T Ha

Summary

Affiliation: University of Illinois
Country: USA

Publications

  1. 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
  2. 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
  3. pmc Spectroscopic observation of RNA chaperone activities of Hfq in post-transcriptional regulation by a small non-coding RNA
    Veronique Arluison
    Institut de Biologie Physico Chimique, CNRS UPR 9073 conventionnee avec l université Paris 7, 13 rue P et M Curie, 75005 Paris, France
    Nucleic Acids Res 35:999-1006. 2007
  4. ncbi request reprint Need for speed: mechanical regulation of a replicative helicase
    Taekjip Ha
    Department of Physics and Institute for Genomic Biology, University of Illinois, Urbana Champaign, and Howard Hughes Medical Institute, Urbana, IL 61801, USA
    Cell 129:1249-50. 2007
  5. ncbi request reprint Single-molecule fluorescence methods for the study of nucleic acids
    T Ha
    Department of Physics and Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Curr Opin Struct Biol 11:287-92. 2001
  6. ncbi request reprint Structural dynamics and processing of nucleic acids revealed by single-molecule spectroscopy
    Taekjip Ha
    Department of Physics and Center for Biophysics and Computational Biology, University of Illinois, Urbana Champaign, Urbana, Illinois 61801, USA
    Biochemistry 43:4055-63. 2004
  7. ncbi request reprint Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase
    Taekjip Ha
    Department of Physics, University of Illinois, Urbana, Illinois 61801, USA
    Nature 419:638-41. 2002
  8. ncbi request reprint Single-molecule fluorescence resonance energy transfer
    T Ha
    Department of Physics, Center for Biophysics and Computational Biology, Urbana 61801, USA
    Methods 25:78-86. 2001
  9. 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
  10. 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

Research Grants

  1. Single Molecule Study of Helicase Mechanisms
    Taekjip Ha; Fiscal Year: 2010
  2. Single Molecule Study of Helicase Mechanisms
    Taekjip Ha; Fiscal Year: 2002
  3. Single Molecule Study of Helicase Mechanisms
    Taekjip Ha; Fiscal Year: 2009
  4. Single Molecule Study of Helicase Mechanisms
    Taekjip Ha; Fiscal Year: 2005
  5. Single Molecule Study of Helicase Mechanisms
    Taekjip Ha; Fiscal Year: 2007
  6. Porous Biomimetric Nanocontainers
    Taekjip Ha; Fiscal Year: 2007
  7. Single Molecule Study of Helicase Mechanisms
    Taekjip Ha; Fiscal Year: 2006
  8. Single Molecule Study of Helicase Mechanisms
    Taekjip Ha; Fiscal Year: 2003
  9. Single Molecule Study of Helicase Mechanisms
    Taekjip Ha; Fiscal Year: 2004
  10. Single Molecule Study of Helicase Mechanisms
    Taekjip Ha; Fiscal Year: 2003

