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22416 CPLC Conference Bags 2014-D 3RD MIDWEST SINGLE MOLECULE WORKSHOP UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN AUGUST 4 - 5, 2014 University of Illinois – Physics Department – 320 Loomis Lab, 1110 W. Green Street – Urbana-Champaign, Illinois 61801 – 217-333-3393 CONTENTS ORGANIZERS Program – 2 Prof. Yann R. Chemla – University of Illinois Oral presentation abstracts – 5 Dr. Jaya Yodh – University of Illinois Poster list – 17 Poster presentation abstracts – 20 Management team: Participants – 45 Angala Meharry – University of Illinois Maps – 49 Sandra Patterson – University of Illinois Contact: VENUE [email protected] Alice Campbell Alumni Center http://cplc.illinois.edu/workshops/MWSMW2014 601 South Lincoln Avenue Urbana, IL 61801 http://www.uiaa.org/alumnicenter/contact.html SPONSORED BY 1 PROGRAM MONDAY, AUGUST 4, 2014 ALICE CAMPBELL ALUMNI CENTER 8:00 a.m. - 8:45 a.m. Registration & refreshments Welcome 8:45 a.m. - 9:00 a.m. Yann Chemla – University of Illinois at Urbana-Champaign Keynote lecture: Stephen Kowalczykowski – University of California, Davis 9:00 a.m. - 10:00 a.m. “Single-Molecule Visualization of Protein-DNA Complexes: Understanding the Physics and Chemistry of Biology, One Molecule at a Time” 10:00 a.m. - 10:20 a.m. Coffee break SESSION I: “Single-Molecule Interactions” Chair: Yann Chemla – University of Illinois at Urbana-Champaign Talk 1: Sanjeevi Sivasankar – Iowa State University 10:20 a.m. - 10:40 a.m. “Conformational Switching in Single Prion Proteins Promotes Oligomerization” Talk 2: Charles Schroeder – University of Illinois at Urbana-Champaign 10:40 a.m. - 11:00 a.m. “Direct Observations of TALE Protein Search Dynamics Along DNA” Talk 3: Yi Luo – The Ohio State University 11:00 a.m. - 11:20 a.m. “Nucleosomes Accelerate Transcription Factor Dissociation” Talk 4: Sujay Ray – Kent State University 11:20 a.m. - 11:40 a.m. “G-quadruplex Formation in Telomeres Enhances POT1/TPP1 Protection Against RPA Binding” Talk 5: Krishna Sigdel – University of Missouri 11:40 a.m. - 12:00 p.m. “Mechanical Insight into Lipid-protein Interactions Using Bee Venom” 12:00 p.m. - 2:30 p.m. LUNCH & POSTER SESSION I (Posters I-1 to I-27) SESSION II: “Molecular machines” Chair: Wei Cheng – University of Michigan Talk 6: Peter Cornish – University of Missouri 2:30 p.m. - 2:50 p.m. “Structured mRNA Induces the Ribosome into a Hyper-rotated State” Talk 7: Julia Widom – University of Michigan 2:50 p.m. - 3:10 p.m. “Dissecting the Functions of RNA Helicases in Splicing by Single-molecule FRET” Talk 8: Maria Spies – University of Iowa 3:10 p.m. - 3:30 p.m. “Single-molecule Studies of FeS-containing DNA Helicases: Kinetics, Conformational Dynamics and Molecular Mechanisms” 2 PROGRAM - continued MONDAY, AUGUST 4, 2014 ALICE CAMPBELL ALUMNI CENTER 3:30 p.m. - 3:50 p.m. Coffee break 3:50 p.m. - 4:10 p.m. Talk 9: Eric Tomko – Washington University in St. Louis “ATP- and NTP-dependent Promoter Opening by the Yeast RNAP II Pre-initiation Complex” 4:10 p.m. - 4:30 p.m. Talk 10: Alfonso Brenlla – Wayne State University “Mechanism of Aromatic Carcinogen Bypass by the Y-family Polymerase Dpo4” 4:30 p.m.- 6:30 p.m. POSTER SESSION II (Posters II-1 to II-25) 7:00 p.m.- 9:00 p.m. RECEPTION – BREAD COMPANY, 706 S. GOODWIN AVENUE, URBANA TUESDAY, AUGUST 5, 2014 ALICE CAMPBELL ALUMNI CENTER 8:50 a.m. - 9:00 a.m. Introduction & announcements SESSION III: “Single molecules in live cells” Chair: Maria Spies – University of Iowa 9:00 a.m. - 9:20 a.m. Talk 11: Kenneth Ritchie – Purdue University “Mobility of TonB and FepA in the Membranes of E. coli” 9:20 a.m. - 9:40 a.m. Talk 12: Wenting Li, University of Wisconsin-Madison “Single Molecule Study of RelA During the Stringent Response in Live E. coli Cells” Talk 13: Rudra Kafle, University of Michigan 9:40 a.m. - 10:00 a.m. “Dynamics of Chromosomal DNA in Escherichia coli” 10:00 a.m. - 10:20 a.m. Coffee break 10:20 a.m. - 10:40 a.m. Talk 14: Taekjip Ha – University of Illinois at Urbana-Champaign “Single Molecules and Cellular Mechanics” 10:40 a.m. - 11:00 a.m. Talk 15: Yan Mei Wang – Washington University in St. Louis “Single-molecule Investigation of Intraflagellar Transport Mechanisms” Talk 16: Qiong Yang – University of Michigan 11:00 a.m. - 11:20 a.m. “From Molecules to Development: Revealing Simple Rules of Biological Clocks” 11:20 a.m. - 11:50 a.m. Business meeting 11:50 a.m. - 12:00 p.m. Poster awards 12:00 p.m. - 1:00 p.m. Lunch 3 PROGRAM - continued TUESDAY, AUGUST 5, 2014 ALICE CAMPBELL ALUMNI CENTER SESSION IV: “New methods” Chair: Taekjip Ha – University of Illinois at Urbana-Champaign Talk 17: Wei Cheng – University of Michigan 1:00 p.m. - 1:20 p.m. “Optical Trapping and Multi-parameter Analysis of Single HIV-1 in Culture Media Reveal the Positive Cooperativity of Envelope Spikes in Mediating Viral Infection” 1:20 p.m. - 1:40 p.m. Talk 18: Richelle Teeling-Smith – The Ohio State University “Exploring Dynamics with Single-Molecule Electron Paramagnetic Resonance” Talk 19: