Comparison of Experimental and Theoretical Melting Behavior of DNA

Abstract

ABSTRACTHigh resolution melting curves of total nuclearDictyostelium discoideumDNA (A×3 strain) are compared to theoretical melting calculated from GENBANK sequences(1.74 % of total) by the statistical thermodynamics program MELTSIM, parameterized for long DNA sequences(1,2). The lower and upper limits of simulated melting agree quantitatively with the experimental melting of total DNA. Calculated melting of coding, intron and flanking regions indicate that intron and flanking DNAs are extremely (A+T)-rich and account for the earliest melting DNA. There is no temperature overlap of these regions with coding DNA. A theoretical denaturation map of DNA containing the ribosomal DNA genes showed excellent agreement with subtransition positions of these genes in experimental curves. Agreement between these calculated and experimental melting data demonstrates our ability to accurately simulate DNA melting in complex eukaryotic genomes. This has important consequences for the understanding of sequence dependent energetic properties of nucleic acids and their potential use as biomaterials.