Locations of frequently opening regions on natural DNAs and their relation to functional loci.

Abstract

AbstractThe probability of each base pair being in open state under premelting conditions was calculated and plotted against the base number for nine DNA genomes whose entire nucleotide sequences have been determined. The base‐pair opening profiles thus obtained were compared with the functional maps. Origins of DNA replication fall on frequently opening regions for five of six DNA genomes with known initiation sites of replication. Coincidence of frequently opening regions with promoters and terminators of transcription is most prominent for DNAs with block heterogeneity in sequence such as papovavirus DNAs, a Colicin El‐related plasmid pAO3, pBR322, and Transposon 3 (Tn 3) DNAs, while this coincidence is less apparent in DNAs with random sequence such as the replicative form of ϕX174 and G4 phage DNAs. In fd phage DNA, about half the promoters are located in frequently opening regions, although the strength of a promoter is not correlated with the frequency of opening of base pairs. Correlation of frequently opening regions and gene boundaries is not so obvious as claimed previously. As a whole, coincidence of functional loci and frequently opening regions defined in base‐pair opening profiles is far from perfect but much better than that previously inferred from the conventional running average of local A + T content, theoretical denaturation mapping, or electron microscopy of partially denatured DNA molecules.