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STAFF OF THE HA GROUP

GROUP LEADER: Taekjip Ha Complete CV

Contents

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POST-GRADUATES

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Hamza Balci, PhD

Joined group: Apr. 2007

Current Publications:

  • H. Balci, T. Ha, H. L. Sweeney, and P. R. Selvin, "Interhead Distance Measurements in Myosin VI via SHRImP supported a Simplified Hand-overHand model", Biophysical Journal (2005)
  • Joo, C., H. Balci, Y. Ishitsuka, C. Buranachai, and T. Ha , "Advances in Single-Molecule Fluorescence Methods for Molecular Biology", Annual Review of Biochemistry 77, 51-76 (2008)
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Matt Comstock, PhD

Joined group: Mar. 2008

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Peter Cornish, PhD

Joined group: Nov. 2005

Current Publications:

  • P.V. Cornish, D.N. Ermolenko, H.F. Noller, and T. Ha, "Spontaneous Intersubunit Rotation in Single Ribosomes", Molecular Cell 30, 578-88 (2008).
  • P.V. Cornish and T. Ha, "A Survey of Single Molecule Techniques in Chemical Biology", ACS Chemical Biology 2, 53-61 (2006).
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Yuji Ishitsuka, PhD

Joined group: Nov. 2006

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Gwangrog Lee, PhD

Joined group: Nov. 2006

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Sua Myong, PhD

Joined group: Jan. 2002

B.A. in Molecular Cell Biology, U.C. Berkeley (1994)

Ph.D in Nutritional Science & Toxicology, U.C. Berkeley (2001)

Currently Research Assistant Professor in the Institute for Genomic Biology, University of Illinois, Urbana.

Current Publications:

  • S. Myong, M. M. Bruno, A. M. Pyle and T. Ha, "Spring-loaded mechanism of DNA unwinding by HCV NS3 helicase," Science 317, 513-516 (2007).
  • C. Joo, S. A McKinney, M. Nakamura, I. Rasnik, S. Myong, and T. Ha, "Real Time Observation of RecA Filament Dynamics with Single Monomer Resolution", Cell 126, 515-527 (2006).
  • I. Rasnik, S. Myong, and T. Ha, "Unraveling Helicase Mechanism One Molecule at a Time", Nucleic Acids Research 34, 4225-4231 (2006).
  • S. Myong, B. Stevens, and T. Ha, "Bridging Conformational Dynamics and Function using Single-Molecule Spectroscopy", Structure 14, 633-643 (2006).
  • S. Myong, I. Rasnik, C. Joo, T. M. Lohman, and T. Ha, "Repetitive Shuttling of a Motor Protein on DNA", Nature 437, 1321-1325 (2005).
  • I. Rasnik+, S. Myong+, W. Cheng, T. M. Lohman, and T. Ha, "DNA-binding Orientation and Domain Conformation of the E. Coli Rep Helicase Monomer Bound to a Partial Duplex Junction: Single-molecule Studies of Flourescently Labeled Enzymes", Journal of Molecular Biology 336, 395-408 (2004). (+co-authorship)
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Eli Rothenberg, PhD

Joined group as post-doctoral fellow: Aug. 2005

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Xinghua Shi, PhD

Joined group as post-doctoral fellow: July 2007

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Jaya Yodh, PhD

Joined group: Aug. 2006


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GRADUATE STUDENTS

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Sinan Arslan

Joined group: May 2006, dept: physics

  • Talks:
    • 51st Biophysical Society Annual Meeting, "Single Molecule Study Reveals Step Size and Mechanistic Details of Rep Helicase Translocation on Single Stranded DNA", March 5, 2007, Baltimore, MD
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Michael Brenner

Joined group: Sep. 2006, dept: chemistry

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Ibrahim Cisse

Joined group: Jun. 2004, dept: physics

Current Publications:

  • I. Cisse, B. Okumus, C. Joo, T. Ha, "Fueling protein-DNA interactions inside porous nanocontainers", PNAS, (2007) (In Print)
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Jiajie Diao

Joined group: Aug. 2005, dept: physics

Sept. 16 ~ Sept. 23, 2007: made 27 PEG slides

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Sultan Doganay

Joined group: Jan. 2008, dept: biophysics

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Ankur Jain

Joined group: Dec. 2007, dept: biophysics

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Prakrit Jena

Joined group: Jan. 2006, dept: physics

Current publications:

  • Hong Jin, Esther S. Jeng, Daniel A. Heller, Prakrit V. Jena, Robert Kirmse, Jörg Langowski, and Michael S. Strano, "Divalent Ion and Thermally Induced DNA Conformational Polymorphism on Single-walled Carbon Nanotubes", ACS Macromolecules (2007)
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Kyung Suk Lee

Joined group: Aug. 2006, dept: physics

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Cheng Liu

Joined group: May 2005, dept: physics

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Jeehae Park

Joined group: Jan. 2005, dept: biophysics

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Kaushik Ragunathan

Joined group: Jan. 2006, dept: biophysics

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Maria Sorokina

Joined group: Nov. 2006

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Reza Vafabakhsh

Joined group: Aug. 2006, dept: physics

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Ruobo Zhou

Joined group: May 2006, dept: physics

Current publications:

  • S. Hohng, R. Zhou, M. K. Nahas, J. Yu, K. Schulten, D. M. J. Lilley and T. Ha, "Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the Holliday junction", Science 318, 279-283(2007)


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SUPPORT STAFF

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Salman Syed

  • Technician/Grad. Student
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Julia Wright

  • Administrative Assistant (joined group October 2006)


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FORMER MEMBERS

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Sungchul Hohng, PhD

Joined group as post-doctoral fellow: Jan. 2002
Left group: Aug. 2006

Current location: Seoul National University, Physics Department (Assistant Professor) (http://smb.snu.ac.kr)

Contact: shohng AT phya DOT snu DOT ac DOT kr

  • S. Hohng, R. Zhou, M. K. Nahas, J. Yu, K. Schulten, D. M. J. Lilley and T. Ha, "Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the Holliday junction", Science 318, 279-283(2007)
  • V. Arluison+, S. Hohng+, R. Roy, O. Pellegrini, P. Regnier and T. Ha, "Spectroscopic observation of RNA chaperone activities of Hfq in post-transcriptional regulation by a small non-coding RNA", Nucleic Acids Research, (2006) (+co-authorship)
  • S. Hohng and T. Ha, "Single-molecule Quantum Dot FRET", ChemPhysChem 6, 956-960 (2005)
  • Nahas, T. J. Wilson, S. Hohng, K. Jarvie, D. M. J. Lilley and T. Ha, "Observation of Internal Cleavage and Ligation Reactions of a Ribozyme", Nature Structural & Molecular Biology 11, 1107-1113 (2004)
  • S. Hohng, C. Joo, and T. Ha, "Single-Molecule Three-color FRET", Biophysical Journal 87, 1328-1337 (2004)
  • S. Hohng and T. Ha, "Near-Complete Suppression of Quantum Dot Blinking in Ambient Conditions", Journal of American Chemical Society 126, 1324-1325 (2004)
  • S. Hohng, E. Tan, T. J. Wilson, R. M. Clegg, D. M. J. Lilley, and T. Ha, "Conformational Flexibility of Four-way Junctions in RNA", Journal of Molecular Biology 336, 69-79 (2004)
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Chirlmin Joo, PhD

Joined group as graduate student: January 2003
Received PhD in physics: May 2007
Joined group as post-doctoral fellow: May 2007 Left group: August 2008

Current location: V. Narry Kim's Lab; Seoul National University (http://www.narrykim.org)

Contact: chirlmin AT gmail DOT com (http://www.chirlmin.net)