Collaborators

Detail Information

Publications73

  1. 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...
  2. 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...
  3. pmc Spectroscopic observation of RNA chaperone activities of Hfq in post-transcriptional regulation by a small non-coding RNA
    Veronique Arluison
    Institut de Biologie Physico Chimique, CNRS UPR 9073 conventionnee avec l université Paris 7, 13 rue P et M Curie, 75005 Paris, France
    Nucleic Acids Res 35:999-1006. 2007
    ..Overall, our data suggests that Hfq not only promotes strand exchange by binding rapidly to both DsrA and rpoS but also possesses RNA chaperoning properties that facilitates dynamic RNA-RNA interactions...
  4. ncbi request reprint Need for speed: mechanical regulation of a replicative helicase
    Taekjip Ha
    Department of Physics and Institute for Genomic Biology, University of Illinois, Urbana Champaign, and Howard Hughes Medical Institute, Urbana, IL 61801, USA
    Cell 129:1249-50. 2007
    ..In this issue, Johnson et al. (2007) shed light on this conundrum using a single molecule approach to dissect the behavior of the T7 DNA helicase...
  5. ncbi request reprint Single-molecule fluorescence methods for the study of nucleic acids
    T Ha
    Department of Physics and Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Curr Opin Struct Biol 11:287-92. 2001
    ..An exciting new opportunity of combining fluorescence methods and biomechanical tools to study the structural changes and functions of enzymes that participate in nucleic acid metabolism has also arisen...
  6. ncbi request reprint Structural dynamics and processing of nucleic acids revealed by single-molecule spectroscopy
    Taekjip Ha
    Department of Physics and Center for Biophysics and Computational Biology, University of Illinois, Urbana Champaign, Urbana, Illinois 61801, USA
    Biochemistry 43:4055-63. 2004
    ..The most recent examples are discussed, including the hairpin ribozyme, Holliday junction, G-quadruplex, Rep helicase, reverse transcriptase, and combination with mechanical manipulation...
  7. ncbi request reprint Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase
    Taekjip Ha
    Department of Physics, University of Illinois, Urbana, Illinois 61801, USA
    Nature 419:638-41. 2002
    ..We expect that these techniques will be useful for dynamic studies of other helicases and protein-DNA interactions...
  8. ncbi request reprint Single-molecule fluorescence resonance energy transfer
    T Ha
    Department of Physics, Center for Biophysics and Computational Biology, Urbana 61801, USA
    Methods 25:78-86. 2001
    ..Here, we discuss practical considerations for its implementation including experimental apparatus, fluorescent probe selection, surface immobilization, single-molecule FRET analysis schemes, and interpretation...
  9. 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...
  10. 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...
  11. 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...
  12. 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...
  13. 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...
  14. 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
    ....
  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 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...
  17. 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...
  18. 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
    ....
  19. 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...
  20. 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...
  21. 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
    ....
  22. 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...
  23. ncbi request reprint Structural dynamics of individual Holliday junctions
    Sean A McKinney
    Physics Department, University of Illinois, Urbana Champaign, 61801, USA
    Nat Struct Biol 10:93-7. 2003
    ..This provides a mechanism whereby the sequence-dependent conformational bias could determine the extent of genetic exchange upon junction resolution...
  24. ncbi request reprint Single-molecule studies of DNA and RNA four-way junctions
    S A McKinney
    Department of Physics, University of Illinois, Urbana Champaign, Urbana, IL 61801, USA
    Biochem Soc Trans 32:41-5. 2004
    ..The most definitive evidence for this is the observation of three-state folding in single-hairpin ribozymes, the intermediate state of which is populated due to the intrinsic properties of the junction...
  25. 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...
  26. 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
    ....
  27. 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...
  28. 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...
  29. 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
    ....
  30. 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
    ....
  31. 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...
  32. 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
    ....
  33. 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...
  34. 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...
  35. 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...
  36. 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...
  37. 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...
  38. 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...
  39. 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...
  40. 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
    ....
  41. pmc A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate
    Elliot Tan
    Department of Physics and Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Proc Natl Acad Sci U S A 100:9308-13. 2003
    ..Dynamic interplay between structural elements, as we demonstrate for the hairpin ribozyme, may be a general theme for other functional RNA molecules...
  42. 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...
  43. 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...
  44. 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...
  45. 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
    ....
  46. 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...
  47. 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...
  48. 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...
  49. 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...
  50. 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...
  51. 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...
  52. 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...
  53. pmc Multiple intermediates in SNARE-induced membrane fusion
    Tae Young Yoon
    Howard Hughes Medical Institute, Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Proc Natl Acad Sci U S A 103:19731-6. 2006
    ..The ability to monitor the time course of fusion events between two proteoliposomes should be useful for addressing many important issues in SNARE-mediated membrane fusion...
  54. 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
    ....
  55. 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...
  56. 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
    ....
  57. 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...
  58. 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...
  59. 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
    ....
  60. pmc Conformational model of the Holliday junction transition deduced from molecular dynamics simulations
    Jin Yu
    Beckman Institute, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Nucleic Acids Res 32:6683-95. 2004
    ..The results show that magnesium ions stabilize the stacked-X form and destabilize the open and tetrahedral intermediates. Overall, our study provides a detailed dynamic model of the Holliday junction undergoing a conformer transition...
  61. 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...
  62. 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...
  63. 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...
  64. 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...
  65. 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...
  66. pmc Single-molecule high-resolution imaging with photobleaching
    Matthew P Gordon
    Department of Physics and Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Proc Natl Acad Sci U S A 101:6462-5. 2004
    ..In addition to bridging the gap in optical resolution, this technique may be useful for biophysical or genomic applications, including the generation of super-high-density maps of single-nucleotide polymorphisms...
  67. pmc Extreme conformational diversity in human telomeric DNA
    J Y Lee
    Department of Physics, Seoul National University, Seoul 151 742, Korea
    Proc Natl Acad Sci U S A 102:18938-43. 2005
    ..The extremely diverse conformations of the human telomeric DNA may have mechanistic implications for the proteins and drugs that recognize G-rich sequences...
  68. pmc Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids
    Asif Iqbal
    Cancer Research United Kingdom Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
    Proc Natl Acad Sci U S A 105:11176-81. 2008
    ..Our data unequivocally establish that Förster transfer obeys the orientation dependence as expected for a dipole-dipole interaction...
  69. pmc Transcription initiation in a single-subunit RNA polymerase proceeds through DNA scrunching and rotation of the N-terminal subdomains
    Guo Qing Tang
    Department of Biochemistry, University of Medicine and Dentistry of New Jersey Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
    Mol Cell 30:567-77. 2008
    ..The observed stepwise conformational changes provide a basis to understand abortive RNA synthesis during early stages of initiation and promoter escape during the later stages that allows transition to processive elongation...
  70. ncbi request reprint Stereospecific effects determine the structure of a four-way DNA junction
    Jia Liu
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
    Chem Biol 12:217-28. 2005
    ..It is likely that the stereochemical environment of the methyl group affects the interaction with metal ions in the center of the junction...
  71. pmc Single-molecule conformational analysis of G-quadruplex formation in the promoter DNA duplex of the proto-oncogene c-kit
    Pravin S Shirude
    Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
    J Am Chem Soc 129:7484-5. 2007
  72. ncbi request reprint RNA folding and the origins of catalytic activity in the hairpin ribozyme
    Timothy J Wilson
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee DD1 5EH, UK
    Blood Cells Mol Dis 38:8-14. 2007
    ..We observe significant rates of cleavage and ligation, and a bell-shaped pH dependence for both...
  73. pmc Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules
    Harold D Kim
    Department of Applied Physics and Physics, Stanford University, Stanford, CA 94305 4060, USA
    Proc Natl Acad Sci U S A 99:4284-9. 2002
    ..This version of FCS/FRET on immobilized single molecules is demonstrated to be a powerful technique in the study of conformational dynamics of biomolecules over time scales ranging from microseconds to seconds...

