Arluison, Véronique, Hohng, Sungchul, Roy, Rahul, Pellegrini, Olivier, Régnier, Philippe, Ha, Taekjip
Hfq protein is vital for the function of many non-coding small (s)RNAs in bacteria but the mechanism by which Hfq facilitates the function of sRNA is still debated. We developed a fluorescence...
Arluison, Véronique, Hohng, Sungchul, Roy, Rahul, Pellegrini, Olivier, Régnier, Philippe, Ha, Taekjip
Hfq protein is vital for the function of many non-coding small (s)RNAs in bacteria but the mechanism by which Hfq facilitates the function of sRNA is still debated. We developed a fluorescence...
Defocused orientation and position imaging (DOPI) of myosin V. (2006)
Toprak, Erdal, Enderlein, Joerg, Syed, Sheyum, McKinney, Sean A., Petschek, Rolfe G., Ha, Taekjip, ...
The centroid of a fluorophore can be determined within approximately 1.5-nm accuracy from its focused image through fluorescence imaging with one-nanometer accuracy (FIONA). If, instead, the sample...
Unraveling helicase mechanisms one molecule at a time (2006)
Rasnik, Ivan, Myong, Sua, Ha, Taekjip
Recent years have seen an increasing number of biological applications of single molecule techniques, evolving from a proof of principle type to the more sophisticated studies. Here we compare the...
Unraveling helicase mechanisms one molecule at a time (2006)
Rasnik, Ivan, Myong, Sua, Ha, Taekjip
Recent years have seen an increasing number of biological applications of single molecule techniques, evolving from a proof of principle type to the more sophisticated studies. Here we compare the...
Unraveling helicase mechanisms one molecule at a time (2006)
Rasnik, Ivan, Myong, Sua, Ha, Taekjip
Recent years have seen an increasing number of biological applications of single molecule techniques, evolving from a proof of principle type to the more sophisticated studies. Here we compare the...
Surfaces and orientations: much to fret about? (2004)
Rasnik, Ivan, McKinney, Sean A., Ha, Taekjip
Single molecule FRET (fluorescence resonance energy transfer) is a powerful technique for detecting real-time conformational changes and molecular interactions during biological reactions. In this...
Yu, Jin, Ha, Taekjip, Schulten, Klaus
Homologous recombination plays a key role in the restart of stalled replication forks and in the generation of genetic diversity. During this process, two homologous DNA molecules undergo strand...
Thesis (Ph. D. in Physics)--University of California, Berkeley, Dec. 1996.
Fluorescence spectroscopy of single molecules at room temperature and its applications / (1996)
Thesis (Ph. D. in Physics)--University of California, Berkeley, Dec. 1996.
Single-Molecule Three-Color FRET (1328)
Sungchul Hohng, Chirlmin Joo, Taekjip Ha
ABSTRACT Fluorescence resonance energy transfer (FRET) measured at the single-molecule level can reveal conformational changes of biomolecules and intermolecular interactions in physiologically...
Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism
Ha, Taekjip, Ting, Alice Y., Liang, Joy, Caldwell, W. Brett, Deniz, Ashok A., Chemla, Daniel S., ...
Fluorescence resonance energy transfer and fluorescence polarization anisotropy are used to investigate single molecules of the enzyme staphylococcal nuclease. Intramolecular fluorescence resonance...
Ligand-induced conformational changes observed in single RNA molecules
Ha, Taekjip, Zhuang, Xiaowei, Kim, Harold D., Orr, Jeffrey W., Williamson, James R., Chu, Steven
We present the first demonstration that fluorescence resonance energy transfer can be used to track the motion of a single molecule undergoing conformational changes. As a model system, the...
Fluorescence quenching: A tool for single-molecule protein-folding study
Zhuang, Xiaowei, Ha, Taekjip, Kim, Harold D., Centner, Thomas, Labeit, Siegfried, Chu, Steven
By using titin as a model system, we have demonstrated that fluorescence quenching can be used to study protein folding at the single molecule level. The unfolded titin molecules with multiple dye...
Deniz, Ashok A., Dahan, Maxime, Grunwell, Jocelyn R., Ha, Taekjip, Faulhaber, Ann E., Chemla, Daniel S., ...
Photon bursts from single diffusing donor-acceptor labeled macromolecules were used to measure intramolecular distances and identify subpopulations of freely diffusing macromolecules in a...
Kim, Harold D., Nienhaus, G. Ulrich, Ha, Taekjip, Orr, Jeffrey W., Williamson, James R., Chu, Steven
Fluorescence correlation spectroscopy (FCS) of fluorescence resonant energy transfer (FRET) on immobilized individual fluorophores was used to study the Mg2+-facilitated conformational change of an...
