THEORETICFAL ASPECTS OF DNA SUPERCOILING

Project Details

Description

The three-dimensional spatial arrangements of double helical DNA
deformed along various supercoiled trajectories will be generated
by direct computer modeling and Monte Carlo simulations and then
analyzed at the detailed molecular level. The extent to which the
regular linear duplex can be forced to bend and twist will then be
monitored by semiempirical potential energy calculations. Bond
lengths, valence angles, and torsion angles will be kept within
normally prescribed limits, and steric and electrostatic
interactions of nonbonded atoms and groups will be estimated with
standard functions. Of particular interest will be the effects of
base sequence on overall conformation and the long-range effects
associated with close contacts of sequentially distant chain
residues. Long-range ionic effects will be included to access the
stabilities of various three-dimensional forms (e.g., toroidal,
interwound, circular, etc.). The relative contributions of bending
and twisting to the total energy will be computed directly and
compared with elastic models of supercoiling. The ability of the
potential energy functions to account for macroscopic properties
of the supercoils will be tested using established statistical
mechanical procedures. The major objective of the work is to understand and visualize the
structure and properties of supercoiled DNA. The immediate goal
is to describe average chain structure and properties in terms of
realistic molecular models. The studies may clarify the role of
the primary base sequence and the polyelectrolyte sugar-phosphate
backbone on the folding of the chain. A more long-range goal is
to uncover structural details of supercoil-induced transitions of
DNA, including the possible formation of Z-DNA, cruciforms, and
local melted regions.
StatusFinished
Effective start/end date12/31/893/31/21

Funding

  • National Institute of General Medical Sciences: $194,375.00
  • National Institute of General Medical Sciences: $194,375.00
  • National Institute of General Medical Sciences
  • National Institute of General Medical Sciences
  • National Institute of General Medical Sciences: $223,373.00
  • National Institute of General Medical Sciences
  • National Institute of General Medical Sciences
  • National Institute of General Medical Sciences: $223,312.00
  • National Institute of General Medical Sciences
  • National Institute of General Medical Sciences: $329,297.00
  • National Institute of General Medical Sciences
  • National Institute of General Medical Sciences
  • National Institute of General Medical Sciences: $225,197.00
  • National Institute of General Medical Sciences: $292,323.00
  • National Institute of General Medical Sciences
  • National Institute of General Medical Sciences: $188,376.00
  • National Institute of General Medical Sciences: $282,536.00
  • National Institute of General Medical Sciences
  • National Institute of General Medical Sciences: $191,118.00
  • National Institute of General Medical Sciences
  • National Institute of General Medical Sciences: $327,145.00
  • National Institute of General Medical Sciences
  • National Institute of General Medical Sciences: $223,507.00
  • National Institute of General Medical Sciences
  • National Institute of General Medical Sciences
  • National Institute of General Medical Sciences: $253,392.00
  • National Institute of General Medical Sciences
  • National Institute of General Medical Sciences: $194,375.00
  • National Institute of General Medical Sciences: $330,421.00
  • National Institute of General Medical Sciences: $328,204.00
  • National Institute of General Medical Sciences: $293,258.00
  • National Institute of General Medical Sciences: $290,332.00

ASJC

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Computational Mathematics
  • Physics and Astronomy(all)
  • Genetics
  • Polymers and Plastics
  • Molecular Biology
  • Biochemistry
  • Computer Graphics and Computer-Aided Design

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