Superthelical structure of DNA and regulation of gene expression.

Abstract

Specific base sequences have been found in common in genes and regarded as regulatory signals on the level of the primary structure. However DNA constructs higher-order forms in cells and superhelix is an essential structure of DNA in construction of chromatin and in packaging DNA. If DNA is viewed on the basis of superhelix, common features or specific higher-order structures appear among sequences nonhomologous to each other, or far-off sequences are situated side by side. The structural perturbation resulting from negative superhelix induces torsional underwinding which causes local melting, cruciform formation, or conformational shift from B-form to Z-form. Evidence has accumulated which suggests that these comformations of DNA play important roles as recognition and target sites of proteins involved in transcription, replication, and recombination. In addition to the primary structure, superhelix of DNA seems to be a key part of regulatory mechanism of gene expression.In this article, I will summarize common features of DNA in transcription, and the data on the conformational alteration of double stranded DNA related to regulation of gene expression. I will discuss regulation of gene expression from a view-point of structural perturbation of double helix.