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Conference Program
 
Nucleic Acids
June 3-8, 2007
Salve Regina University
Newport, RI

Nucleic acids are the core of life. The Gordon Research Conference on Nucleic Acids has played a key historical role in the development of molecular biology. In 2007, we continue the long tradition of mixing speakers in areas of DNA and RNA biology, chemistry and biophysics. These crossroads nurture innovation, creativity and discovery. Keynote Lectures presented by Jacqueline Barton, speaking on DNA charge transport, and Ignacio Tinoco, speaking on RNA structural investigations, will open the meeting on Sunday evening. A total of 8 sessions will be held over the next 4 days, including many of the world’s leading scientists in nucleic acids research. Topics will include transcription initiation and activation, recognition and processing of DNA damage, DNA dynamics and the nucleosome, translation and its regulation, splicing, RNA interference, ribozymes and riboswitches, and a novel session on emerging technologies leading to synthetic biology. While the sessions represent a broad survey of the nucleic acids field, each dives into considerable depth. An overview of the questions defining the frontier of each topic will be provided by the session chair. Sessions will occur in the morning and evening with afternoons free for poster sessions and discussion among participants. The Nucleic Acids Gordon Conference has central importance in disseminating new information to the broader community of nucleic acid biologists and chemists and is an important vehicle to engage students and young researchers into the community.


Contributors
We are grateful to the following organizations for financial support:

American Chemical Society Publications
Dharmacon, Inc.
Glen Research Corporation
Oxford University Press
RNA Society
Signal Pharmaceutical
Trilink Biotechnologies, Inc.
US Biochemicals
Carl Storm Underrepresented Minority Fellowships Program
Alnylam Pharmaceuticals
Cell Press
Molecular BioSystems (Royal Society of Chemistry)