A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate
Tan, Elliot, Wilson, Timothy J., Nahas, Michelle K., Clegg, Robert M., Lilley, David M. J., Ha, Taekjip
The natural form of the hairpin ribozyme comprises two major structural elements: a four-way RNA junction and two internal loops carried by adjacent arms of the junction. The ribozyme folds into its...
Single-molecule high-resolution imaging with photobleaching
Gordon, Matthew P., Ha, Taekjip, Selvin, Paul R.
Conventional light microscopy is limited in its resolving power by the Rayleigh limit to length scales on the order of 200 nm. On the other hand, spectroscopic techniques such as fluorescence...
Conformational model of the Holliday junction transition deduced from molecular dynamics simulations
Yu, Jin, Ha, Taekjip, Schulten, Klaus
Homologous recombination plays a key role in the restart of stalled replication forks and in the generation of genetic diversity. During this process, two homologous DNA molecules undergo strand...
Early steps of supported bilayer formation probed by single vesicle fluorescence assays.
Johnson, Joseph M, Ha, Taekjip, Chu, Steve, Boxer, Steven G
We have developed a single vesicle assay to study the mechanisms of supported bilayer formation. Fluorescently labeled, unilamellar vesicles (30-100 nm diameter) were first adsorbed to a quartz...
Probing Single-Stranded DNA Conformational Flexibility Using Fluorescence Spectroscopy
Murphy, M.C., Rasnik, Ivan, Cheng, Wei, Lohman, Timothy M., Ha, Taekjip
Single-stranded DNA (ssDNA) is an essential intermediate in various DNA metabolic processes and interacts with a large number of proteins. Due to its flexibility, the conformations of ssDNA in...
Single-Molecule Three-Color FRET
Hohng, Sungchul, Joo, Chirlmin, Ha, Taekjip
Fluorescence resonance energy transfer (FRET) measured at the single-molecule level can reveal conformational changes of biomolecules and intermolecular interactions in physiologically relevant...
Vesicle Encapsulation Studies Reveal that Single Molecule Ribozyme Heterogeneities Are Intrinsic
Okumus, Burak, Wilson, Timothy J., Lilley, David M. J., Ha, Taekjip
Single-molecule measurements have revealed that what were assumed to be identical molecules can differ significantly in their static and dynamic properties. One of the most striking examples is the...
Extreme conformational diversity in human telomeric DNA
Lee, J. Y., Okumus, Burak, Kim, D. S., Ha, Taekjip
DNA with tandem repeats of guanines folds into G-quadruplexes made of a stack of G-quartets. In vitro, G-quadruplex formation inhibits telomere extension, and POT1 binding to the single-stranded...
Interhead Distance Measurements in Myosin VI via SHRImP Support a Simplified Hand-Over-Hand Model
Balci, Hamza, Ha, Taekjip, Sweeney, H. Lee, Selvin, Paul R.
Myosin VI walks in a hand-over-hand fashion with an average step size of 30 nm, which is much larger than its 10 nm lever arm. Recent experiments suggest that the myosin VI structure has an unfolded...
Defocused orientation and position imaging (DOPI) of myosin V
Toprak, Erdal, Enderlein, Joerg, Syed, Sheyum, McKinney, Sean A., Petschek, Rolfe G., Ha, Taekjip, ...
The centroid of a fluorophore can be determined within ≈1.5-nm accuracy from its focused image through fluorescence imaging with one-nanometer accuracy (FIONA). If, instead, the sample is moved...
Unraveling helicase mechanisms one molecule at a time
Rasnik, Ivan, Myong, Sua, Ha, Taekjip
Recent years have seen an increasing number of biological applications of single molecule techniques, evolving from a proof of principle type to the more sophisticated studies. Here we compare the...
Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism
Ha, Taekjip, Ting, Alice Y., Liang, Joy, Caldwell, W. Brett, Deniz, Ashok A., Chemla, Daniel S., ...
Fluorescence resonance energy transfer and fluorescence polarization anisotropy are used to investigate single molecules of the enzyme staphylococcal nuclease. Intramolecular fluorescence resonance...
Ligand-induced conformational changes observed in single RNA molecules
Ha, Taekjip, Zhuang, Xiaowei, Kim, Harold D., Orr, Jeffrey W., Williamson, James R., Chu, Steven
We present the first demonstration that fluorescence resonance energy transfer can be used to track the motion of a single molecule undergoing conformational changes. As a model system, the...
Fluorescence quenching: A tool for single-molecule protein-folding study
Zhuang, Xiaowei, Ha, Taekjip, Kim, Harold D., Centner, Thomas, Labeit, Siegfried, Chu, Steven
By using titin as a model system, we have demonstrated that fluorescence quenching can be used to study protein folding at the single molecule level. The unfolded titin molecules with multiple dye...