Ph. D. in Physics, University of Illinois at Urbana-Champaign, USA (2007)
B.S. in Physics, Seoul National University, Korea (2002)

Current Publications:

  • C. Joo, H. Balci, Y. Ishitsuka, C. Buranachai, T. Ha "Advances in Single-Molecule Fluorescence Methods for Molecular Biology", Ann. Rev. Biochemistry (2008)
  • C. Joo and T. Ha "Single Molecule FRET with Total Internal Reflection Microscopy" In 'Single Molecule Techniques: A Laboratory Manual' (ed P. Selvin and T. Ha) (Cold Spring Harbor Laboratory Press, 2008)
  • I. Cisse, B. Okumus, C. Joo, T. Ha, "Fueling protein-DNA interactions inside porous nanocontainers", PNAS, (2007)
  • C. Joo, Single-Molecule FRET Study on the RecA-Mediated DNA Repair Doctoral Thesis, University of Illinois (2007)
  • S. A. McKinney, C. Joo, and T. Ha, "Analysis of Single Molecule FRET Trajectories using Hidden Markov Modeling", Biophysical Journal 91, 1941-1951 (2006)
  • C. Joo, S. A McKinney, M. Nakamura, I. Rasnik, S. Myong, and T. Ha, "Real Time Observation of RecA Filament Dynamics with Single Monomer Resolution", Cell 126, 515-527 (2006)
  • S. Myong, I. Rasnik, C. Joo, T. M. Lohman, and T. Ha, "Repetitive Shuttling of a Motor Protein on DNA", Nature 437, 1321-1325 (2005)
  • S. Hohng, C. Joo, and T. Ha, "Single-Molecule Three-color FRET", Biophysical Journal 87, 1328-1337 (2004)
  • C. Joo, S. A. McKinney, D. M. J. Lilley and T. Ha, "Exploring Rare Conformational Species and Ionic Effects in DNA Holliday Junctions using Single-Molecule Spectroscopy", Journal of Molecular Biology 341, 739-751 (2004)
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Sunghyun Kim

Joined group: Mar. 2007 Left group: Aug. 2007

Current location: Interdisciplinary Program of Integrated Biotechnology, Sogang University, Korea

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Yongsun Kim

Joined group as undergraduate: May 2006
Left group: May 2007

Current location: MIT, Physics Department (graduate student) (http://web.mit.edu/physics/)

Contact: kingmking AT gmail DOT com

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Hye Ran Koh

Joined group: Dec. 2006, chemistry, SNU, Korea

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Zigurts Majumdar, Ph.D.

Joined group as post-doctoral fellow: January 2006
Left group: May 2006

Currently location: National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892

Contact: zmajumdar AT gmail DOT com

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Mary C. McKinney, PhD

Joined group as graduate student: May 2001
Received PhD in biophysics: May 2006
Left group: Aug. 2006

Current: Brant Weinstein's Lab; NIH, Child Health and Human Development, Bethesda, MD (http://dir.nichd.nih.gov/lmg/uvo/WEINSLAB.html)

Contact: mckinnyc AT mail DOT nih DOT gov

  • Y. Lin, C. E. Guzman, M. C. McKinney, S. K. Nair, T. Ha, and I. K. O. Cann, "Methanosarcina Acetivorans Flap Endonuclease 1 Activity is Inhibited by a Cognate Single-Stranded DNA-Binding Protein", J. Bacteriology 188, 6153-6167 (2006)
  • J. B. Robbins+, M. C. McKinney+, C. E. Guzman, B. Srinatana, S. Fits-Gibbon, T. Ha, and I. K. O. Cann, "The Euryarchaeota: Nature's Medium for Engineering of Single-stranded DNA Binding Proteins", J. Biol. Chem. 280, 15325-15339 (2005) (+co-authorship)
  • J. B. Robbins+, M. C. Murphy+, B. A. White, R. I. Mackie, T. Ha, and I. K. O. Cann, "Functional Analysis of Multiple Single-stranded DNA-binding Proteins from Methanosarcina Acetivorans and their Effects of DNA Synthesis by PolBI", Journal of Biological Chemistry 279, 6315-6326 (2004) (+co-authorship)
  • M. C. Murphy, I. Rasnik, W. Cheng, T. M. Lohman, and T. Ha, "Probing Single Stranded DNA Conformational Flexibility using Flourescence Spectroscopy", Biophysical Journal 86, 2530-2537 (2004)
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Sean A. McKinney, PhD

