Department of Physics, University of Illinois at Urbana Champaign, 61801, USA
    Annu Rev Phys Chem 63:595-617. 2012
    ..Understanding photophysics is critical in the design and interpretation of single-molecule experiments...
  10. ncbi request reprint The euryarchaeota, nature's medium for engineering of single-stranded DNA-binding proteins
    Justin B Robbins
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    J Biol Chem 280:15325-39. 2005
    ..Although the diversity shown by archaeal single-stranded DNA-binding proteins is unparalleled, the presence of their simplest form in many organisms across all domains of life is of greater evolutionary consequence...
  11. ncbi request reprint Single-molecule quantum-dot fluorescence resonance energy transfer
    Sungchul Hohng
    Physics Department, University of Illinois, Urbana Champaign, Urbana, Illinois 61801, USA
    Chemphyschem 6:956-60. 2005
    ....
  12. pmc Single-molecule nanopositioning: structural transitions of a helicase-DNA complex during ATP hydrolysis
    Hamza Balci
    Physics Department, University of Illinois, Urbana, Illinois, USA
    Biophys J 101:976-84. 2011
    ..We discuss the possible implications of this newly observed conformation...
  13. pmc SSB protein diffusion on single-stranded DNA stimulates RecA filament formation
    Rahul Roy
    Center for Biophysics and Computational Biology, University of Illinois, Urbana Champaign, Illinois 61801, USA
    Nature 461:1092-7. 2009
    ..This observation of diffusional movement of a protein on ssDNA introduces a new model for how an SSB protein can be redistributed, while remaining tightly bound to ssDNA during recombination and repair processes...
  14. pmc Single-molecule analysis reveals differential effect of ssDNA-binding proteins on DNA translocation by XPD helicase
    Masayoshi Honda
    Department of Biochemistry, University of Illinois at Urbana Champaign, 61801, USA
    Mol Cell 35:694-703. 2009
    ..In contrast, RPA2 did not interfere with XPD-ssDNA binding but markedly slowed down XPD translocation. Mechanistic models of bypassing DNA-bound proteins by the Rad3 family helicases and their biological implications are discussed...
  15. ncbi request reprint Observation of internal cleavage and ligation reactions of a ribozyme
    Michelle K Nahas
    Physics Department, University of Illinois, Urbana Champaign, Urbana, Illinois 61801, USA
    Nat Struct Mol Biol 11:1107-13. 2004
    ....
  16. pmc How directional translocation is regulated in a DNA helicase motor
    Jin Yu
    Beckman Institute, University of Illinois at Urbana Champaign, Champaign, Illinois and Howard Hughes Medical Institute, Urbana, Illinois, USA
    Biophys J 93:3783-97. 2007
    ..We identify a set of essential residues coevolutionarily coupled in related helicases that should be involved in the allosteric regulation of these motor proteins...
  17. ncbi request reprint Bridging conformational dynamics and function using single-molecule spectroscopy
    Sua Myong
    Department of Physics, University of Illinois, Urbana Champaign, Urbana, Illinois 61801, USA
    Structure 14:633-43. 2006
    ....
  18. ncbi request reprint Repetitive shuttling of a motor protein on DNA
    Sua Myong
    Physics Department, University of Illinois, Urbana Champaign, Urbana, Illinois 61801, USA
    Nature 437:1321-5. 2005
    ..Thus, the binding of a single Rep monomer to a stalled replication fork can lead to repetitive shuttling along the single-stranded region, possibly keeping the DNA clear of toxic recombination intermediates...
  19. pmc Engineering of functional replication protein a homologs based on insights into the evolution of oligonucleotide/oligosaccharide-binding folds
    Yuyen Lin
    Department of Animal Sciences, University of Illinois at Urbana Champaign, 1207 West Gregory Drive, Urbana, IL 61801, USA
    J Bacteriol 190:5766-80. 2008
    ..On the basis of these results, different models that attempt to explain how intramolecular and intermolecular homologous recombination can generate novel forms of SSB or RPAs are proposed...
  20. pmc Single molecule nanocontainers made porous using a bacterial toxin
    Burak Okumus
    Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, USA
    J Am Chem Soc 131:14844-9. 2009
    ..Moreover, engineered mutants of the utilized toxin can potentially be exploited in the future applications...
