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73rd Harden Conference - Machines on genes II - The central dogma at the interface of biology, chemistry and physics

19—23 August 2012

St Anne's College, Oxford, UK



Meeting background

The replication, maintenance and transcription of the genome require an array of protein machines including polymerases, helicases, translocases, nucleases, recombinases and topoisomerases, often functioning as components of multi-protein complexes. Machines on Genes II will bring together scientists with an interest in multi- and inter-disciplinary approaches for unravelling the anatomy, architecture and mechanisms of these remarkable molecular machines. The conference will cover topics in DNA replication, recombination, repair and transcription and will showcase the latest work of world leaders in the fields of structural biology, chemical biology and novel biophysical methods including single-molecule detection.

Organizers:
Achillefs Kapanidis (University of Oxford, United Kingdom)
Mark Dillingham (University of Bristol, United Kingdom)
Marshall Stark (University of Glasgow, United Kingdom)
Richard Bowater (University of East Anglia, United Kingdom)
Sunday 19 August 2012
12:00 - 14:00 Registration with lunch

Session 1

 

Chair:
Mark Dillingham (University of Bristol, United Kingdom)
Sunday 19 August 2012
14:00 - 14:10
Opening remarks
The organizers
14:10 - 14:50
In vivo single-molecule biochemistry of bacterial chromosome replication and segregation
David Sherratt (University of Oxford, United Kingdom)
14:50 - 15:10
Unpair to repair or degrade-specific phosphate diester hydrolysis at DNA and RNA duplex ends
Selected oral communication - Jane Grasby (University of Sheffield, United Kingdom)
15:10 - 15:30
Single-molecule characterization of Fen1-PCNA complexes acting on flap DNA substrates
Selected oral communication - Carlos Penedo (University of St Andrews, United Kingdom)
15:30 - 16:00 Coffee/tea break

16:00 - 16:40
Single-molecule studies of DNA replication
Antoine van Oijen (Groningen University, The Netherlands)
16:40 - 17:20
Structure and Mechanism of CRISPR interference machines for antiviral defence
Malcolm White (St Andrews University, United Kingdom)
17:20 - 17:40
Direct observation of stalled fork restart and lesion bypass via fork regression in T4 replication system
Selected oral communication - Maria Manosas (University of Barcelona, Spain)
17:40 - 18:30 Drinks reception with poster viewing

18:30 - 20:00 Dinner

Session 2

 

Chair:
Jane Grasby (University of Sheffield, United Kingdom)
Sunday 19 August 2012
20:00 - 21:00
The 1st RSC Nucleic Acids Group Michael J. Gait Lecture sponsored by Idera Pharmaceuticals
Single molecule visualization of protein-DNA complexes: watching machines at work
Steve Kowalczykowski (University of California, Davis, U.S.A.)

Session 3

 

Chair:
Marshall Stark (University of Glasgow, United Kingdom)
Monday 20 August 2012
09:00 - 09:40
Bottom-up reconstruction of DNA repair pathways at single-molecule resolution
Terence Strick (Institut Jacques Monod, France)
09:40 - 10:00
The xeroderma pigmentosum group E mutation (K244E) in DDB2 of a UV-damaged DNA-binding protein (UV-DDB) results in DNA sliding and loss of damage binding specificity
Selected oral communication - Bennett Van Houten (University of Pittsburgh Cancer Institute, U.S.A.)
10:00 - 10:20
Novel insights into Nucleotide Excision DNA repair revealed by single molecule imaging on DNA tightropes
Selected oral communication - Neil Kad (University of Essex, United Kingdom)
10:20 - 10:40
Initial steps of bacterial MMR studied by combined crosslinking/fluorescence analysis
Selected oral communication - Peter Friedhoff (Justus-Liebig Universitat, Germany)
10:40 - 11:10 Coffee/tea break

11:10 - 11:50
DNA integration and excision by the site-specific serine recombinase, phiC31 integrase
Maggie Smith (University of Aberdeen, United Kingdom)
11:50 - 12:10
Topological analysis of site-specific recombination by ΦC31 integrase
Selected oral communication - Femi Olorunniji (University of Glasgow, United Kingdom)
12:10 - 12:30
Big bang versus a steady state: the emergent properties of a DNA-looping reaction control the trajectory of a genomic invasion by a mariner transposon
Selected oral communication - Ronald Chalmers (University of Nottingham, United Kingdom)
12:30 - 14:00 Lunch

Session 4

 

Chair:
Steve Kowalczykowski (University of California, Davis, U.S.A.)
Monday 20 August 2012
14:00 - 14:40
Quantifying how DNA stretches, melts and changes twist under tension
Gijs Wuite (VU University Amsterdam, The Netherlands)
14:40 - 15:00
Local and global structure of branched DNA revealed using high-resolution single-molecule FRET
Selected oral communication - Steven Magennis (University of Manchester, United Kingdom)
15:00 - 15:30 Coffee/tea break

15:30 - 16:10
DNA- and nucleotide-driven conformational changes in gyrase coordinate DNA binding, strand passage and supercoiling with the nucleotide cycle
Dagmar Klostermeier (University of Muenster, Germany)
16:10 - 16:30
Tracking BRCA2-GFP entities in living mammalian cells using oblique-illumination laser excitation
Selected oral communication - Marcel Reuter (Erasmus University Medical Center, The Netherlands)
16:30 - 16:50
Visualization and quantification of RAD51-filament formation at single-monomer resolution
Selected Oral Communication - Andrea Candelli (VU University Amsterdam, The Netherlands)
16:50 - 19:00 Poster session (odd numbers)

19:00 - 20:30 Dinner

Session 5

 

