Comparison of Experimental with Theoretical Melting of the Yeast Genome and Individual Yeast Chromosome Denaturation Mapping Using the Program Meltsim

Abstract

The yeast S. cereviseae represents the first eukaryotic organism whose genome has been entirely sequenced as a result of the Human Genome Project(1). In this report we demonstrate the good agreement between an experimental high resolution melting curve of total nuclear S. cereviseae DNA and the theoretical melting calculated for the complete yeast DNA genome (12,067,277 bp: Saccharomyces Genome Database) by the statistical thermodynamics program MELTSIM, parameterized for long DNA sequences(2,3). The experimental and theoretical melting curves are both fairly symmetrical and possess nearly identical T_m values. Calculated melting of coding and flanking DNA regions indicates that flanking DNAs are more (A+T)-rich than coding sequences and account for the earliest melting DNA. Calculated melting curves of the 16 individual yeast chromosomes are very similar and with few exceptions exhibit symmetric melting curves. MELTSIM was also used to calculate a theoretical denaturation map of Chromosome III DNA. The agreement between MELTSIM calculated and experimental melting data demonstrates our ability to accurately simulate long DNA sequence melting in complex eukaryotic genomes, whose sequences are becoming increasingly available for study in public databases. This has important consequences for the understanding of sequence dependent energetic properties of DNA in their biological sequence context and also for their potential use in biomaterials applications.