  21. ncbi request reprint A single vesicle-vesicle fusion assay for in vitro studies of SNAREs and accessory proteins
    Jiajie Diao
    Department of Physics, University of Illinois at Urbana Champaign, Illinois, USA
    Nat Protoc 7:921-34. 2012
    ..These assays can be used to study the roles of various SNARE proteins, accessory proteins and effects of different lipid compositions on specific fusion steps. The total time required to finish one round of this protocol is 3–6 d...
  22. pmc PcrA helicase dismantles RecA filaments by reeling in DNA in uniform steps
    Jeehae Park
    Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Cell 142:544-55. 2010
    ....
  23. pmc Branch migration enzyme as a Brownian ratchet
    Ivan Rasnik
    Physics Department, University of Illinois, Urbana Champaign, Urbana, IL, USA
    EMBO J 27:1727-35. 2008
    ....
  24. pmc Protein-guided RNA dynamics during early ribosome assembly
    Hajin Kim
    1 Department of Physics, Center for the Physics of Living Cells and Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA 2 Howard Hughes Medical Institute, Urbana, Illinois 61801, USA 3 4 School of Nano Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 689 798, Republic of Korea H K Department of Biochemistry and Biophysics, University of California at San Francisco, 600 16th Street, San Francisco, California 94143 2200, USA M M Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, LHRRB 517, Boston, Massachusetts 02115 5730, USA K R
    Nature 506:334-8. 2014
    ..These protein-guided dynamics offer an alternative explanation for induced fit in RNA-protein complexes. ..
  25. pmc A practical guide to single-molecule FRET
    Rahul Roy
    Department of Physics, University of Illinois at Urbana Champaign, 1110 West Green Street, Urbana, Illinois 61801, USA
    Nat Methods 5:507-16. 2008
    ..We also describe how a smFRET-capable instrument can be built at a reasonable cost with off-the-shelf components and operated reliably using well-established protocols and freely available software...
  26. pmc Temperature-independent porous nanocontainers for single-molecule fluorescence studies
    Yuji Ishitsuka
    Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Anal Chem 82:9694-701. 2010
    ..The permeability of the biofriendly nanocontainer over a wide range of temperature would be effectively applied to other surface-based high-throughput measurements and sensors beyond the single-molecule fluorescence measurements...
  27. ncbi request reprint Ultrafast redistribution of E. coli SSB along long single-stranded DNA via intersegment transfer
    Kyung Suk Lee
    Department of Physics, Center for Physics in Living Cells and Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801 2902, USA
    J Mol Biol 426:2413-21. 2014
    ..Our work suggests that SSB can also migrate via a long-range intersegment transfer on long ssDNA. The force dependence of SSB movement on ssDNA further supports this interpretation. ..
  28. ncbi request reprint Functional analysis of multiple single-stranded DNA-binding proteins from Methanosarcina acetivorans and their effects on DNA synthesis by DNA polymerase BI
    Justin B Robbins
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    J Biol Chem 279:6315-26. 2004
    ..Although bacterial SSB and eukaryotic RPA have been shown to stimulate DNA synthesis by their cognate DNA polymerases, our findings provide the first in vitro biochemical evidence for the conservation of this property in an archaeon...
  29. pmc Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic
    Burak Okumus
    Physics Department, University of Illinois, Urbana Champaign, Urbana, Illinois USA
    Biophys J 87:2798-806. 2004
    ..This strongly indicates that the observed heterogeneity in dynamic properties does not arise as an artifact of surface attachment, but is intrinsic to the nature of the molecules...
  30. pmc Reverse-chaperoning activity of an AAA+ protein
    Cheng Liu
    Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana Champaign, Champaign, Illinois, USA
    Biophys J 100:1344-52. 2011
    ..This PCNA assembly activity required the ATP-bound conformation of RFC. Our work demonstrates a reverse-chaperoning activity for an AAA+ protein that can act as a template for the assembly of another protein complex...
  31. ncbi request reprint Exploring rare conformational species and ionic effects in DNA Holliday junctions using single-molecule spectroscopy
    Chirlmin Joo
    Physics Department, University of Illinois, Urbana Champaign, Urbana, IL 61801, USA
    J Mol Biol 341:739-51. 2004
    ..This further supports the notion that electrostatic stabilization of the stacked structures dictates the interconversion rates between different structural forms...