SUNDAY
2:00 pm - 11:00 pmArrival and Check-in
6:00 pmDinner
7:30 pm - 7:40 pmWelcome / Introductory Comments by GRC Site Staff
7:40 pm - 9:30 pm KEYNOTE SPEAKERS: FRONTIERS OF DNA & RNA RESEARCH
Discussion Leaders: Cynthia Burrows (University of Utah) and Jody Puglisi (Stanford University)
7:40 pm - 8:25 pmJacqueline Barton (Caltech)
"DNA-mediated charge transport for long range signaling"
8:25 pm - 8:35 pmDiscussion
8:35 pm - 9:20 pmIgnacio Tinoco (UC Berkeley)
"Codon-by-codon translation of messenger RNA"
9:20 pm - 9:30 pmDiscussion
MONDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pm MOLECULAR RECOGNITION AND PROCESSING OF DNA DAMAGE
9:00 am - 9:05 amDiscussion Leader: Susan Wallace (University of Vermont)
9:05 am - 9:30 amOrlando Schärer (SUNY Stony Brook)
"Mechanisms of damage recognition and dual incision in human nucleotide excision repair"
9:30 am - 9:35 amDiscussion
9:35 am - 10:00 amJim Stivers (Johns Hopkins University)
"Enzymatic detection of damaged bases in DNA"
10:00 am - 10:05 amDiscussion
10:05 amCoffee Break / Group Photo
10:35 am - 11:00 amSteve West (Cancer Center UK)
"Aprataxin: a proof-reader for abortive DNA ligation events"
11:00 am - 11:05 amDiscussion
11:05 am - 11:30 amSusan Wallace (University of Vermont)
"Replicative polymerases meet oxidative DNA damages"
11:30 am - 11:35 amDiscussion
11:35 am - 12:00 pmTom Kunkel (NIEHS)
"Evidence that DNA polymerase epsilon participates in leading strand DNA replication"
12:00 pm - 12:05 pmDiscussion
12:05 pm - 12:25 pmZucai Suo (Ohio State University)
"Mechanism of DNA lesion bypass catalyzed by a Y-family DNA polymerase"
12:25 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session I: White
6:00 pmDinner
7:30 pm - 9:30 pm NUCLEOSOMES AND DNA DYNAMICS
Discussion Leader: Leemor Joshua-Tor (Cold Spring Harbor)
7:30 pm - 7:55 pmJonathan Widom (Northwestern University)
"The genomic code for nucleosome positioning"
7:55 pm - 8:00 pmDiscussion
8:00 pm - 8:25 pmGeeta Narlikar (UC, San Francisco)
"Mechanisms of ATP-dependent chromatin remodeling enzymes"
8:25 pm - 8:30 pmDiscussion
8:30 pm - 8:55 pmSteve Kowalczykowski (UC, Davis)
"Single-molecule visualization of translocation by DNA-remodeling motor proteins"
8:55 pm - 9:00 pmDiscussion
9:00 pm - 9:25 pmLeemor Joshua-Tor (Cold Spring Harbor)
"DNA translocation in a replicative hexameric helicase"
9:25 pm - 9:30 pmDiscussion
TUESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pm RIBOZYMES AND RIBOSWITCHES: STRUCTURAL BASIS FOR FUNCTION
9:00 am - 9:05 amDiscussion Leader: Adrian Ferre-d’Amare (Hutchinson Cancer Center)
9:05 am - 9:30 amDavid Lilley (University of Dundee)
"Structure and mechanism of the VS ribozyme"
9:30 am - 9:35 amDiscussion
9:35 am - 9:45 amDinggeng Chai (University of Calgary)
"3D Model of a group II intron and its interaction with the intron-encoded reverse transcriptase"
9:45 am - 9:50 amDiscussion
9:50 am - 10:15 amAdrian Ferre-d’Amare (Hutchinson Cancer Center)
"The glmS ribozyme-riboswitch: structural analysis of a coenzyme-dependent catalytic RNA"
10:15 am - 10:20 amDiscussion
10:20 amCoffee Break
10:45 am - 10:55 amMaumita Mandal (UC, Berkeley)
"Dynamics of conformational switching in single molecules of guanine-responsive riboswitch"
10:55 am - 11:00 amDiscussion
11:00 am - 11:25 am Dan Herschlag (Stanford University)
"Demystifying RNA folding"
11:25 am - 11:30 amDiscussion
11:30 am - 11:55 am Jennifer Doudna (UC, Berkeley)
"Control of mRNA recruitment to human ribosomes"
11:55 am - 12:00 pmDiscussion
12:00 pm - 12:10 pmMarcia Levitus (Arizona State Univ.)
"Measuring conformational dynamics in nucleic acids: A new FCS-FRET approach"
12:10 pm - 12:15 pmDiscussion
12:15 pm - 12:25 pmPeter Qin (University of Southern California)
"Mapping global structures of nucleic acids using site-directed spin labeling"
12:25 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session I: White
6:00 pmDinner
7:30 pm - 9:30 pm EMERGING TECHNOLOGIES: SYNTHETIC BIOLOGY
Discussion Leader: Floyd Romesberg (Scripps)
7:30 pm - 7:55 pmFloyd Romesberg (Scripps Research Institute)
"Efforts to expand the genetic alphabet"
7:55 pm - 8:00 pmDiscussion
8:00 pm - 8:25 pmChristina Smolke (Caltech)
"Engineering RNA devices as general tools in programming cellular function"
8:25 pm - 8:30 pmDiscussion