Research Grants12

  1. Single Molecule Study of Helicase Mechanisms
    Taekjip Ha; Fiscal Year: 2010
    ..In all of our studies, bulk-phase biochemical experiments, crystallography, and computational studies through collaboration will help us design and interpret our measurements. ..
  2. Single Molecule Study of Helicase Mechanisms
    Taekjip Ha; Fiscal Year: 2002
    ..For example, we will measure both the number of helicase monomers bound to DNA and DNA unwinding to determine if the active form of SF1 helicase is monomer or dimer. ..
  3. Single Molecule Study of Helicase Mechanisms
    Taekjip Ha; Fiscal Year: 2009
    ..In all of our studies, bulk-phase biochemical experiments, crystallography, and computational studies through collaboration will help us design and interpret our measurements. ..
  4. Single Molecule Study of Helicase Mechanisms
    Taekjip Ha; Fiscal Year: 2005
    ..For example, we will measure both the number of helicase monomers bound to DNA and DNA unwinding to determine if the active form of SF1 helicase is monomer or dimer. ..
  5. Single Molecule Study of Helicase Mechanisms
    Taekjip Ha; Fiscal Year: 2007
    ..In all of our studies, bulk-phase biochemical experiments, crystallography, and computational studies through collaboration will help us design and interpret our measurements. ..
  6. Porous Biomimetric Nanocontainers
    Taekjip Ha; Fiscal Year: 2007
    ..Furthermore we will use these techniques to make new biological discoveries on the activities of RNA enzymes and helicases. ..
  7. Single Molecule Study of Helicase Mechanisms
    Taekjip Ha; Fiscal Year: 2006
    ..For example, we will measure both the number of helicase monomers bound to DNA and DNA unwinding to determine if the active form of SF1 helicase is monomer or dimer. ..
  8. Single Molecule Study of Helicase Mechanisms
    Taekjip Ha; Fiscal Year: 2003
    ..For example, we will measure both the number of helicase monomers bound to DNA and DNA unwinding to determine if the active form of SF1 helicase is monomer or dimer. ..
  9. Single Molecule Study of Helicase Mechanisms
    Taekjip Ha; Fiscal Year: 2004
    ..For example, we will measure both the number of helicase monomers bound to DNA and DNA unwinding to determine if the active form of SF1 helicase is monomer or dimer. ..
  10. Single Molecule Study of Helicase Mechanisms
    Taekjip Ha; Fiscal Year: 2003
    ..For example, we will measure both the number of helicase monomers bound to DNA and DNA unwinding to determine if the active form of SF1 helicase is monomer or dimer. ..