  32. pmc BLM helicase measures DNA unwound before switching strands and hRPA promotes unwinding reinitiation
    Jaya G Yodh
    Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    EMBO J 28:405-16. 2009
    ..The reported activities may facilitate BLM processing of stalled replication forks and illegitimately formed recombination intermediates...
  33. pmc Tyrosine phosphorylation enhances RAD52-mediated annealing by modulating its DNA binding
    Masayoshi Honda
    Department of Biochemistry, University of Illinois Urbana Champaign, Urbana, IL, USA
    EMBO J 30:3368-82. 2011
    ..We propose that phosphorylation at Y104 enhances ssDNA annealing activity of RAD52 by attenuating dsDNA binding. Implications of phosphorylation-mediated activation of RAD52 annealing activity are discussed...
  34. pmc Structure-based model of the stepping motor of PcrA helicase
    Jin Yu
    Beckman Institute, Department of Physics, and Howard Hughes Medical Institute, University of Illinois at Urbana Champaign, Urbana, IL, USA
    Biophys J 91:2097-114. 2006
    ..By combining short timescale (nanoseconds) molecular dynamics and long timescale (milliseconds) stochastic-dynamics descriptions, our study suggests a structure-based mechanism of the ATP-powered unidirectional movement of PcrA helicase...
  35. doi request reprint Advances in single-molecule fluorescence methods for molecular biology
    Chirlmin Joo
    Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Annu Rev Biochem 77:51-76. 2008
    ..In this exciting era of transitioning from in vitro to in vivo and in situ conditions, it is anticipated that SM fluorescence methodology will become a common tool of molecular biology...
  36. ncbi request reprint Real-time observation of RecA filament dynamics with single monomer resolution
    Chirlmin Joo
    Howard Hughes Medical Institute and Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Cell 126:515-27. 2006
    ..This supports the proposal for a passive role of RecA-loading machineries in SSB removal...
  37. pmc Interhead distance measurements in myosin VI via SHRImP support a simplified hand-over-hand model
    Hamza Balci
    Physics and Biophysics Departments, University of Illinois, Urbana Champaign, Illinois 61801, USA
    Biophys J 89:413-7. 2005
    ..To clarify these issues, we used a new technique, SHRImP, to measure the interhead distance of nearly rigor myosin VI molecules. Our data show a single peak at 29.3 +/- 0.7 nm, in agreement with the straightforward hand-over-hand model...
  38. pmc Human Rad52-mediated homology search and annealing occurs by continuous interactions between overlapping nucleoprotein complexes
    Eli Rothenberg
    Howard Hughes Medical Institute and Center for the Physics of Living Cells, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Proc Natl Acad Sci U S A 105:20274-9. 2008
    ..In light of these observations we propose a model for hRad52-mediated DNA annealing where ssDNA release and dsDNA zippering are coordinated through successive rearrangement of overlapping nucleoprotein complexes...
  39. pmc Defocused orientation and position imaging (DOPI) of myosin V
    Erdal Toprak
    Center for Biophysics and Computational Biology and Physics Department, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Proc Natl Acad Sci U S A 103:6495-9. 2006
    ..When beta changes, the probe rotates +/-27 degrees azimuthally around actin and then rotates back again on the next step. Our results remove degeneracy in angles and the appearance of nontilting lever arms that were reported...
  40. pmc Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction
    Sungchul Hohng
    Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Science 318:279-83. 2007
    ..This method of mapping two-dimensional reaction landscapes at low forces is readily applicable to other nucleic acid systems and their interactions with proteins and enzymes...
  41. pmc Fueling protein DNA interactions inside porous nanocontainers
    Ibrahim Cisse
    Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Proc Natl Acad Sci U S A 104:12646-50. 2007
    ..This method provides a biofriendly and simple alternative to surface tethering that is ideal for the study of transient and weakly interacting biological complexes...
  42. pmc Human Rad52 binds and wraps single-stranded DNA and mediates annealing via two hRad52-ssDNA complexes
    Jill M Grimme
    Department of Biochemistry, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Nucleic Acids Res 38:2917-30. 2010
    ....
  43. pmc SSB functions as a sliding platform that migrates on DNA via reptation
    Ruobo Zhou
    Department of Physics and Center for the Physics of Living Cells, University of Illinois, Urbana Champaign, IL 61801, USA
    Cell 146:222-32. 2011
    ....