Joined group as graduate student: May 2001
Received PhD in physics: May 2006
Left group: Aug. 2006

Current: Loren Looger’s Lab; Janelia Farm, HHMI (http://www.hhmi.org/research/groupleaders/looger_bio.html)

Contact: mckinneys AT janelia DOT hhmi DOT org

  • I. Rasnik, S. A. McKinney, and T. Ha, "Nonblinking and Long-lasting Single Molecule Fluorescence Imaging", Nature Methods , (2006)
  • C. Joo, S. A McKinney, M. Nakamura, I. Rasnik, S. Myong, and T. Ha, "Real Time Observation of RecA Filament Dynamics with Single Monomer Resolution", Cell 126, 515-527 (2006)
  • S. A. McKinney, C. Joo, and T. Ha, "Analysis of Single Molecule FRET Trajectories using Hidden Markov Modeling", Biophysical Journal 91, 1941-1951 (2006)
  • E. Toprak, J. Enderlein, Sh. Syed, S. McKinney, R. G. Perschek, T. Ha, Y. E. Goldman, and P. R. Selvin, "Defocused Orientation and Position Imaging (DOPI) of Myosin V", Proc. Nat. Acad. Sci. U.S.A. 103, 6495-6499 (2006)
  • C. Buranachai, S. A. McKinney, and T. Ha, "Single Molecule Nanometronome", Nano Letters 102, 18938-18943 (2006)
  • I. Rasnik, S. A. McKinney, and T. Ha, "Surfaces and Orientations: Much to FRET about?", Accounts of Chemical Research 38, 542-548 (2005) (pdf)
  • S. A. McKinney, A. Freeman, D. M. J. Lilley and T. Ha, "Observing Spontaneous Branch Migration fo Holliday Junctions One Step at a Time", Proc. Nat. Acad. Sci. U.S.A. 102, 5715-5720 (2005)
  • J. Liu, A. C. Daclias, S. A. McKinney, T. Ha, D. G. Norman, and D. M. J. Lilley, "stereospecific Effects Determine the Structure of a four-way DNA Junction", Chemistry & Biology 12, 217-288 (2005)
  • C. Joo, S. A. McKinney, D. M. J. Lilley and T. Ha, "Exploring Rare Conformational Species and Ionic Effects in DNA Holliday Junctions using Single-Molecule Spectroscopy", Journal of Molecular Biology 341, 739-751 (2004)
  • Yildiz, J. Forkey, S. A. McKinney, T. Ha, Y. Goldman, and P. R. Selvin, "Myosin V Walks Hand over Hand: Single Flourophore Imaging with 1.5 Nanometer Localization", Science 300, 2061-2065 (2003)
  • S. A. McKinney, A. C. Declais, D. M. J. Lilley, and T. Ha, "Structural Dynamics of Individual Holiday Junctions", Nature Structural Biology 10, 93-97 (2003)
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Michelle Nahas, PhD

Joined group as graduate student: May 2002
Received PhD in physics: December, 2006
Joined group as post-doctoral fellow: December 2006
Left Group: May 2007 Currently: BD Biosciences, North Carolina

Publications:

  • T. J. Wilson, M. Nahas, L. Araki, S. Harusawa, T. Ha, D. M. Lilly, "RNA folding and the origins of catalytic activity in the hairpin ribozyme." Blood Cells Mol Dis. 38 (1), 8-14 (2007).
  • M. K. Nahas, Folding and catalysis of hairpin ribozyme. Doctoral Thesis, University of Illinois (2006).
  • M. K. Nahas, T. J. Wilson, S. Hohng, K. Jarvie, D. M. J. Lilley and T. Ha, "Observation of Internal Cleavage and Ligation Reactions of a Ribozyme." Nature Structural & Molecular Biology 11, 1107-1113 (2004).
  • S. A. McKinney, E. Tan, T. J. Wilson, M. K. Nahas, A. C. Declias, R. M. Clegg, D. M. J. Lilley, and T. Ha, "Single Molecule Studies of DNA and RNA Four-way Junctions." Biochemical Society Transactions 32, 41-45 (2004).
  • E. Tan, T. J. Wilson, M. K. Nahas, R. M. Clegg, D. M. J. Lilley, and T. Ha, "A Four-way Junction Accelerates Hairpin Ribozyme Folding via a Discrete Intermediate." Proc. Natl. Acad. Sci. U.S.A. 100, 9308 (2003).
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Muneaki Nakamura

Joined group as REU undergraduate: June 2006
Left group: Aug. 2006

Current location: Stanford University, Department of Chemistry (graduate student) (http://www.stanford.edu/dept/chemistry/)

Contact: mrn AT stanford DOT edu

  • C. Joo, S. A McKinney, M. Nakamura, I. Rasnik, S. Myong, and T. Ha, "Real Time Observation of RecA Filament Dynamics with Single Monomer Resolution", Cell 126, 515-527 (2006)
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Burak Okumus, PhD

Joined group as graduate student: January 2001
Received PhD in biophysics: September 2006
Joined group as post-doctoral fellow: October 2006
Left group: May 2007

Current location: Paulsson Lab
Department of Systems Biology
Harvard Medical School
200 Longwood Ave, Alpert 536
Boston, MA 02115

Contact: burakokumus AT yahoo DOT com

Publications:

  • B. Okumus, "Exploring novel techniques for the single molecule toolkit: Vesicle encapsulation and immobilization", Ph.D. Thesis, University of Illinois (2007).
  • P. S. Shirude, B. Okumus, L. Ying, T. Ha and S. Balasubramanian, "Single Molecule Conformational Analysis of G-Quadruplex Formation in the Promoter DNA Duplex of the Proto-Oncogene C-kit", JACS, (2007) (In Print)
  • I. Cisse, B. Okumus, C. Joo, T. Ha, "Fueling protein-DNA interactions inside porous nanocontainers", PNAS, (2007) (In Print)
  • T. Yoon+, B. Okumus+, F. Zhang+, Y.K. Shin and T. Ha, "Multiple intermediates in SNARE-induced membrane fusion", PNAS 103, 19731-19736 (2006) (+co-authorship)
  • J. Y. Lee+, B. Okumus+, D. S. Kim, and T. Ha, "Extreme Conformational Diversity in Human Telomeric DNA", Proc. Nat. Acad. Sci. U.S.A. 102, 18938-18943 (2005) (+co-authorship)
  • B. Okumus, T. J. Wilson, D. M. J. Lilley, and T. Ha, "Vesicle Encapsulation Studies Reveal that Single Molecule Ribozyme Heterogeneities are Intrinsic", Biophysical Journal 87, 2798-2806 (2004)
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Ivan Rasnik, PhD

Joined group as post-doctoral fellow: December 2000
Left group: Aug. 2005

Current location: Emory University, Department of Physics (Assistant Professor) (http://www.physics.emory.edu/faculty/rasnik/)