Deniz, Ashok A., Dahan, Maxime, Grunwell, Jocelyn R., Ha, Taekjip, Faulhaber, Ann E., Chemla, Daniel S., ...
Photon bursts from single diffusing donor-acceptor labeled macromolecules were used to measure intramolecular distances and identify subpopulations of freely diffusing macromolecules in a...
Kim, Harold D., Nienhaus, G. Ulrich, Ha, Taekjip, Orr, Jeffrey W., Williamson, James R., Chu, Steven
Fluorescence correlation spectroscopy (FCS) of fluorescence resonant energy transfer (FRET) on immobilized individual fluorophores was used to study the Mg2+-facilitated conformational change of an...
A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate
Tan, Elliot, Wilson, Timothy J., Nahas, Michelle K., Clegg, Robert M., Lilley, David M. J., Ha, Taekjip
The natural form of the hairpin ribozyme comprises two major structural elements: a four-way RNA junction and two internal loops carried by adjacent arms of the junction. The ribozyme folds into its...
Single-molecule high-resolution imaging with photobleaching
Gordon, Matthew P., Ha, Taekjip, Selvin, Paul R.
Conventional light microscopy is limited in its resolving power by the Rayleigh limit to length scales on the order of 200 nm. On the other hand, spectroscopic techniques such as fluorescence...
Conformational model of the Holliday junction transition deduced from molecular dynamics simulations
Yu, Jin, Ha, Taekjip, Schulten, Klaus
Homologous recombination plays a key role in the restart of stalled replication forks and in the generation of genetic diversity. During this process, two homologous DNA molecules undergo strand...
Observing spontaneous branch migration of Holliday junctions one step at a time
McKinney, Sean A., Freeman, Alasdair D. J., Lilley, David M. J., Ha, Taekjip
Genetic recombination occurs between homologous DNA molecules via a four-way (Holliday) junction intermediate. This ancient and ubiquitous process is important for the repair of double-stranded...
Early steps of supported bilayer formation probed by single vesicle fluorescence assays.
Johnson, Joseph M, Ha, Taekjip, Chu, Steve, Boxer, Steven G
We have developed a single vesicle assay to study the mechanisms of supported bilayer formation. Fluorescently labeled, unilamellar vesicles (30-100 nm diameter) were first adsorbed to a quartz...
Probing Single-Stranded DNA Conformational Flexibility Using Fluorescence Spectroscopy
Murphy, M.C., Rasnik, Ivan, Cheng, Wei, Lohman, Timothy M., Ha, Taekjip
Single-stranded DNA (ssDNA) is an essential intermediate in various DNA metabolic processes and interacts with a large number of proteins. Due to its flexibility, the conformations of ssDNA in...
Single-Molecule Three-Color FRET
Hohng, Sungchul, Joo, Chirlmin, Ha, Taekjip
Fluorescence resonance energy transfer (FRET) measured at the single-molecule level can reveal conformational changes of biomolecules and intermolecular interactions in physiologically relevant...
Vesicle Encapsulation Studies Reveal that Single Molecule Ribozyme Heterogeneities Are Intrinsic
Okumus, Burak, Wilson, Timothy J., Lilley, David M. J., Ha, Taekjip
Single-molecule measurements have revealed that what were assumed to be identical molecules can differ significantly in their static and dynamic properties. One of the most striking examples is the...
Extreme conformational diversity in human telomeric DNA
Lee, J. Y., Okumus, Burak, Kim, D. S., Ha, Taekjip
DNA with tandem repeats of guanines folds into G-quadruplexes made of a stack of G-quartets. In vitro, G-quadruplex formation inhibits telomere extension, and POT1 binding to the single-stranded...
Interhead Distance Measurements in Myosin VI via SHRImP Support a Simplified Hand-Over-Hand Model
Balci, Hamza, Ha, Taekjip, Sweeney, H. Lee, Selvin, Paul R.
Myosin VI walks in a hand-over-hand fashion with an average step size of 30 nm, which is much larger than its 10 nm lever arm. Recent experiments suggest that the myosin VI structure has an unfolded...
Defocused orientation and position imaging (DOPI) of myosin V
Toprak, Erdal, Enderlein, Joerg, Syed, Sheyum, McKinney, Sean A., Petschek, Rolfe G., Ha, Taekjip, ...
The centroid of a fluorophore can be determined within ≈1.5-nm accuracy from its focused image through fluorescence imaging with one-nanometer accuracy (FIONA). If, instead, the sample is moved...
Unraveling helicase mechanisms one molecule at a time
Rasnik, Ivan, Myong, Sua, Ha, Taekjip
Recent years have seen an increasing number of biological applications of single molecule techniques, evolving from a proof of principle type to the more sophisticated studies. Here we compare the...