  44. pmc A rule of seven in Watson-Crick base-pairing of mismatched sequences
    Ibrahim I Cisse
    Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
    Nat Struct Mol Biol 19:623-7. 2012
    ....
  45. ncbi request reprint Surfaces and orientations: much to FRET about?
    Ivan Rasnik
    Physics Department and Center for Biophysics and Computational Biology, University of Illinois, Urbana Champaign, Urbana, Illinois 61801, USA
    Acc Chem Res 38:542-8. 2005
    ....
  46. pmc Observing spontaneous branch migration of Holliday junctions one step at a time
    Sean A McKinney
    Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Proc Natl Acad Sci U S A 102:5715-20. 2005
    ....
  47. pmc Dynamic structural rearrangements between DNA binding modes of E. coli SSB protein
    Rahul Roy
    Center for Biophysics and Computational Biology, University of Illinois, Urbana Champaign, IL 61801, USA
    J Mol Biol 369:1244-57. 2007
    ....
  48. pmc Detecting intramolecular conformational dynamics of single molecules in short distance range with subnanometer sensitivity
    Ruobo Zhou
    Department of Physics and Center for the Physics of Living Cells, University of Illinois, Urbana Champaign, Illinois 61801, United States
    Nano Lett 11:5482-8. 2011
    ....
  49. pmc Direct imaging of single UvrD helicase dynamics on long single-stranded DNA
    Kyung Suk Lee
    Department of Physics, Center for Physics in Living Cells and Institute for Genomic Biology, University of Illinois, Urbana Champaign, Urbana, Illinois 61801 2902, USA
    Nat Commun 4:1878. 2013
    ....
  50. ncbi request reprint Conformational flexibility of four-way junctions in RNA
    Sungchul Hohng
    Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    J Mol Biol 336:69-79. 2004
    ....
  51. pmc Spontaneous intersubunit rotation in single ribosomes
    Peter V Cornish
    Department of Physics, University of Illinois, 1110 West Green Street, Urbana, IL 61801, USA
    Mol Cell 30:578-88. 2008
    ..Our results provide direct evidence that the intersubunit rotation that underlies ribosomal translocation is thermally driven...
  52. pmc Spring-loaded mechanism of DNA unwinding by hepatitis C virus NS3 helicase
    Sua Myong
    Physics Department, University of Illinois, 1110 West Green Street, Urbana, IL 61801, USA
    Science 317:513-6. 2007
    ..Such repetitive unwinding behavior over a short stretch of duplex may help to keep secondary structures resolved during viral genome replication...
  53. pmc Real-time observation of strand exchange reaction with high spatiotemporal resolution
    Kaushik Ragunathan
    Center for Biophysics and Computational Biology, Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Structure 19:1064-73. 2011
    ..This finding could have important implications for the irreversibility of strand exchange. Our model for strand exchange links structural models of RecA to its catalytic function...
  54. ncbi request reprint DNA-binding orientation and domain conformation of the E. coli rep helicase monomer bound to a partial duplex junction: single-molecule studies of fluorescently labeled enzymes
    Ivan Rasnik
    Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    J Mol Biol 336:395-408. 2004
    ..Therefore, the closed form of Rep bound to a partial duplex DNA appears to be an inhibited form of the enzyme...
  55. pmc Single-molecule three-color FRET
    Sungchul Hohng
    Physics Department, University of Illinois, Urbana Champaign, Urbana, Illinois, USA
    Biophys J 87:1328-37. 2004
    ..Our data further suggest that Holliday junction does not spend measurable time with any of the helices unstacked, and that the parallel conformations are not populated to a detectable degree...
  56. ncbi request reprint Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization
    Ahmet Yildiz
    Center for Biophysics and Computational Biology, University of Illinois, Urbana Champaign, IL 61801, USA
    Science 300:2061-5. 2003
    ..These results strongly support a hand-over-hand model of motility, not an inchworm model...
  57. pmc Methanosarcina acetivorans flap endonuclease 1 activity is inhibited by a cognate single-stranded-DNA-binding protein
    Yuyen Lin
    Department of Animal Sciences, University of Illinois at Urbana Champaign, 1207 West Gregory Drive, IL 61801, USA
    J Bacteriol 188:6153-67. 2006
    ..Despite these interesting observations, further biochemical and genetic analyses are required to gain a deeper understanding of the physiological implications of our findings...