Randall Goldsmith – University of Wisconsin-Madison 1:40 p.m. - 2:00 p.m. “What to do when the (fluorescent) lights go out: toward single molecule spectroscopy with optical microresonators” Talk 20: Margaret Rodgers – University of Wisconsin-Madison 2:00 p.m. - 2:20 p.m. “A dual-functioning genetic tag for simultaneous isolation and observation of single fluorescent complexes from whole cell extract” 2:20 p.m. - 2:40 p.m. Talk 21: Aleksei Aksimentiev – University of Illinois at Urbana-Champaign “Probing DNA-protein association through atomistic and coarse-grained simulations” Talk 22: Michael Hudoba – The Ohio State University 2:40 p.m. - 3:00 p.m. “Design of Force-Sensitive DNA Origami Components” 3:00 p.m. Closing remarks & departure 4 ORAL PRESENTATION ABSTRACTS KEYNOTE LECTURE Single-Molecule Visualization of Protein-DNA Complexes: Understanding the Physics and Chemistry of Biology, One Molecule at a Time Stephen Kowalczykowski University of California, Davis It is now possible to image individual proteins acting on single molecules of DNA. Such imaging affords unprecedented interrogation of fundamental biophysical processes. Visualization is achieved through the application of two complementary procedures. In one, a single DNA molecule is attached to a polystyrene bead, which is captured in an optical trap. The DNA, a worm-like coil, is extended either by the force of solution flow in a micro-flow cell, or by capturing the opposite DNA end in a second optical trap. In the second procedure, DNA is attached by one end to a glass surface. The coiled DNA is elongated either by continuous solution flow or by subsequently tethering the opposite end to the surface. Proteins and DNA are visualized via fluorescent reporters. Individual molecules are imaged using either epifluorescence microscopy or total internal reflection fluorescence (TIRF) microscopy. Molecules are introduced and supramolecular complexes are built, one component at a time, using microfluidic flowcells. Using these approaches, we have watched proteins functioning in the repair, replication, and manipulation of DNA. We have imaged unwinding of DNA by helicases, translocation along DNA by motor proteins, self-assembly of protein filaments on DNA as well as regulation of nucleation and growth, the search for DNA sequence homology protein-DNA filaments, replication of DNA, and nucleosome structure and it’s remodeling. I will summarize how these experiments were done, what we’ve learned, and prospects for the future. 5 MONDAY AUGUST 4, 2014 SESSION I: SINGLE-MOLECULE INTERACTIONS Talk 1: Conformational Switching in Single Prion Proteins Promotes Oligomerization Sanjeevi Sivasankar Iowa State University Transmissible spongiform encephalopathies which include neurodegenerative diseases like Creutzfeldt–Jakob disease, bovine spongiform encephalopathy, chronic wasting disease and scrapie, are characterized by the misfolding and oligomerization of prion proteins into protease resistant neurotoxic aggregates. However, the molecular mechanisms of prion misfolding and aggregation are unclear. Here we report, at the single molecule level, the role of the structured and disordered regions of prion proteins and different divalent ion co-factors in their protease resistance and oligomerization. Using a single molecule fluorescence based protease resistance assay, we demonstrate that prion monomers misfold to a protease resistant conformation before oligomer assembly; the intrinsically disordered N-terminal region and Cu2+ ions are obligatory for this conformational switching. Using single molecule force measurements with an Atomic Force Microscope (AFM) we show that the protease resistant conformation has a 900-fold higher association constant compared to the native conformation. The high binding affinity of protease resistant prions indicates that they serve as monomeric seeds for the subsequent formation of neurotoxic aggregates. Talk 2: Direct Observation of TALE Protein Search Dynamics Along DNA Charles M. Schroeder University of Illinois at Urbana-Champaign In this talk, we discuss the direct observation of transcription activator-like effector (TALE) protein dynamics along DNA templates using single molecule techniques. TALE proteins are robust, programmable DNA-binding proteins that can be fused to a nuclease domain to generate the TALEN system, a leading technology in the field of genetic engineering. In recent years, powerful methods for gene editing have been developed, including zinc finger nucleases, the CRISPR/Cas9 system, and TALENs. Despite great promise for treating human disease, however, we still lack a complete understanding of the mechanisms governing TALE search dynamics and the role of off-target binding events that threaten to inhibit clinical implementation. From this view, our work aims to develop a molecular-level understanding of TALE binding and target sequence search on DNA, which will facilitate the design of new and efficient TALEN systems.
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