Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
June 17-21 2003

Sequence-Dependent DNA Condensation and the Electrostatic Zipper Motif

Sequence-dependent configuration changes and condensation of double-stranded (ds) poly(dG-dC)·(dG-dC) (GC-DNA) and ds poly(dA-dT)·(dA-dT) (AT-DNA) were observed by AFM in the presence of Ni(II) (1). Less condensing agent was required to generate configuration changes in GC-DNA as compared to AT-DNA. In the presence of Ni(II) cations, GC-DNA adopted a Z-type conformation and underwent a step-wise condensation, starting with partial intramolecular folding, followed by intermolecular condensation of two to several molecules and ending with the formation of toroids, rods, and jumbles. GC-DNA condensates were unusual in that the most highly condensed regions were surrounded by loops of ds GC-DNA. In contrast, AT-DNA retained its B-type conformation and displayed only minor condensation even at high Ni(II) concentrations. The Ni(II)-dependent differences in condensation between GC-DNA and AT-DNA are predicted by an extension of the electrostatic zipper motif (2) in which we account for shorter than Debye screening length surface separations between the DNA molecules and for the Ni(II)-induced conformation change of GC-DNA to Z-DNA.

Helen G. Hansma*
John C. Sitko
Eduard M. Mateescu

Department of Physics
University of California
Santa Barbara, CA 93106
Phone: 805 8933881
Fax: 805 8938315

References and Footnotes
  1. Sitko, J. C., Mateescu, E. M. & Hansma, H. G. Biophysical Journal 84, 419-431 (2003).
  2. Kornyshev, A. A. & Leikin, S. Physical Review Letters 82, 4138-41 (1999).