  58. pmc Assembly of the five-way junction in the ribosomal small subunit using hybrid MD-Gō simulations
    Ke Chen
    Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    J Phys Chem B 116:6819-31. 2012
    ....
  59. pmc Single-molecule pull-down for studying protein interactions
    Ankur Jain
    Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
    Nat Protoc 7:445-52. 2012
    ..SiMPull is generally applicable to proteins from a variety of cellular contexts and to endogenous proteins. Starting with the cell extracts and passivated slides, the assay requires 1.5-2.5 h for data acquisition and analysis...
  60. doi request reprint Single-molecule FRET analysis of helicase functions
    Eli Rothenberg
    Department of Physics, NSF Center for the Physics of Living Cells, University of Illinois at Urbana Champaign, Urbana, IL, USA
    Methods Mol Biol 587:29-43. 2010
    ..In this chapter we provide a general guide for the construction and execution of single-molecule FRET assays for the study of helicase properties and functionalities...
  61. pmc Following movement of the L1 stalk between three functional states in single ribosomes
    Peter V Cornish
    Department of Physics, University of Illinois, 1110 West Green Street, Urbana, IL 61801, USA
    Proc Natl Acad Sci U S A 106:2571-6. 2009
    ....
  62. pmc Cytosolic viral sensor RIG-I is a 5'-triphosphate-dependent translocase on double-stranded RNA
    Sua Myong
    Institute for Genomic Biology, University of Illinois at Urbana Champaign, 1206 West Gregory Drive, Champaign, IL 61801, USA
    Science 323:1070-4. 2009
    ..This functional integration of two RNA molecular patterns may provide a means to specifically sense and counteract replicating viruses...
  63. pmc Unraveling helicase mechanisms one molecule at a time
    Ivan Rasnik
    Department of Physics, Emory University, Atlanta, GA 30322, USA
    Nucleic Acids Res 34:4225-31. 2006
    ..Unexpected phenomena have also been observed from individual molecules suggesting extended or alternative functionality of helicases in vivo...
  64. ncbi request reprint Nonblinking and long-lasting single-molecule fluorescence imaging
    Ivan Rasnik
    Department of Physics, Emory University, Atlanta, Georgia 30322, USA
    Nat Methods 3:891-3. 2006
    ....
  65. ncbi request reprint A dendritic single-molecule fluorescent probe that is monovalent, photostable and minimally blinking
    Si Kyung Yang
    Department of Chemistry, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Nat Chem 5:692-7. 2013
    ..These interesting properties greatly simplify use of the fluorophore...
  66. doi request reprint A comparative study of multivariate and univariate hidden Markov modelings in time-binned single-molecule FRET data analysis
    Yang Liu
    Center for the Physics of Living Cell, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    J Phys Chem B 114:5386-403. 2010
    ..We also show that, in the case of multiple trajectories, analyzing them simultaneously gives better results than averaging over individual analysis results...
  67. pmc Multivector fluorescence analysis of the xpt guanine riboswitch aptamer domain and the conformational role of guanine
    Michael D Brenner
    Department of Chemistry, University of Illinois atUrbana Champaign, Urbana, Illinois 61801, USA
    Biochemistry 49:1596-605. 2010
    ....
  68. doi request reprint Real-time observation of G-quadruplex dynamics using single-molecule FRET microscopy
    Burak Okumus
    Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL, USA
    Methods Mol Biol 608:81-96. 2010
    ....
  69. ncbi request reprint Dissecting metal ion-dependent folding and catalysis of a single DNAzyme
    Hee Kyung Kim
    Department of Chemistry, University of Illinois at Urbana Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
    Nat Chem Biol 3:763-8. 2007
    ..These features may contribute to the unusually fast Pb2+-dependent reaction of the DNAzyme. These results suggest that DNAzymes can use all modes of activation that metalloproteins use...
  70. pmc Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy
    M C Murphy
    Physics Department, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Biophys J 86:2530-7. 2004
    ..The persistence length thus estimated ranges from 1.5 nm in 2 M NaCl to 3 nm in 25 mM NaCl...
  71. pmc Analysis of single-molecule FRET trajectories using hidden Markov modeling
    Sean A McKinney
    Department of Physics and Howard Hughes Medical Institute, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
    Biophys J 91:1941-51. 2006
    ..The algorithm is then applied to the analysis of the binding and dissociation of three RecA monomers on a DNA construct...
