Structural junctions in DNA: the influence of flanking sequence on nuclease digestion specificities

When a protein binds to DNA, the affinity of this protein for its primary site of interaction may be influenced by the nature of flanking sequences. This is thought to be a consequence of local cooperativity in the DNA molecule, where the conformation at one point along the helix can influence the c...

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Bibliographic Details
Published in:Nucleic acids research 1985-06, Vol.13 (12), p.4445-4467
Main Authors: Drew, Horace R., Travers, Andrew A.
Format: Article
Language:English
Subjects:
Analytical, structural and metabolic biochemistry
Base Sequence
Biological and medical sciences
Chemical Phenomena
Chemistry
Deoxyribonuclease I - metabolism
Distamycins
DNA
DNA Restriction Enzymes - metabolism
Dna, deoxyribonucleoproteins
Echinomycin
Endodeoxyribonucleases - metabolism
Fundamental and applied biological sciences. Psychology
Nucleic acids
Substrate Specificity
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Summary:When a protein binds to DNA, the affinity of this protein for its primary site of interaction may be influenced by the nature of flanking sequences. This is thought to be a consequence of local cooperativity in the DNA molecule, where the conformation at one point along the helix can influence the conformation at another, and thereby modulate the free energy of protein-DNA recognition. In order to learn more about this process, we have carried out experiments of two sorts. First, we have constructed sequences of the type (dA)11 (dG)8, where the conformational preferences of the DNA molecule switch from one extreme to another over just a single base pair, and subjected them to digestion by DNAase I and DNAase II. This is to learn whether the structure changes abruptly at the Junction point, or more gradually with an influence extending into residues on either side. Secondly, we have subjected long plasmid DNA to digestion by restriction enzymes Fnu DII, Hae III, Hha I and Msp I, to look for correlations between cutting rate and the identity of nucleotides on either side of the restriction site. The influence of flanking sequence on nuclease digestion specificities is clearly evident in both kinds of experiment, but the rules governing this seem complex and not easily formulated. The best that can be done at present is to divide the problem into two parts, “analogue” and “digital”, representing sugar-phosphate and base components of recognition
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/13.12.4445