Contact: irasnik AT physics DOT emory DOT edu

  • I. Rasnik, S. A. McKinney, and T. Ha, "Nonblinking and Long-lasting Single Molecule Fluorescence Imaging", Nature Methods , (2006)
  • C. Joo, S. A McKinney, M. Nakamura, I. Rasnik, S. Myong, and T. Ha, "Real Time Observation of RecA Filament Dynamics with Single Monomer Resolution", Cell 126, 515-527 (2006)
  • I. Rasnik, S. Myong, and T. Ha, "Unraveling Helicase Mechanism One Molecule at a Time", Nucleic Acids Research 34, 4225-4231 (2006)
  • S. Myong, I. Rasnik, C. Joo, T. M. Lohman, and T. Ha, "Repetitive Shuttling of a Motor Protein on DNA", Nature 437, 1321-1325 (2005)
  • I. Rasnik, S. A. McKinney, and T. Ha, "Surfaces and Orientations: Much to FRET about?", Accounts of Chemical Research 38, 542-548 (2005)
  • I. Rasnik, S. Myong, W. Cheng, T. M. Lohman, and T. Ha, "DNA-binding Orientation and Domain Conformation of the E. Coli Rep Helicase Monomer Bound to a Partial Duplex Junction: Single-molecule Studies of Flourescently Labeled Enzymes", Journal of Molecular Biology 336, 395-408 (2004)
  • M. C. Murphy, I. Rasnik, W. Cheng, T. M. Lohman, and T. Ha, "Probing Single Stranded DNA Conformational Flexibility using Flourescence Spectroscopy", Biophysical Journal 86, 2530-2537 (2004)
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Richard Renfrew

Left group: May. 2007 (computer technician)

Current location: Univesity of Illinois, Urbana.

Contact: renfrew AT uiuc DOT edu

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Rahul Roy, PhD

Joined group as graduate student: January 2002
Received PhD in biophysics: May 2007
Post-doctoral fellow, June - Sept 2007

Current: Xie Lab, Harvard University, Cambridge (http://bernstein.harvard.edu/)

Contact: rahulfx16 AT gmail DOT edu

Current Publications:

  • R. Roy, A. G. Kozlov, T. M. Lohman and T. Ha, "Dynamic structural rearrangments between DNA binding modes of E. coli SSB protein", Journal of Molecular Biology, 369 (5): 1244-1257 (2007)
  • R. Roy, Single molecule FRET studies of DNA binding and RNA polymerizing proteins. Ph.D. Thesis, University of Illinois (2007).
  • V. Arluison, S. Hohng, R. Roy, O. Pellegrini, P. Regnier and T. Ha, "Spectroscopic observation of RNA chaperone activities of Hfq in post-transcriptional regulation by a small non-coding RNA", Nucleic Acids Research, 35 (3): 999-1006 (2007).
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Benjamin C. Stevens, PhD

Joined group as graduate student: May 2001
Received PhD in physics: May 2006
Left group: Aug. 2006

Current: Visigen Inc., Houston, TX (http://www.visigenbio.com/)

Contact: benstevens2 AT gmail DOT com

  • S. Myong, B. Stevens, and T. Ha, "Bridging Conformational Dynamics and Function using Single-Molecule Spectroscopy", Structure 14, 633-643 (2006)
  • B. C. Stevens and T. Ha, "Discrete and Heterogeneous Rotational Dynamics of Single Membrane Probe Dyes in Gel Phase Supported Bilayers", Journal of Chemical Physics 120, 2020-2029 (2004)


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Nathan VanHoudnos

Joined group: May 2007, dept: physics Worked on: Single, Double, hadata.igb, phyhaclu Left group: September 2008

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Tae-Young Yoon, PhD

Joined group as post-doctoral fellow: Aug. 2005 Left group: Dec. 2007

  • T. Yoon+, B. Okumus+, F. Zhang+, Y.K. Shin and T. Ha, From the cover: "Multiple intermediates in SNARE-induced membrane fusion", PNAS 103, 19731-19736 (2006) (+co-authorship)

Current: http://physics.kaist.ac.kr/english/taeyoung_yoon.htm

Email: tyyoon AT kaist DOT ac DOT kr

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