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Albany 2001

category image Biomolecular
Stereodynamics
SUNY at Albany
June 19-23, 2001

Stabilization of DNA duplex and triplex structures by intercalating agents: Construction of 3D phase diagrams

Previous studies have shown that some nucleic acid intercalating agents can stabilize duplex and triplex secondary structures. However, the variety of experimental conditions used in past investigations make it difficult to directly compare the stabilizing effects of oligonucleotide length, nature of intercalating agent and relative/absolute concentration of nucleic acid and intercalating agent. In a systematic approach to this problem, we are constructing 3D phase diagrams for DNA secondary structure (i.e., single stranded, duplex, triplex) as a function of oligonucleotide length, nucleic acid/intercalator concentration and temperature. Phase diagrams are being constructed for different intercalating agents, and for identical DNA samples in the absence of intercalating agents. One objective of this work is to aid our design of temperature and concentration pathways that allow temporal control over the assembly and disassembly of multi-stranded nucleic acid structures. Our ultimate goal is to develop methods for the assembly of mono- and oligonucleotides on nucleic acid templates as part of a cyclic process for the artificial replication of RNA-like polymers. How intercalating agents could facilitate this process will be discussed. The intercalation-mediated process envisioned for nucleic replication has a number of potential advantages over previous approaches to protein-free replication. These same advantages also suggest that intercalation may have played a central role in replication during the RNA world (1). The implications of our recent results on this proposal will also be discussed.

References and Footnotes
  1. Nicholas V. Hud and Frank. A. L. Anet, "Intercalation-Mediated Synthesis and Replication: A New Approach to the Origin of Life," J.Ttheor. Biol. 205, 543-562 (2000).

Matjaz Polak and Nicholas V. Hud

School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA 30332-0400
Phone: 404-385-1162, Fax: 404-894-2295, E-mail: hud@chemistry.gatech.edu