  72. pmc Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization
    Reza Vafabakhsh
    Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Science 337:1097-101. 2012
    ..Many biologically important protein-DNA interactions that involve looping and bending of DNA below 100 bp likely use this intrinsic bendability of DNA...
  73. ncbi request reprint A single vesicle-vesicle fusion assay for in vitro studies of SNAREs and accessory proteins
    Jiajie Diao
    Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
    Nat Protoc 7:921-34. 2012
    ..These assays can be used to study the roles of various SNARE proteins, accessory proteins and effects of different lipid compositions on specific fusion steps. The total time required to finish one round of this protocol is 3-6 d...
  74. pmc A single-vesicle content mixing assay for SNARE-mediated membrane fusion
    Jiajie Diao
    Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Nat Commun 1:54. 2010
    ..We found that the yeast SNARE complex alone without any accessory proteins can expand the fusion pore large enough to transmit ~11 kDa cargoes...
  75. pmc Monovalent, clickable, uncharged, water-soluble perylenediimide-cored dendrimers for target-specific fluorescent biolabeling
    Si Kyung Yang
    Department of Chemistry, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    J Am Chem Soc 133:9964-7. 2011
    ..Single-molecule studies and target-specific biolabeling are reported, including the highly specific labeling of proteins on the surface of living bacterial and mammalian cells...
  76. ncbi request reprint Inching over hurdles: how DNA helicases move on crowded lattices
    Maria Spies
    Howard Hughes Medical Institute, Department of Biochemistry and Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA
    Cell Cycle 9:1742-9. 2010
    ..We then propose that the selective ability of some helicases to bypass or displace a specific ssDNA binding protein may be important for activation of these enzymes for particular DNA maintenance tasks...
  77. pmc The role of L1 stalk-tRNA interaction in the ribosome elongation cycle
    Leonardo G Trabuco
    Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    J Mol Biol 402:741-60. 2010
    ....
  78. pmc Insight into helicase mechanism and function revealed through single-molecule approaches
    Jaya G Yodh
    Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Q Rev Biophys 43:185-217. 2010
    ..The contributions of these sm investigations to our understanding of helicase mechanism and function will be discussed...
  79. doi request reprint Force-fluorescence spectroscopy at the single-molecule level
    Ruobo Zhou
    Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
    Methods Enzymol 475:405-26. 2010
    ..The possibility to place fluorescent labels at nearly any desired position and a sophisticated design of the experiment increases the amount of information that can be extracted in contrast to pure mechanical or fluorescence experiments...
  80. pmc Dynamic association of ORCA with prereplicative complex components regulates DNA replication initiation
    Zhen Shen
    Department of Cell and Developmental Biology, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
    Mol Cell Biol 32:3107-20. 2012
    ..We propose that the dynamic association of ORCA with pre-RC components modulates the assembly of its interacting partners on chromatin and facilitates DNA replication initiation...
  81. ncbi request reprint MCM forked substrate specificity involves dynamic interaction with the 5'-tail
    Eli Rothenberg
    Department of Physics, University of Illinois at Urbana Champaign, 1110 West Green Street, Urbana, IL 61801, USA
    J Biol Chem 282:34229-34. 2007
    ..This interaction contributes to substrate selectivity and increases the stability of the forked DNA-MCM complex, with possible implications for the MCM unwinding mechanism...
  82. pmc Single molecule nanometronome
    Chittanon Buranachai
    Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, 61801, USA
    Nano Lett 6:496-500. 2006
    ..Since the device displays clearly distinguishable responses even with a single base pair difference, it may lead to a single molecule sensor of minute sequence differences of a target DNA...
  83. pmc C2AB: a molecular glue for lipid vesicles with a negatively charged surface
    Jiajie Diao
    Department of Physics, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Langmuir 25:7177-80. 2009
    ..Furthermore, highly charged liposomes are beneficial in preventing spontaneous fusion before applying the molecular glue...
  84. pmc Acidification of the oxygen scavenging system in single-molecule fluorescence studies: in situ sensing with a ratiometric dual-emission probe
    Xinghua Shi
    Howard Hughes Medical Institute, Department of Physics, and Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Anal Chem 82:6132-8. 2010
    ..This in situ assay should be applicable to a large variety of future single-molecule fluorescence studies...
