Use of DNA melting simulation software for in silico diagnostic assay design: targeting regions with complex melting curves and

Background: DNA melting curve analysis using double-stranded DNA-specific dyes such as SYTO9 produce complex and reproducible melting profiles, resulting in the detection of multiple melting peaks from a single amplicon and allowing the discrimination of different species. We compare the melting curves of several Naegleria and Cryptosporidium amplicons generated in vitro with in silico DNA melting simulations using the programs POLAND and MELTSIM., then test the utility of these programs for assay design using a genetic marker for toxin production in cyanobacteria. Results: The SYTO9 melting curve profiles of three species of Naegleria and two species of Cryptosporidium were similar to POLAND and MELTSIM melting simulations, excepting some differences in the relative peak heights and the absolute melting temperatures of these peaks. MELTSIM and POLAND were used to screen sequences from a putative toxin gene in two different species of cyanobacteria and identify regions exhibiting diag...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: John P. Rasmussen, Christopher P. Saint, Paul T. Monis
• Keywords: BMCBI 2007, Melting Curve, Melting Profiles, Simulations