Distribution of sequence-dependent curvature in genomic DNA sequences.
The distribution of inherent, sequence-dependent curvature was calculated for a number of prokaryotic (M. genitalium, H. influenzae, M. jannaschii), viral (adenovirus 2, equine herpes virus 1), phage (M13, lambda), eukaryotic (S. cerevisiae) and mitochondrial genomes as well as E. coli and human genomic fragments. The genomic averages are in the range of 6-8 degrees/helical turn and only about 20% of DNA is curved less than 3 degrees/helical turn. The prokaryotes and phages appear to have a consistently higher frequency of curved DNA in their genomes than the other genomes tested. Long, highly curved segments, similar to artificially designed curved DNA, are apparently absent from the genomes. Short, curved segments, differing in G+C content may provide environmentally modulated conformational signals for gene regulation. A WWW-server was constructed for the prediction of curved sites from DNA sequences (http://icgeb.trieste.it/dna/curve_it.html/)..
Gabrielian
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A
International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park, Trieste, Italy.
Vlahovicek
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K
Pongor
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S
D000818:Animals; D004269:DNA, Bacterial / Q000737:chemistry*; D004272:DNA, Mitochondrial / Q000737:chemistry*; D004279:DNA, Viral / Q000737:chemistry*; D016678:Genome; D006801:Humans; D009690:Nucleic Acid Conformation
D004269:DNA, Bacterial; D004272:DNA, Mitochondrial; D004279:DNA, Viral