Computation With 3D DNA Structures

Natasha Jonoska, Department of Mathematics, University of South Florida

National Science Foundation, October 1, 1999

Abstract

We propose use of three dimensional structures (knots or graphs) made of DNA molecules as a computational tool. A k-armed branched junction molecule is taken as a basic building block to form graphs. The main idea is presented through an example of solving 3-vertex colorability problem that potentially reduces the number of laboratory (computational) steps. Some mathematical problems that arise from this approach are presented. Current experiments in detecting and removing certain partially double stranded molecules are discussed. Use of recombinases, topoisomerases and different DNA forms (B,Z,H) is proposed.

Natasha Jonoska

Last modified: Mon Sep 27 13:17:20 EDT 1999