NUCLEIC ACID ELECTROSTATIC PROPERTIES FROM CRYSTALS
Project Number7R01GM039513-10
Contact PI/Project LeaderCRAVEN, BRYAN M
Awardee OrganizationINDIANA UNIVERSITY OF PENNSYLVANIA
Description
Abstract Text
Electrostatic properties of the nucleic acids will be determined from X-
ray and neutron single crystal diffraction studies of simple nucleic acid
components ranging up to minihelical dinucleotide structures. Emphasis
will be on mapping the electrostatic potential, either within the crystal
unit cell, or for molecules extracted from the crystal lattice. We have
shown that the electrostatic potential can he experimentally determined
more easily than other molecular properties such as the charge density or
the electric field. With a simple structure model including only two
atomic charge parameters in addition to the atomic parameters used in
conventional crystal structure determinations, we expect to obtain
physically meaningful maps of electrostatic potential for molecules
containing at least 50 atoms.
Such results will be of particular significance for the nucleic acids
which have strongly ionic character and contain many polar groups. The H
bonding of the bases, their stacking, the binding of counterions and polar
molecules such as water, all involve interactions which are predominantly
electrostatic. We will map the electrostatic potential in the voids of
nucleotide crystal structures after water molecules, cations and
intercalated drugs are completely or selectively removed from the
pseudoatom model, and in this way we will study their binding sites.
An important characteristic of this project is that experimental
electrostatic potentials will be carefully cross-checked for consistency
with each other and with results from simple benchmark crystal structures.
We outline a new procedure for representing the electron density, the
modulus of the electric field, or the electrostatic potential as the sum
of contributions from spherically symmetric atomic charges. Our procedure
overcomes the disadvantages inherent in fitting procedures that are based
on the points of a grid and occur within a finite volume in space. The aim
is to compile a database of atomic charges which can be conveniently
incorporated as part of a standardized force field for molecular mechanics
and molecular dynamics calculations.
Public Health Relevance Statement
Data not available.
NIH Spending Category
No NIH Spending Category available.
Project Terms
X ray crystallographyadductadenosinechemical modelscomputer program /softwarecrystallizationcytidinedinucleotidedrug interactionselectron densityguanosineionic bondmathematical modelneutron diffractionnucleic acid structureoligonucleotidesphysical model
No Sub Projects information available for 7R01GM039513-10
Publications
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Clinical Studies
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