Metal-activated hydrolytic cleavage of DNA

Basile, Lena A.; Raphael, Adrienne L.; Barton, Jacqueline K.

doi:10.1021/ja00258a061

Cited by 155 publications

(81 citation statements)

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“…A number of metal ion complexes have been shown to hydrolyze phosphate esters (13,14) as well as RNA with various efficiencies (15)(16)(17)(18); however, these complexes are unable to hydrolyze the phosphate diester backbone of DNA. The only reported metal-catalyzed DNA hydrolysis thus far is effected by Cu2+, Zn2+, Cd2+, or Pb2+ complexed to a polyamine ligand tethered to a DNA-binding [Ru(phen)3]2+ derivative (19), which afforded nicked (single-stranded break) pBR322 at 37°C after 5-7 hr. Here we report a dinuclear iron complex, Fe2(HPTB)(OH)(NO3)4 (where HPTB is N,N,N',N'-tetrakis (2-benzimidazolylmethyl)-2-hydroxy-1,3-diaminopropane (20, 21), which in concert with H202 or 02 effects double-stranded cleavage of pBR322 via a "hydrolytic" mechanism.…”

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confidence: 99%

Double-stranded cleavage of pBR322 by a diiron complex via a "hydrolytic" mechanism.

Hanson

Que

1994

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

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Treatment of plasmid pBR322 with Fe2-(HPTB)(OH)(NO3)4(HPTB =N,N,N',N '-tetrakis(2-benzimidazolylmethyl The complex Fe2(HPTB)(OH)(NO3)4 was synthesized according to published procedures (20). This complex has been shown to interact with H202 to form a 1:1 adduct (20).Plasmid pBR322 was purchased from Promega and transformed into Escherichia coli strains JM109 and HB101 by using CaCl2 (22). The cells were grown in Luria-Bertani broth containing tetracycline, amplified with chloramphenicol, and harvested; the plasmid was purified according to published procedures (23). Purity and quantity of DNA were determined by measuring the A26o/A280 ratio, using a Hoefer fluorometer and gel electrophoresis.Linearization of pBR322 with Fe2(HPTB)(OH)(NO34. The cleavage of pBR322 by Fe2(HPTB)(OH)(NO3)4/H202 was accomplished by mixing (in order) 1 ,ul of (0.15 mg/ml) pBR322, 1 ,ul of 0.1 M Tris HCl (pH 8.0) buffer, 1,ul (0.1 mM) of Fe2(HPTB)(OH)(NO3)4, 6 ,l of H20, and 1 ,ul of 9.0 mM H202 at 25°C. Immediately after mixing, the DNA solution was subjected to electrophoresis on a 1% agarose gel in TAE (40 mM Tris acetate/i mM EDTA) (24) and stained with ethidium bromide solution at 0.5 pg/ml to observe the cleaved DNA products. The amount of DNA was quantitated by photographing the fluorescence under UV light and analyzing the band intensities with a Pharmacia densitometer. The fluorescence intensities were corrected for the different binding affinities ofethidium bromide to form I vs. forms II and III (25). Lengthening the reaction time did not affect the amounts of nicked and linearized pBR322. The linearized pBR322 was recovered from the agarose gel by electroelution ofthe excised gel fragment, followed by phenol/chloroform extraction and precipitation with 3.0 M NaOAc and ethanol (24).Control experiments with Fe(EDTA)/H202 were done under conditions identical to those of Fe2(HPTB)(OH)(NO3)4/ Abbreviations:

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confidence: 99%

Double-stranded cleavage of pBR322 by a diiron complex via a "hydrolytic" mechanism.

Hanson

Que

1994

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

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“…35 This strategy coupled to a DNA binding functionality has also been exploited, albeit inefficiently, in the hydrolytic cleavage of doublehelical DNA by Ru(DIPhMacro with Zn 2 +, Cd 2 +, or Pb 2 + added in situ. 36 In this complex (see Figure 8.6), the central portion of the molecule, held together by the ruthenium(II), is responsible for DNA binding. Tethered onto the coordinatively saturated ruthenium complex are two diethylenetriamine functionalities (in the Macro ligand), however, and these serve to coordinate hydrolytically active metal ions such as Zn(II) and Co(II) , which promote DNA hydrolysis once delivered to the sugar-phosphate backbone by the DNA-binding domain.…”

Section: Hydrolytic Chemistrymentioning

confidence: 99%

“…34 (B) Ru(DIPhMacro, a metal complex constructed to contain a central DNA-binding domain (Ru(DIP)32+) with two tethered amine arms to chelate additional metal ions (Zn 2 +) to deliver to the sugar-phosphate backbone and promote hydrolytic strand cleavage. 36 (C) RNA site-specificially hydrolyzed by lead ion. Diagram of the proposed mechanism of sugar-phosphate backbone cleavage between residue D 17 and G I8 in yeast RNA…”

Section: Hydrolytic Chemistrymentioning

confidence: 99%

Metal–nucleic acid interactions

2014

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“…Such agents can be used for a great variety of applications, e.g., for DNA footprinting [2], location of base mismatches and loop regions [3], identification of conformational variations in DNA [4], and as chemotherapeutic agents [5]. It has been reported that the DNA-cleaving ability of metal complexes varies not only from metal to metal [6], but is also influenced by the coordinating groups [7] [8]. Because DNA cleavage with metal complexes is a radical-based process [2] [9] that gives rise to products lacking 3'-or 5'-phosphate groups [10] (not being amenable to further enzymatic manipulation), their use has been limited.…”

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Ternary Zinc(II)-Dipeptide Complexes for the Hydrolytic Cleavage of DNA at Physiological pH

Reddy

Mohan

Rao

2005

C&B

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A series of Zn(II) complexes with cysteinylglycine (CysGly) and histidylserine (HisSer), and of CysGly and histidylphenylalanine (HisPhe) were investigated. Complex stabilities were determined potentiometrically, and binding geometries were probed by means of 1H-NMR spectroscopy, using Co(II) instead of Zn(II) as a spectroscopic marker. The ternary 1:1:1 complexes [Zn(II)(CysGly)(HisSer)] and [Zn(II)(CysGly)(HisPhe)] were shown by UV experiments, fluorescence titration, and gel electrophoresis to intercalate with DNA, and to hydrolytically cleave supercoiled DNA (form-I), partly also circular (form-II) DNA, under physiological conditions (37 degrees, H2O, pH 7.5).

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Metal-activated hydrolytic cleavage of DNA

Cited by 155 publications

References 0 publications

Double-stranded cleavage of pBR322 by a diiron complex via a "hydrolytic" mechanism.

Double-stranded cleavage of pBR322 by a diiron complex via a "hydrolytic" mechanism.

Metal–nucleic acid interactions

Ternary Zinc(II)-Dipeptide Complexes for the Hydrolytic Cleavage of DNA at Physiological pH

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