Biomaterial Database

Strand-specific cleavage of mismatch-containing DNA by deoxyinosine 3'-endonuclease from Escherichia coli. 1994

M Yao, and Y W Kow

Department of Microbiology and Molecular Genetics, University of Vermont, Markey Center for Molecular Genetics, Burlington 05405.

A deoxyinosine-specific endonuclease, deoxyinosine 3'-endonuclease (Yao, M., Hatahet, Z., Melamede, R. J., and Kow, Y. W. (1994) J. Biol. Chem. 269, 16260-16268), from Escherichia coli was found to recognize mismatches in DNA. Using DNA duplexes containing a unique mismatch, the enzyme was found to hydrolyze the second phosphodiester bond 3' to the mismatch. The cleavage efficiency of deoxyinosine 3'-endonuclease on mismatch-containing DNA was affected by the nature of the mismatches. The cleavage activity was also affected by the sequence context surrounding the mismatches. The presence of a G/C or C/G pair immediately 3' or 5' to the mismatch substantially reduced the ability of the enzyme to nick the mismatch-containing DNA. The presence of two G/C pairs, one 5' and the other 3' to the mismatch, abolishes the ability of the enzyme to recognize the mismatch. Interestingly, deoxyinosine 3'endonuclease showed strong strand specificity on DNA containing mismatches, and only one strand of the mismatch-containing DNA was nicked by the enzyme. This strand specificity of mismatch cleavage was not affected by the nature of the mismatch. Preliminary data suggest that the strand specificity is terminus dependent; the enzyme cleaves the strand with the mismatch closer to its 5' terminus. However, when DNA duplexes containing deoxyinosine were used as substrates, deoxyinosine 3'-endonuclease cleaved exclusively the strand containing deoxyinosine. Deoxyinosine 3'-endonuclease also cleaved single-stranded DNA containing deoxyinosine, but not DNA containing normal deoxynucleotides or deoxynebularine, suggesting the enzyme uses different mechanisms of recognition for deoxyinosine and mismatches in DNA.

UI	MeSH Term	Description	Entries
D007288	Inosine	A purine nucleoside that has hypoxanthine linked by the N9 nitrogen to the C1 carbon of ribose. It is an intermediate in the degradation of purines and purine nucleosides to uric acid and in pathways of purine salvage. It also occurs in the anticodon of certain transfer RNA molecules. (Dorland, 28th ed)
D008969	Molecular Sequence Data	Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.	Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D009838	Oligodeoxyribonucleotides	A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.	Oligodeoxynucleotide,Oligodeoxyribonucleotide,Oligodeoxynucleotides
D002413	Cations, Divalent	Positively charged atoms, radicals or groups of atoms with a valence of plus 2, which travel to the cathode or negative pole during electrolysis.	Divalent Cations
D004260	DNA Repair	The removal of DNA LESIONS and/or restoration of intact DNA strands without BASE PAIR MISMATCHES, intrastrand or interstrand crosslinks, or discontinuities in the DNA sugar-phosphate backbones.	DNA Damage Response
D004706	Endodeoxyribonucleases	A group of enzymes catalyzing the endonucleolytic cleavage of DNA. They include members of EC 3.1.21.-, EC 3.1.22.-, EC 3.1.23.- (DNA RESTRICTION ENZYMES), EC 3.1.24.- (DNA RESTRICTION ENZYMES), and EC 3.1.25.-.
D004720	Endonucleases	Enzymes that catalyze the hydrolysis of the internal bonds and thereby the formation of polynucleotides or oligonucleotides from ribo- or deoxyribonucleotide chains. EC 3.1.-.	Endonuclease
D004926	Escherichia coli	A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.	Alkalescens-Dispar Group,Bacillus coli,Bacterium coli,Bacterium coli commune,Diffusely Adherent Escherichia coli,E coli,EAggEC,Enteroaggregative Escherichia coli,Enterococcus coli,Diffusely Adherent E. coli,Enteroaggregative E. coli,Enteroinvasive E. coli,Enteroinvasive Escherichia coli
D001080	Apurinic Acid	Hydrolysate of DNA in which purine bases have been removed.	Acid, Apurinic
D001483	Base Sequence	The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.	DNA Sequence,Nucleotide Sequence,RNA Sequence,DNA Sequences,Base Sequences,Nucleotide Sequences,RNA Sequences,Sequence, Base,Sequence, DNA,Sequence, Nucleotide,Sequence, RNA,Sequences, Base,Sequences, DNA,Sequences, Nucleotide,Sequences, RNA