Book of Abstracts: Albany 2003

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Abstract Book
June 17-21 2003

Theory of the Dependence of Configurations of Intrinsically Curved DNA on Salt Concentration

Our group has recently developed an efficient method of calculating the influence of screened electrostatic forces on the equilibrium configurations of intrinsically curved DNA obeying a theory (1) of sequence-dependent DNA elasticity which permits one to take into account information about the variation in elastic properties from one base-pair step to another. Figures will be presented showing how the minimum energy configuration of curved DNA extends as the concentration c of (monovalent) salt is lowered. The theory of counterion condensation employed for the calculations is applicable for values of c for which the Debye radii are less than the distance of closest approach of the DNA segment to itself. There are cases in which several equilibrium configurations can occur at one ionic strength with some locally stable and others unstable. In such cases bifurcation diagrams can be constructed with ionic strength taken as independent variable. Detailed results will be shown for a 500 base pair (bp) segment that in its stress-free configuration is close to a helix with a radius and pitch such that each of its 150 bp subsegments has a shape not far from that of a closed circular ring. In that example, if the segment is, for each c, in the configuration that minimizes its total energy (i.e., the sum of its elastic and electrostatic energy), then the distance between its end points increases 9-fold as c decreases from 1 M to 5×10-6 M . An example will be given of a 300 bp segment that has multiple equilibrium configurations at each c in a broad range of c.

Bernard D. Coleman1,*
Yoav Biton1
David Swigon2

1Department of Mechanics & Materials Science
Rutgers University
School of Engineering
98 Brett Road, Piscataway, NJ 08854
Phone: 732-445-5558
Fax: 732-445-0085
2Department of Chemistry & Chemical Biology
Rutgers University
Wright-Rieman Laboratories
610 Taylor Road, Piscataway, NJ 08854
Phone: 732-445-4619
Fax: 732-445-5958

References and Footnotes
  1. B. D. Coleman, W. K. Olson, & D. Swigon, J. Chem. Phys., Scheduled to appear in April 2003.