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A DNA minor groove electronegative potential genome map based on photo-chemical probing

Lindemose, Søren, Nielsen, Peter Eigil, Hansen, Morten, Møllegaard, Niels Erik
Nucleic acids research 2011 v.39 no.14 pp. 6269-6276
DNA, RNA, algorithms, binding sites, gene expression, genome, models, nucleosomes
The double-stranded DNA of the genome contains both sequence information directly relating to the protein and RNA coding as well as functional and structural information relating to protein recognition. Only recently is the importance of DNA shape in this recognition process being fully appreciated, and it also appears that minor groove electronegative potential may contribute significantly in guiding proteins to their cognate binding sites in the genome. Based on the photo-chemical probing results, we have derived an algorithm that predicts the minor groove electronegative potential in a DNA helix of any given sequence. We have validated this model on a series of protein-DNA binding sites known to involve minor groove electrostatic recognition as well as on stable nucleosome core complexes. The algorithm allows for the first time a full minor groove electrostatic description at the nucleotide resolution of any genome, and it is illustrated how such detailed studies of this sequence dependent, inherent property of the DNA may reflect on genome organization, gene expression and chromosomal condensation.