Nuclease activity of 1,10-phenanthroline-copper ion: reaction with CGCGAATTCGCG and its complexes with netropsin and EcoRI

Kuwabara, Michio D.; Yoon, Chun; Goyne, Thomas; Thederahn, Theodore; Sigman, David S.

doi:10.1021/bi00371a023

Cited by 186 publications

(148 citation statements)

References 31 publications

(27 reference statements)

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“…This suggests that the enzyme binds only to the DNA strand containing deoxyinosine and makes no contact with the opposite strand. Furthermore, no footprinting was observed when the DNA digestion was performed with 1,10-phenanthroline-copper ion system (17,18), suggesting that the protein interacts with the DNA along the major groove (data not shown).…”

Section: Duplex Dmentioning

confidence: 98%

Interaction of Deoxyinosine 3′-Endonuclease from Escherichia coli with DNA Containing Deoxyinosine

Yao¹,

Kow²

1995

Journal of Biological Chemistry

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By using a band mobility shift assay, deoxyinosine 3-endonuclease, an Escherichia coli enzyme which recognizes deoxyinosine, AP site, urea residue, and base mismatches in DNA, was shown to bind tightly to deoxyinosine-containing oligonucleotide duplexes. Two distinct protein-DNA complexes were observed, the faster migrating complex (complex I, K d ‫؍‬ 4 ؋ 10 ؊9 M) contained one molecule of deoxyinosine 3-endonuclease, while the slower migrating complex (complex II, K d ‫؍‬ 4 ؋ 10 ؊7 M) contained two molecules of the protein bound to every molecule of duplex DNA. The endonucleolytic activity of deoxyinosine 3-endonuclease paralleled the formation of the complex I. Interestingly, deoxyinosine 3-endonuclease exhibited similar affinities for both the substrate and the nicked duplex product and thus remained bound to the DNA after the cleavage reaction. The formation of a stable complex required the presence of a duplex structure 5 to the deoxyinosine residue. DNase I footprinting revealed that deoxyinosine 3-endonuclease protected 4 -5 nucleotides 5 to the deoxyinosine, and when complex II was formed, at least 13 nucleotides 3 to deoxyinosine were protected. Based on these results, a model is proposed for the interaction of deoxyinosine 3-endonuclease with DNA containing deoxyinosine.Deoxyinosine in DNA can arise from deamination of deoxyadenosine, which can be spontaneous or promoted by exposure of DNA to ionizing radiation, UV light, or nitrous acid (1-3). Deoxyinosine in DNA is premutagenic and can lead to A/T to C/G transition mutations (4). Deoxyinosine in DNA was thought to be removed by hypoxanthine DNA glycosylase, which has been partially purified from Escherichia coli as well as other eukaryotic sources (5-8). However, it was reported recently (9) that a well characterized repair enzyme, 3-methyladenine DNA glycosylase II, encoded by alkA gene in E. coli possesses hypoxanthine DNA glycosylase activity and releases hypoxanthine from deoxyinosine-containing DNA, suggesting that both 3-methyladenine DNA glycosylase and hypoxanthine DNA glycosylase activities reside in the same protein. It has also been shown that 3-methyladenine DNA glycosylase from human (ANPG protein), rat (APDG protein), and yeast (MAG protein) are able to excise hypoxanthine from DNA (9).Recently, we identified and purified a novel deoxyinosine specific endonuclease from E. coli, deoxyinosine 3Ј-endonuclease (10). The enzyme hydrolyzes the second phosphodiester bond 3Ј to the deoxyinosine residue. In addition to deoxyinosine, deoxyinosine 3Ј-endonuclease also recognizes AP site, urea residue, and base mismatches in DNA and exhibits strand-specific cleavage of base mismatches in DNA (11). In contrast to hypoxanthine DNA glycosylase, deoxyinosine 3Ј-endonuclease does not remove deoxyinosine or other lesions from the DNA (10). Therefore, it is likely that other proteins are required to complete the repair process initiated by deoxyinosine 3Ј-endonuclease.The initial binding of a protein to DNA is critical for multiprotein interaction with DN...

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Section: Duplex Dmentioning

confidence: 98%

Interaction of Deoxyinosine 3′-Endonuclease from Escherichia coli with DNA Containing Deoxyinosine

Yao¹,

Kow²

1995

Journal of Biological Chemistry

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“…The 1,lOphenanthroline-copper complex [ (OP)2Cu+] is an artificial nuclease with hydrogen peroxide as a coreactant. The reagent generates hydroxyl radicals that cleave B-DNA by oxidation of the deoxyribose near the binding site of the complex in the minor groove (Sigman, 1986;Kuwabara et al, 1986). The reactivity of (OP)&u+ with B-DNA is sequence dependent.…”

Section: C8mentioning

confidence: 99%

“…The reactivity of (OP)&u+ with B-DNA is sequence dependent. That is, different sequences show different hyperreactive sites because of local variations in the minor groove conformation that influence binding of the complex (Veal & Rill, 1988); left-handed Z-DNA or single-stranded DNA incapable of forming secondary structures are not cleaved (Marshall et al, 1981;Pope & Sigman, 1984), while a DNA-RNA hybrid in the A conformation with the characteristic shallow minor groove is digested at only one-third the rate of B-DNA (Sigman, 1986).…”

