Chapter

Systems and Synthetic Biology

pp 241-254

Date:

DNA Structure and Promoter Engineering

  • Venkata Rajesh YellaAffiliated withMolecular Biophysics Unit, Indian Institute of Science
  • , Aditya KumarAffiliated withMolecular Biophysics Unit, Indian Institute of Science
  • , Manju BansalAffiliated withMolecular Biophysics Unit, Indian Institute of Science Email author 

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Abstract

Transcription initiation is the first step in the regulation of gene expression. Promoters are the regions of genomic DNA where transcription initiation machinery assembles and are generally characterized by presence of short nucleotide sequence motifs like TATA-box, Inr element, BRE, etc. However, apart from these motifs, promoter regions have been reported to have structural properties, such as lower stability, lesser bendability and more curvature compared to other genomic regions. Interestingly, these properties are conserved from archaea to mammals, with little differences. Several algorithms have been developed to differentiate promoter regions from non promoters, using DNA structural properties. Here we show that, in E. coli and S. cerevisiae, genes with different experimentally determined expression levels, differ in their structural features. Promoters of highly expressed or less responsive genes are less stable, less bendable and more curved compared to promoters of lowly expressed or more responsive genes. This suggests that these structural properties can be used to design promoters to modulate gene expression.

Keywords

Promoter engineering DNA structural properties DNA duplex stability DNA bendability Intrinsic curvature NUCRADGEN Transcription factor binding sites (TFBSs)