Drosophila Rrp1 3'-exonuclease: demonstration of DNA sequence dependence and DNA strand specificity.
Drosophila Rrp1 (recombination repair protein 1) is a DNA repair enzyme whose nuclease activities include AP-endonuclease, 3'-exonuclease, 3'-phosphodiesterase and 3'-phosphatase. This study investigates the sequence specificity of the dsDNA 3'-exonuclease activity of Rrp1. We demonstrate that the activity is more efficient in purine-rich regions of dsDNA than in pyrimidine-rich regions. Rrp1 exonuclease activity is examined at 3'-terminal homopurine or homopyrimidine tracts, at junctions between purine- and pyrimidine-rich sequences and upon encountering repeated dinucleotide runs. The data show that purine-purine and 3'-pyrimidine-5'-purine dinucleotide bonds are cleaved faster than 3'-purine-5'-pyrimidine or pyrimidine-pyrimidine bonds. Thus, the base occupying the penultimate position in the 3'-terminal dinucleotide may be important in determining the relative efficiency of bond cleavage by Rrp1. These findings may reflect upon specific DNA-protein interactions in the enzyme active site.
Sander
M
M
Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
Benhaim
D
D
D000818:Animals; D004260:DNA Repair / Q000235:genetics; D004330:Drosophila; D029721:Drosophila Proteins; D004591:Electrophoresis, Polyacrylamide Gel; D005092:Exonucleases / Q000378:metabolism*; D009713:Nucleotidyltransferases / Q000378:metabolism*; D009838:Oligodeoxyribonucleotides / Q000737:chemistry / Q000378:metabolism; D011743:Pyrimidines / Q000494:pharmacology; D012091:Repetitive Sequences, Nucleic Acid; D013379:Substrate Specificity
D029721:Drosophila Proteins; D009838:Oligodeoxyribonucleotides; D011743:Pyrimidines; D009713:Nucleotidyltransferases; C061900:Rrp1 protein, Drosophila; D005092:Exonucleases