DNA Secondary Structures for Probe Design

Visualizing DNA secondary structures is essential to fast and efficient design of probes for DNA chips. There are several programs available for visualizing single-stranded RNA secondary structures, but these programs cannot be used to draw DNA secondary structures formed by several hundred to thousand primers and target genes. We have developed an algorithm and program for visualizing DNA secondary structures formed by multiple strands. We believe the program will be a valuable tool for designing primers and probes in DNA chips. This work was supported by the Korea Science and Engineering Foundation (KOSEF) under grant R01-2003-000-10461-0