THEORETICAL ASPECTS OF DNA SUPERCOILING

Project Details

Description

The three-dimensional spatial arrangements of double helical DNA deformed
along various supercoiled trajectories will be generated mathematically and
then analyzed 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 long-range effects associated with close contacts of
sequentially distant chain residues. Long-range ionic effects will be
examined using a newly modified Coulombia potential that reproduces the
electrostatic interactions between charges on the surface of a dielectric
cylinder immersed in salt water. The stabilities of various
three-dimensional forms (e.g., toroidal, interwound, circular, etc.) will
be compared and the detailed conformational variations of the standard
double helical secondary structure examined. 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.
Various secondary structural forms (e.g., A-, B-, Z-DNA) will be deformed
along the superhelical trajectories in an attempt to understand the
supercoil-induced conformational transitions of the DNA duplex.
StatusFinished
Effective start/end date8/1/853/31/20

Funding

  • National Institutes of Health
  • National Institutes of Health: $290,332.00
  • National Institutes of Health
  • National Institutes of Health
  • National Institutes of Health: $253,392.00
  • National Institutes of Health
  • National Institutes of Health: $292,323.00
  • National Institutes of Health: $194,375.00
  • National Institutes of Health: $223,312.00
  • National Institutes of Health: $153,792.00
  • National Institutes of Health: $282,536.00
  • National Institutes of Health: $327,145.00
  • National Institutes of Health: $172,551.00
  • National Institutes of Health: $223,507.00
  • National Institutes of Health
  • National Institutes of Health: $223,373.00
  • National Institutes of Health
  • National Institutes of Health
  • National Institutes of Health
  • National Institutes of Health: $183,451.00
  • National Institutes of Health: $328,204.00
  • National Institutes of Health: $329,297.00
  • National Institutes of Health
  • National Institutes of Health: $225,197.00
  • National Institutes of Health: $194,375.00
  • National Institutes of Health: $194,375.00
  • National Institutes of Health: $293,258.00
  • National Institutes of Health: $191,118.00
  • National Institutes of Health: $131,492.00
  • National Institutes of Health: $188,376.00
  • National Institutes of Health
  • National Institutes of Health: $330,421.00
  • National Institutes of Health

ASJC

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)

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