Open AccessProperties of DNase I digestion of the deoaxyoligonucleotide:5′d(ATCGTACGAT)23′
Author(s) -
Emily L. Fish,
John N. Vournakis
Publication year - 1987
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/15.22.9417
Subject(s) - deoxyribonuclease i , footprinting , phosphodiester bond , deoxyribonuclease , dna , oligomer , biology , dna footprinting , substrate (aquarium) , enzyme , cleavage (geology) , endonuclease , digestion (alchemy) , biochemistry , stereochemistry , chemistry , dna binding protein , chromatography , rna , base sequence , organic chemistry , ecology , paleontology , fracture (geology) , gene , transcription factor
Deoxyribonuclease I digestion of the deoxyoligodecamer 5'd(ATCGTACGAT)2(3') has been examined in detail to study the kinetic and structural properties of this enzyme substrate system in solution. In addition, these studies have defined, in general, those DNase I conditions to be used in future drug-DNA footprinting experiments. Special attention has been taken of those properties of DNase I that are critical for quantitation of ligand binding to small DNA fragments, and that aid in designing oligomers to be used in footprinting experiments. Enzyme activity was observed at all phosphodiester bonds in the decamer studied with varying affinity, except for the first four bonds at the 5' end of the oligomer. The DNA substrate concentration is always in excess, in order to achieve conditions of no more than one DNase I cleavage per DNA molecule. Reactions were controlled so that 65% or more of the initial amount of decamer substrate remained after DNase I digestion. It was observed that the rate of enzyme reactivity decreases with digestion time and is sensitive to the experimental conditions.