Book of Abstracts: Albany 2003

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

Ions, Bonding and Bending in DNA/Protein Recognition

The problem of how a specific protein recognizes a particular sequence of base pairs in DNA has gone through three phases: (a) patterned hydrogen-bonding, (b) sequence-dependent local helix deformability, and (c) localized binding of cations ? certainly divalent, and more hypothetically monovalent as well. Elementary hydrogen-bonding patterns as proposed first by Seeman, Rosenberg and Rich (1) proved to be too simple, provoking a baffled Brian Matthews to entitle a 1988 Nature review: "Protein-DNA interaction. No code for recognition?" (2). Attention then shifted to differences in local helix structure that might assist binding to a recognition protein, with helix bending being the most striking feature (3, 4). The issue, of course, was not one of rigid sequence-determined bending per se, but of sequence-dependent bendability when the recognition protein was encountered. More recently, divalent cations, which have long been observed in DNA/protein complexes, have been implicated as possible players in the recognition process. That is the principal subject of this symposium

Richard E. Dickerson
Mary L. Kopka
Ann Maris
Gye-Won Han

Molecular Biology Institute
Boyer Hall
University of California, Los Angeles
Los Angeles,CA 90095-1570

References and Footnotes
  1. N. C. Seeman, J. M. Rosenberg & A. Rich, Proc. Natl. Acad. Sci. USA 73, 804-808 (1977).
  2. B. W. Matthews, Nature 335, 294-295 (1988).
  3. R. E. Dickerson, Nucleic Acids Research 26, 1906-1926 (1998).
  4. R. E. Dickerson & T. K. Chiu, Biopolymers (Nucleic Acid Sciences) 44, 361-403 (1997).