Lin, Yuyen, Guzman, Claudia E., McKinney, Mary C., Nair, Satish K., Ha, Taekjip, Cann, Isaac K. O.
The oligonucleotide/oligosaccharide-binding (OB) fold is central to the architecture of single-stranded- DNA-binding proteins, which are polypeptides essential for diverse cellular processes,...
Arluison, Véronique, Hohng, Sungchul, Roy, Rahul, Pellegrini, Olivier, Régnier, Philippe, Ha, Taekjip
Hfq protein is vital for the function of many non-coding small (s)RNAs in bacteria but the mechanism by which Hfq facilitates the function of sRNA is still debated. We developed a fluorescence...
Multiple intermediates in SNARE-induced membrane fusion
Yoon, Tae-Young, Okumus, Burak, Zhang, Fan, Shin, Yeon-Kyun, Ha, Taekjip
Membrane fusion in eukaryotic cells is thought to be mediated by a highly conserved family of proteins called SNAREs (soluble N-ethyl maleimide sensitive-factor attachment protein receptors). The...
Analysis of Single-Molecule FRET Trajectories Using Hidden Markov Modeling
McKinney, Sean A., Joo, Chirlmin, Ha, Taekjip
The analysis of single-molecule fluorescence resonance energy transfer (FRET) trajectories has become one of significant biophysical interest. In deducing the transition rates between various states...
Structure-Based Model of the Stepping Motor of PcrA Helicase
Yu, Jin, Ha, Taekjip, Schulten, Klaus
DNA helicases are ubiquitous molecular motors involved in cellular DNA metabolism. They move along single-stranded DNA (ssDNA) and separate duplex DNA into its component strands, utilizing the free...
Fueling protein–DNA interactions inside porous nanocontainers
Cisse, Ibrahim, Okumus, Burak, Joo, Chirlmin, Ha, Taekjip
Vesicle encapsulation offers a biologically relevant environment for many soluble proteins and nucleic acids and an optimal immobilization medium for single-molecule fluorescence assays. Furthermore,...
How Directional Translocation is Regulated in a DNA Helicase Motor
Yu, Jin, Ha, Taekjip, Schulten, Klaus
PcrA helicase from Bacillus stearothermophilus is one of the smallest motor proteins structurally known in full atomic detail. It translocates progressively from the 3′ end to the 5′ end of...
Iqbal, Asif, Arslan, Sinan, Okumus, Burak, Wilson, Timothy J., Giraud, Gerard, Norman, David G., ...
We have found that the efficiency of fluorescence resonance energy transfer between Cy3 and Cy5 terminally attached to the 5′ ends of a DNA duplex is significantly affected by the relative...
Lin, Yuyen, Lin, Li-Jung, Sriratana, Palita, Coleman, Kelli, Ha, Taekjip, Spies, Maria, ...
The bacterial single-stranded DNA-binding protein (SSB) and the archaeal/eukaryotic functional homolog, replication protein A (RPA), are essential for most aspects of DNA metabolism. Structural...
Gack, Michaela U., Kirchhofer, Axel, Shin, Young C., Inn, Kyung-Soo, Liang, Chengyu, Cui, Sheng, ...
The caspase recruitment domain (CARD) of intracellular adaptors and sensors plays a critical role in the assembly of signaling complexes involved in innate host defense against pathogens and in the...
Branch migration enzyme as a Brownian ratchet
Rasnik, Ivan, Jeong, Yong-Joo, McKinney, Sean A, Rajagopal, Vaishnavi, Patel, Smita S, Ha, Taekjip
In recent years, it has been shown that helicases are able to perform functions beyond their traditional role in unwinding of double-stranded nucleic acids; yet the mechanistic aspects of these...
Rothenberg, Eli, Grimme, Jill M., Spies, Maria, Ha, Taekjip
The Rad52 protein has critical functions in distinct pathways of the homology-directed DNA repair, one of which is to promote the annealing of complementary strands of DNA. Both yeast and human Rad52...
Following movement of the L1 stalk between three functional states in single ribosomes
Cornish, Peter V., Ermolenko, Dmitri N., Staple, David W., Hoang, Lee, Hickerson, Robyn P., Noller, Harry F., ...
The L1 stalk is a mobile domain of the large ribosomal subunit E site that interacts with the elbow of deacylated tRNA during protein synthesis. Here, by using single-molecule FRET, we follow the...
C2AB: A Molecular Glue for Lipid Vesicles with a Negatively Charged Surface
Diao, Jiajie, Yoon, Tae-Young, Su, Zengliu, Shin, Yeon-Kyun, Ha, Taekjip