Campuses:

DNA sequences

Wednesday, September 19, 2007 - 4:15pm - 4:30pm
Jörg Langowski (Deutsches Krebsforschungszentrum (Cancer Research)(DKFZ))
The higher order structure of chromatin depends crucially on the local geometry of the DNA on the nucleosome. Fluorescence resonance energy transfer (FRET) is a very convenient method to measure intramolecular distances in such large biomolecules and thereby obtain information on the DNA geometry. Varying label positions, DNA fragment length, histone modifications and buffer conditions gives valuable insight into the structure of mono- and trinucleosomes.
Wednesday, September 19, 2007 - 3:45pm - 4:00pm
Nathan Baker (Washington University School of Medicine)
Continuum electrostatics methods have become increasingly popular due to their ability to provide approximate descriptions of solvation energies and forces without the expensive sampling required by all-atom solvent models. In particular, the Poisson–Boltzmann equation (PBE) provides electrostatic potentials, solvation energies, and forces by modeling the solvent as a featureless dielectric material and the mobile ions as a continuous distribution of charge.
Saturday, September 15, 2007 - 3:00pm - 4:00pm
David Swigon (University of Pittsburgh)

  • Worm-like chain model, ring closure, J factor

  • Statistical mechanics of DNA supercoiling

  • Monte Carlo simulations of DNA

  • DNA stretching

  • Extraction of sequence-dependent parameters from statistical
    ensembles

  • DNA denaturation, effect of topological constraints, role in
    transcription regulation

  • Probability of knotting and catenation, removal of
    knots/catenanes



DNA dynamics

Sunday, September 16, 2007 - 9:15am - 10:15am
Richard Lavery (Centre National de la Recherche Scientifique (CNRS))
DNA can easily be deformed by external factors including molecular interactions and applied forces. We have
used molecular modeling and simulation to investigate the structural and energetic nature of these deformations
both in generic terms and, more finely, to understand their sequence dependence and therefore to decode their
role in recognition processes.
Thursday, September 20, 2007 - 3:00pm - 4:00pm
James Maher (Mayo Clinic)
Duplex DNA, the genetic material in living cells, is an unusually inflexible biopolymer. The persistence length of duplex DNA corresponds to 150 base pairs under physiological conditions. Surprisingly, the physical origin of this DNA stiffness is unknown. In particular, the contribution of the high negative charge density of DNA to its stiffness remains both uncertain and controversial. The intrinsic inflexibility of DNA is managed in living cells by the formation of nucleoprotein complexes in which DNA is often dramatically bent, kinked and looped.
Thursday, September 20, 2007 - 1:30pm - 2:30pm
Jason Kahn (University of Maryland)
DNA looping allows protein transcription factors to act at a distance along DNA. Looping is also a test bed for theories on DNA and protein structure and flexibility. However, most natural DNA loops are not stable enough for structural studies. We have designed and constructed bent DNA molecules that form hyperstable DNA loops anchored by the Lac repressor.
Thursday, September 20, 2007 - 9:00am - 10:00am
Andrew Travers (MRC Laboratory of Molecular Biology)
In both bacteria and eukaryotes, maintaining DNA compaction is
a sine qua non of chromatin function. At the same time
accessibility to transcribing, replicating and recombining
enzymes must be maintained. I will argue that these twin
requirements can be viewed in the context of the overall
topology of, for bacteria, the DNA itself, and of, for
eukaryotes, the 30 nm chromatin fibre. In particular, the
plectonemic form of supercoiled ropes, either DNA or 30 nm
fibres, must, in principle, contain distinguishable structures
Tuesday, September 18, 2007 - 1:30pm - 2:30pm
John Marko (Northwestern University)
In experiments where DNA is pulled at constant force and twisted, a mixed
state of extended twisted DNA and plectonemically supercoiled DNA is
easily obtained. I will review the thermodynamics of this state
coexistence phenomenon. A particularly elegant use of
plectoneme-extended DNA coexistence is as a source of constant torque for
single-DNA experiments. I will discuss the estimation of torques and free
energies in such experiments, and I will provide some useful closed-form
Tuesday, September 18, 2007 - 10:30am - 11:30am
Ariel Prunell (Institut Jacques Monod)
Single chromatin fibers were reconstituted in vitro
by salt dialysis from purified histone octamers and 2×18 tandem
repeats of the 5S DNA positioning sequence. The fibers were
flanked by naked ∼600 bp DNA spacers and ∼500 bp DNA stickers
modified with digoxigenin and biotin destined to be linked
respectively to the coated bottom of the flow cell and to the
paramagnetic bead. This construction is then placed under the
rotating magnet of a magnetic tweezers set-up to exert a torque
and a pulling force on the fiber.
Sunday, September 16, 2007 - 4:45pm - 5:00pm
Irwin Tobias (Rutgers, The State University Of New Jersey )
DNA twist step-parameters are in common use in the
community of structural biologists. If, for a molecule with a
closed axial curve, the writhing number, a measure of the
chiral distortion of the axial curve of the molecule from
planarity, is added to the sum over all steps of such twists,
the result has no particular significance. This is in marked
contrast to the properties of the value obtained . the
topological invariant, an integer called the linking number -
when the same writhe is added to the total twist we obtain by

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