Occurrence of potential cruciform and H-DNA forming sequences in genomic DNA

GP Schroth, PS Ho - Nucleic acids research, 1995 - academic.oup.com
Nucleic acids research, 1995academic.oup.com
We have used computer-assisted methods to search large amounts of the human, yeast and
Escherichla coll genomes for inverted repeat (IR) and mirror repeat (MR) DNA sequence
patterns. In highly supercoiled DNA some IRs can form cruclforms, while some MRs can
form intramolecular triplexes, or H-DNA. We find that total IR and MR sequences are highly
enriched in both eukaryotic genomes. In E. coll, however, only total IRs are enriched, while
total MRs only occur as frequently as In random sequence DNA. We then used a set of …
Abstract
We have used computer-assisted methods to search large amounts of the human, yeast and Escherichla coll genomes for inverted repeat (IR) and mirror repeat (MR) DNA sequence patterns. In highly supercoiled DNA some IRs can form cruclforms, while some MRs can form intramolecular triplexes, or H-DNA. We find that total IR and MR sequences are highly enriched in both eukaryotic genomes. In E.coll , however, only total IRs are enriched, while total MRs only occur as frequently as In random sequence DNA. We then used a set of experimentally derived criteria to predict which of the total IRs and MRs are most likely to form crucrforms or H-DNA in supercoiled DNA. We show that strong cruciform forming sequences occur at a relatively high frequency in yeast (1/19 700 bp) and humans (1/41 800 bp), but that H-DNA forming sequences are abundant only in humans (1/49 400 bp). Strong cruciform and H-DNA forming sequences are not abundant In the E.coll genome. These results suggest that crucrforms and H-DNA may have a functional role in eukaryotes, but probably not prokaryotes.
Oxford University Press