Section: C8mentioning

confidence: 99%

Substrate properties of 25-nt parallel-stranded linear DNA duplexes

Rippe¹,

Jovin²

1989

Biochemistry

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Four 25-nt oligonucleotides consisting of sequences of dA and dT (Dl-4) have been synthesized. As shown in a companion paper (Rippe et al., 1989), the two combinations D1-D3 and D2nD4 form normal antiparallel duplexes, whereas the pairs DlsD2 and D3sD4 constitute duplexes with the same sequences, but with the two strands parallel to each other. The activities of the following D N A processing enzymes and chemical reagents on the parallel stranded (ps) and antiparallel stranded (aps) duplexes were tested. Physicochemical studies have demonstrated that given an appropriate selection of sequences two oligonucleotides will form parallel-stranded DNA duplexes instead of the conventional antiparallel B-DNA structure Germann et al., 1988;Rippe et al., 1989). Parallel-stranded DNA has distinctive spectroscopic properties and a thermodynamic stability only slightly less than that of normal B-DNA (Ramsing et al., 1989). Besides the parallel orientation of the two constituent strands, the structural feature of note is the reverse Watson-Crick base pairing between dA and dT residues of the two constituent strands (Pattabiraman, 1986;. Although direct confirmation of the psl-DNA structure by crystallographic and 'H NMR techniques is still not available, the experimental results presented to date are compatible with expectation. Thus, for example, the pattern of chemical methylation by dimethyl sulfate was the same for ps and aps hairpin molecules , excluding the existence of the Hoogsteen base pairs observed with other DNA structures involving parallelstranded interactions.An assessment of the biological relevance of ps-DNA requires the evaluation of its interactions with proteins and other reagents with known specificities for certain DNA conformations. To pursue this point, we synthesized and characterized (Rippe et al., 1989) a set of four 2 5 4 oligonucleotides selected so as to form two pairs of ps and aps duplexes. These molecules were radiolabeled at the 5' ends with 32P and evaluated as substrates for a number of DNA-dependent enzymes and chemical nucleases. MATERIALS AND METHODSOligonucleotide Synthesis and End Labeling. Oligonucleotides D1-4 were synthesized and end labeled with 32P as described elsewhere (Rippe et al., 1989).Reaction Conditions. For the enzymatic and chemical nuclease reactions the samples were incubated at 25 OC, unless

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“…Products of the reaction include 5'-and 3'-monophosphate ester termini, free bases, and minor amounts of 3'-phosphoglycolate (3,4).…”

mentioning

confidence: 99%

Nuclease activity of 1,10-phenanthroline-copper: sequence-specific targeting.

Chen¹,

Sigman²

1986

Proc. Natl. Acad. Sci. U.S.A.

158

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The nuclease activity of 1,10-phenanthrolinecopper ion can be targeted to specific DNA sequences by attachment of the ligand to the 5' end of complementary deoxyoligonucleotides via a phosphoramidate linkage. To synthesize the adduct, the phosphotimidazolide of the deoxyoligonudeotide is prepared using a water-soluble carbodiimide and is then coupled to 5-glycylamido-1,10-phenanthroline. After hybridization to the target DNA, sequence-specific cleavage is observed upon the addition of cupric ion and 3-mercaptopropionic acid. Two methods of assaying the cutting of the operator sequence of the lac operon have been employed using the oligonucleotide 5'-AATTGTTATCCGCTCACAAT-T-3' representing sequence positions 21-1 of the template strand. In the first, the single-stranded DNA of the phage M13mp8 was the target, and cuts were detected using a primer-extension assay. In the second, the substrate was an EcoRI fragment 3' labeled in the nontemplate strand. After denaturation and reannealing to the oligonucleotide-1,10-phenanthroline adduct, cupric ion and 3-mercaptopropionic acid were added, and the products were analyzed directly on a sequencing gel. With the phenanthroline moiety attached to position 21 of the oligonucleotide carrier, cutting was observed at positions 20-25 using both assays.The 1,10-phenanthroline-cuprous complex [(OP)2Cu'] with hydrogen peroxide as a coreactant cleaves DNA by oxidatively degrading the deoxyribose moiety (1, 2). The proposed mechanism for the cleavage reaction involves the reversible binding of the coordination complex to the minor groove prior to the one-electron oxidation by hydrogen peroxide to produce the hydroxyl radical, species directly responsible for the scission reaction as in the following equation:Products of the reaction include 5'-and 3'-monophosphate ester termini, free bases, and minor amounts of 3'-phosphoglycolate (3, 4).The artificial nuclease activity is conformation dependent even though the oxidation of the deoxyribose is independent of the base linked to it. The B-DNA strand of poly(dA-T) is the preferred substrate for the nuclease activity. A-DNA in heteroduplexes composed of poly(rA)-poly(T) is cut at onethird the rate of B-DNA, but poly(dG-dC) in the Z structure and noncomplementing single-stranded DNAs are not good substrates (2,5). The sequence-dependent reactivity preferences that have been observed in a restriction fragment derived from the lac operon control region correlate with biochemical function. For example, the promoter conserved region (Pribnow box) is hyperreactive, reflecting a minor groove geometry distinct from the majority of base pairs in the restriction fragment (6-8). Single base changes in the promoter region, which increase promoter strength, dramatically enhance reactivity toward the coordination complex at up to four sequence positions away from the mutational change. These results have demonstrated that mutations in the promoter region can influence biochemical activity by changing DNA conformation as reflected by reactivity...

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Nuclease activity of 1,10-phenanthroline-copper ion: reaction with CGCGAATTCGCG and its complexes with netropsin and EcoRI

Cited by 186 publications

References 31 publications

Interaction of Deoxyinosine 3′-Endonuclease from Escherichia coli with DNA Containing Deoxyinosine

Interaction of Deoxyinosine 3′-Endonuclease from Escherichia coli with DNA Containing Deoxyinosine

Substrate properties of 25-nt parallel-stranded linear DNA duplexes

Nuclease activity of 1,10-phenanthroline-copper: sequence-specific targeting.

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