8:30 pm - 8:55 pmAndreas Marx (University of Konstanz)
"Chemical Biology of DNA Polymerases"
8:55 pm - 9:00 pmDiscussion
9:00 pm - 9:25 pmMilan Stojanovic (Columbia University)
"DNA computing and robotics: Science, fun, and practical applications"
9:25 pm - 9:30 pmDiscussion
WEDNESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pm THE RIBOSOME
9:00 am - 9:05 amDiscussion Leader: Jamie Cate (UC, Berkeley)
9:05 am - 9:30 amJamie Cate (UC, Berkeley)
"Structural basis for antibiotic inhibition of the bacterial ribosome"
9:30 am - 9:35 amDiscussion
9:35 am - 10:00 amVenki Ramakrishnan (Cambridge University)
"Structures of functional complexes of the 70S ribosome"
10:00 am - 10:05 amDiscussion
10:05 am - 10:30 amJamie Williamson (Scripps)
"Assembly of the 30S ribosome in vitro and in cells"
10:30 am - 10:35 amDiscussion
10:35 amCoffee Break
11:00 am - 11:25 amScott Strobel (Yale University)
"Enzymology of the peptidyl transferase reaction"
11:25 am - 11:30 amDiscussion
11:30 am - 11:55 amWolfgang Wintermeyer (University of Witten-Herdecke)
"Signal recognition particle recruitment and membrane targeting of translating ribosomes in E. coli"
11:55 am - 12:00 pmDiscussion
12:00 pm - 12:25 pmMarty Fedor (Scripps Research Institute)
"Architectural contributions to catalysis by the hairpin ribozyme"
12:25 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session II: Gray
6:00 pmDinner
7:00 pm - 7:30 pmBusiness Meeting
(Nominations for the next Vice Chair; Fill out Conference Evaluation Forms; Discuss future Site & Scheduling preferences; Election of the next Vice Chair)
7:30 pm - 9:30 pm RNA SPLICING MECHANISMS
Discussion Leader: Christine Guthrie (UC, San Francisco)
7:30 pm - 7:55 pmChristine Guthrie (UC, San Francisco)
"Catalytic activation of the spliceosome: Regulation of the Brr2 helicase"
7:55 pm - 8:00 pmDiscussion
8:00 pm - 8:25 pmKristen Lynch (UT Southwestern)
"Mechanisms of signal-induced splicing regulation"
8:25 pm - 8:30 pmDiscussion
8:30 pm - 8:55 pmMelissa Moore (Brandeis University)
"Pre-mRNA splicing and RNA quality control"
8:55 pm - 9:00 pmDiscussion
9:00 pm - 9:25 pmCindy Will (Max Planck, Göttingen)
"Structural dynamics of the spliceosome"
9:25 pm - 9:30 pmDiscussion
THURSDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pm TRANSCRIPTION INITIATION AND REGULATION
9:00 am - 9:05 amDiscussion Leader: Anna Mapp (University of Michigan)
9:05 am - 9:30 amAnna Mapp (University of Michigan)
"Chemical control of gene activation"
9:30 am - 9:35 amDiscussion
9:35 am - 10:00 amTom Kodadek (UT Southwestern)
"Understanding the roles of ubiquitin-proteasome pathway proteins In transcription: Chemical and biological approaches"
10:00 am - 10:05 amDiscussion
10:05 am - 10:30 amRichard Ebright (Rutgers University)
"Single-molecule analysis of transcription"
10:30 am - 10:35 amDiscussion
10:35 amCoffee Break
11:05 am - 11:30 amGuillermo Calero (Stanford University)
"Structural studies of RNA polymerase II complexes"
11:30 am - 11:35 amDiscussion
11:35 am - 11:45 amBogdan Olenyuk (University of Arizona)
"Regulation of gene expression through disruption of transcription factor-coactivator interactions"
11:45 am - 11:50 amDiscussion
11:50 am - 12:00 pmPeter Carr (MIT)
"Whole genome engineering and the construction of new genetic codes"
12:00 pm - 12:05 pmDiscussion
12:05 pm - 12:15 pmKatherine Berry (UC, Berkeley)
"Investigating mRNA recruitment by the human ribosome using fluorescence spectroscopy"
12:15 pm - 12:20 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session II: Gray
6:00 pmDinner
7:30 pm - 9:30 pm RNA INTERFERENCE: PATHWAYS TO GENE FUNCTION
7:30 pm - 7:35 pmDiscussion Leader: Peter Sarnow (Stanford University)
7:35 pm - 8:00 pmPeter Sarnow (Stanford University)
"Subversion of a liver-specific microRNA by hepatitis C virus"
8:00 pm - 8:05 pmDiscussion
8:05 pm - 8:30 pmDinshaw Patel (Sloan-Kettering)
"Structural biology of RNA silencing"
8:30 pm - 8:35 pmDiscussion
8:35 pm - 9:00 pmTim Nilsen (Case Western Reserve)
"Mechanisms of microRNA-mediated gene regulation in animal cells"
9:00 pm - 9:05 pmDiscussion
9:05 pm - 9:20 pmFeng Guo (UCLA)
"Heme is involved in microRNA processing"
9:20 pm - 9:25 pmDiscussion
FRIDAY
7:30 am - 8:30 amBreakfast
9:00 amDeparture

 
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