Chair:
Anna Marie Pyle (Yale University, U.S.A.)
Tuesday 21 August 2012
09:00 - 09:40
Structure and mechanism of the INO80 chromatin remodelling complex
Dale Wigley (The Institute of Cancer Research, United Kingdom)
09:40 - 10:20
Structural and functional analysis of RIG-I, a vertebrate nanomachine for detecting and attacking RNA viruses
Anna Marie Pyle (Yale University, U.S.A.)
10:20 - 10:40
A two step RNA packaging mechanism of ssRNA virus studied by single molecule fluorescence correlation spectroscopy
Selected oral communication - Oleksandr Borodavka (University of Leeds, United Kingdom)
10:40 - 11:10 Coffee/tea break

11:10 - 11:50
Single-molecule study of helicases and polymerases using a hairpin substrate
Vincent Croquette (Ecole Normale Supérieure, France)
11:50 - 12:10
Nucleotide-dependent switching between active and passive unwinding in a nidovirus superfamily 1 RNA helicase
Selected oral communication - Aartjan te Velthuis (University of Oxford, United Kingdom)
12:10 - 12:30
The role of ATP hydrolysis in the reaction mechanism of Type III Restriction Endonucleases
Selected oral communication - Julia Toth (University of Bristol, United Kingdom)
12:30 - 14:00 Lunch

Session 6

 

Chair:
Achillefs Kapanidis (University of Oxford, United Kingdom)
Tuesday 21 August 2012
14:00 - 14:40
Antagonistic activities of RecQ helicases during repetitive DNA unwinding
Ralf Seidel (BIOTEC, TU-Dresden, Germany)
14:40 - 15:00
Modulation of the translocation properties of a model helicase by DNA sequence content within the track
Selected oral communication - Fernando Moreno-Herrero (National Center of Biotechnology, CNB-CSIC, Spain)
15:00 - 15:30 Coffee/tea break

15:30 - 16:10
To what extent are the central dogma enzymes machines?
Taekjip Ha (University of Illinois, U.S.A.)
16:10 - 16:30
Structure of a Type I restriction-modification enzyme bound to its target DNA sequence
Selected oral communication - Saikrishnan Kayarat (Indian Institute of Science Education and Research, India)
16:30 - 16:50
A partially-closed DNA polymerase conformation provides an important checkpoint for nucleotide insertion fidelity
Selected oral communication - Johannes Hohlbein (University of Oxford, United Kingdom)
16:50 - 19:00 Poster session (even numbers)

19:00 - 20:30 Dinner

Session 7

 

Chair:
Richard Ebright (Rutgers, U.S.A.)
Wednesday 22 August 2012
09:00 - 09:40
New approaches to single-molecule biophysics
Nynke Dekker (Technical University Delft, The Netherlands)
09:40 - 10:20
Single molecule studies of eukaryotic transcription
Jens Michaelis (Ludwig-Maximilians-Universität München, Germany)
10:20 - 10:40
Single-molecule DNA repair in live bacteria
Selected oral communication - Stephan Uphoff (University of Oxford, United Kingdom)
10:40 - 11:10 Coffee/tea break

11:10 - 11:50
Mechanism of transcriptional activation via AAA ATPases
Xiaodong Zhang (Imperial College London, United Kingdom)
11:50 - 12:10
Investigations of the mechanisms by which mammalian pre-mRNA splice sites are selected and regulated using single molecule and chemical biology approaches
Selected oral communication - Ian Eperon (University of Leicester, United Kingdom)
12:10 - 12:30
Mapping key events in the lifecycle of the transcriptome at nucleotide resolution
Selected oral communication - David Romero A (Faculty of Biological Sciences, United Kingdom)
12:30 - 14:00 Lunch

Session 8

 

Chair:
Maggie Smith (University of Aberdeen, United Kingdom)
Wednesday 22 August 2012
14:00 - 14:40
Structural basis of transcription initiation
Richard Ebright (Rutgers, U.S.A.)
14:40 - 15:00
Control of the phage shock protein (Psp) stress response in E. coli: quantitative live cell imaging at single molecule sensitivity of the PspF and PspA proteins
Selected oral communication - Liming Ying (Imperial College London, United Kingdom)
15:00 - 15:30 Coffee/tea break

15:30 - 16:10
ATP-induced helicase slippage reveals highly coordinated subunits
Michelle Wang (Howard Hughes Medical Institute Cornell University, U.S.A.)
16:10 - 16:30
Architecture of full-length nuclear receptor heterodimer complexes: an integrative structural biology study
Selected oral communication - Natacha Rochel (IGBMC, France)
16:30 - 19:00 Free time with optional punting trip

19:00 - 20:30 Conference dinner followed by a pub crawl

Session 9

 

Chair:
Richard Bowater (University of East Anglia, United Kingdom)
Thursday 23 August 2012
09:00 - 09:40
Molecular machines of DNA break repair: what they look like and how they work
Claire Wyman (Erasmus MC, The Netherlands)
09:40 - 10:20
Analysing the relative importance of different replicative barriers inside cells
Pete McGlynn (University of Aberdeen, United Kingdom)
10:20 - 10:40
New insight on cooperative DNA binding mechanism by the O6-alkyl-guanine DNA alkyl transferase from single molecule imaging
Selected oral communication - Ingrid Tessmer (Rudolf-Virchow-Center, Germany)
10:40 - 11:10 Coffee/tea break

11:10 - 11:50
Early Career Research Award
Structural biology of the type IV secretion system
Vidya Chandran (Indian Institute of Science, India)
11:50 - 12:00 Closing remarks and close of conference