  85. pmc Single-molecule analysis reveals three phases of DNA degradation by an exonuclease
    Gwangrog Lee
    Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Nat Chem Biol 7:367-74. 2011
    ..The rate-limiting step during processive degradation seems to be the post-cleavage melting of the terminal base pair. We also found that an escape from a known pausing sequence requires enzyme backtracking...
  86. pmc Defining single molecular forces required to activate integrin and notch signaling
    Xuefeng Wang
    Department of Physics, Center for the Physics of Living Cells and Institute for Genomic Biology University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Science 340:991-4. 2013
    ..We find that less than 12 pN is required to activate Notch receptors. TGT can also provide a defined molecular mechanical cue to regulate cellular functions...
  87. pmc Single-molecule views of protein movement on single-stranded DNA
    Taekjip Ha
    Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Annu Rev Biophys 41:295-319. 2012
    ....
  88. pmc Ultrahigh-resolution optical trap with single-fluorophore sensitivity
    Matthew J Comstock
    Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
    Nat Methods 8:335-40. 2011
    ....
  89. pmc Forcing a connection: impacts of single-molecule force spectroscopy on in vivo tension sensing
    Michael D Brenner
    Department of Chemistry, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Biopolymers 95:332-44. 2011
    ..Emphasis will be placed on the use of fluorescence reporter systems for the development of in vivo tension sensors that can be used for calibration with single molecule force methods...
  90. pmc Elastic coupling between RNA degradation and unwinding by an exoribonuclease
    Gwangrog Lee
    Department of Physics, University of Illinois at Urbana Champaign, 1110 West Green Street, Urbana, IL 61801, USA
    Science 336:1726-9. 2012
    ....
  91. pmc Complexin and Ca2+ stimulate SNARE-mediated membrane fusion
    Tae Young Yoon
    Howard Hughes Medical Institute, University of Illinois at Urbana Champaign, 1110 West Green Street, Urbana, Illinois 61801 3080, USA
    Nat Struct Mol Biol 15:707-13. 2008
    ..We suggest that SNARE complexes, complexins and phospholipids collectively form a complex substrate for Ca(2+) and Ca(2+)-sensing fusion effectors in neurotransmitter release...
  92. pmc Stepwise translocation of nucleic acid motors
    Sua Myong
    Department of Bioengineering, University of Illinois at Urbana Champaign, IL, USA
    Curr Opin Struct Biol 20:121-7. 2010
    ..Spontaneous dynamics displayed by ribosome ratcheting and SSB (single stranded DNA binding protein) diffusing on DNA were rectified by interacting cofactors and proteins, EF-G and RecA, respectively...
  93. ncbi request reprint Discrete and heterogeneous rotational dynamics of single membrane probe dyes in gel phase supported lipid bilayer
    Benjamin C Stevens
    Department of Physics, University of Illinois, Urbana Champaign, Urbana, Illinois 61801, USA
    J Chem Phys 120:3030-9. 2004
    ..Our results suggest that the gel phase membrane is not uniform at the microscopic level but is highly dynamic with the rigidity of local environments constantly changing...
  94. pmc Single-molecule nanometry for biological physics
    Hajin Kim
    Howard Hughes Medical Institute, Urbana, IL 61801, USA
    Rep Prog Phys 76:016601. 2013
    ..Finally, we will discuss recent progress in combining angstrom-precision optical tweezers with single-molecule fluorescent detection, opening new windows for multi-dimensional single-molecule nanometry for biological physics...
  95. ncbi request reprint A survey of single-molecule techniques in chemical biology
    Peter V Cornish
    Department of Physics, University of Illinois, Urbana Champaign, 1110 West Green Street, Urbana, Illinois 61801 3080, USA
    ACS Chem Biol 2:53-61. 2007
    ..We will end by providing an assessment of what the future holds, including techniques that are currently in development...
  96. ncbi request reprint Photodestruction intermediates probed by an adjacent reporter molecule
    Taekjip Ha
    Department of Physics, University of Illinois at Urbana Champaign, Urbana, Illinois, 61801, USA
    Phys Rev Lett 90:223002. 2003
    ..These intermediates are nonemitting but are still able to quench the fluorescence of the donor at a distance scale shorter than conventional fluorescence resonance energy transfer, suggesting novel biophysical applications...