Recent Studies of Nucleophilic, General-Acid, and Metal Ion Catalysis of Phosphate Diester Hydrolysis

Blaskó, Andrei; Bruice, Thomas C.

doi:10.1021/ar980060y

Cited by 136 publications

(71 citation statements)

References 32 publications

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“…In fact, interaction of the substrate with two electrophilic metal centers favors the nucleophilic attack of a Zn-OH function and thus enhances the rate of the hydrolytic process, as already found in several dinuclear synthetic Zn(II) complexes [33][34][35][36][37][38][39][40][41][42][43][44][45][46][47][48][49][50]. As discussed above, in the dinuclear L2 complexes the two metals can attain a short intermetallic distance, favoring a bridging interaction mode of the phosphate ester.…”

Section: Conversely the Monohydroxo Complex [Zn 2 L2(oh)]mentioning

confidence: 74%

“…BNPP hydrolysis promoted by mono-and dinuclear Zn(II) complexes is generally explained in terms of an "associative" mechanism [33][34][35][36][37][38][39][40][41][42][43][44][45][46][47][48][49][50]71], in which the substrate approaches the Zn(II) complex and the oxygens of BNPP start associating with the electrophilic Zn(II) ion. A zincbound hydroxide operates a simultaneous nucleophilic attack to the phosphorus atom.…”

Section: Bis(p-nitrophenyl)phosphate Hydrolysismentioning

confidence: 99%

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Zn(II) Coordination by Open-chain Polyamine Ligands Containing Dipyridine Units. Highly Active Dinuclear Zn(II) Complexes in Phosphate Ester Hydrolysis

Bazzicalupi¹,

Bencini

Danesi³

et al. 2008

TOICJ

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Abstract:The synthesis and characterization of two new open-chain ligands, L1 and L2, containing two 2,2'-dipyridine units connected respectively by a pentaethylenhexamine and a pentapropylenhexamine chain, is reported. Zn(II) complexation has been studied by means of potentiometric and UV-vis spectrophotometric measurements in aqueous solution. Both ligands form stable mono-and dinuclear complexes, the metal ions being coordinated by a single dipyridine unit and by the adjacent amine groups. The ability of the binuclear Zn(II) complexes as nucleophilic agents in hydrolytic processes has been tested by using bis(p-nitrophenyl) phosphate (BNPP) as substrate. Both complexes display high rate enhancements in BNPP cleavage in aqueous solution. The study outlines that different mechanisms are operative in BNPP cleavage in the presence of the L1 and L2 complexes.

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Section: Conversely the Monohydroxo Complex [Zn 2 L2(oh)]mentioning

confidence: 74%

Section: Bis(p-nitrophenyl)phosphate Hydrolysismentioning

confidence: 99%

Zn(II) Coordination by Open-chain Polyamine Ligands Containing Dipyridine Units. Highly Active Dinuclear Zn(II) Complexes in Phosphate Ester Hydrolysis

Bazzicalupi¹,

Bencini

Danesi³

et al. 2008

TOICJ

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“…On this basis, chemists, biochemists and biologists have long attempted to rewrite the information encoded within DNA using various approaches. One direct and straightforward approach to precisely alter the information contained by DNA is the site-selective scission of DNA at a target site, [1][2][3][4][5][6][7][8][9][10][11] followed by the appropriate manipulation of the DNA at this local site.…”

Section: Introductionmentioning

confidence: 99%

Artificial site-selective DNA cutters to manipulate single-stranded DNA

Aiba

Komiyama

2012

Polym J

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Recent progress regarding the development of artificial site-selective DNA cutters by chemical approaches are reviewed herein, with a special focus on site-selective cutters for single-stranded DNA. We employ a Ce(IV)/EDTA complex to serve as the catalyst, because it efficiently and selectively cuts single-stranded DNA. Using two complementary oligonucleotide additives, a gap structure is formed at the target site in the single-stranded DNA substrate. Owing to the substrate specificity of Ce(IV)/ EDTA, the gap site is preferentially hydrolyzed, resulting in a site-selective DNA scission. The scission site is easily determined using the Watson-Crick base-pairing rule; thus, both the sequence and scission specificity can be tuned according to demand. The site-selective scission is greatly promoted by attaching a multiphosphonate to the termini of the oligonucleotide additives and placing this ligand at the gap site. The scission fragments can be connected with foreign DNA using ligase, and the recombinant DNA expresses the corresponding protein in E. coli. INTRODUCTIONThe role of DNA in storing and carrying genetic information is essential for the function and development of all living organisms. If the information stored within DNA can be rewritten by scientists, numerous applications in a variety of fields will be possible. On this basis, chemists, biochemists and biologists have long attempted to rewrite the information encoded within DNA using various approaches. One direct and straightforward approach to precisely alter the information contained by DNA is the site-selective scission of DNA at a target site, 1-11 followed by the appropriate manipulation of the DNA at this local site.Currently, in molecular biology, DNA is manipulated by the 'cut-and-paste' method. In this approach, DNA is first cut at a predetermined site by naturally occurring restriction enzymes, and the resultant fragment is connected with another DNA fragment using ligases. Here, the target gene is inserted, deleted or altered. This strategy is satisfactorily effective so long as small DNAs such as plasmids (composed of several thousand base pairs) are targeted. Unfortunately, this technology is insufficient for manipulating large DNAs; however, our interests have been gradually focusing on the manipulation of genomic DNAs of higher organisms. The key problem is the low site specificity of naturally occurring restriction enzymes (most of them recognize 4 to 8-bp DNA sequences). Statistically, the scission site of a restriction enzyme with 6-bp

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“…For these reasons, a powerful tool for the manipulation of large DNA has been strongly desired. [1][2][3][4][5][6][7][8] Recently, we have developed artificial restriction DNA cutter (ARCUT) for site-specific hydrolysis of double-stranded DNA. [9][10][11][12] This new tool is composed of Ce(IV)/EDTA complex, which selectively hydrolyzes single-stranded portion in double-stranded DNA, and a pair of pseudo-complementary peptide nucleic acid (pcPNA).…”

Section: Introductionmentioning

confidence: 99%

Site-specific gene cassette insertion by combining artificial restriction DNA cutter and single-stranded DNA specific endonuclease

Katada¹,

Shigi²,

Komiyama³

2008

Arkivoc

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An artificial restriction DNA cutter (ARCUT), which was composed of Ce(IV)/EDTA complex and a pair of pseudo-complementary peptide nucleic acid, was used for construction of recombinant plasmid vector. The plasmid vector was cut by ARCUT only at target site, and resultant specific overhangs were blunted by treatment with Mung Bean Nuclease and Klenow fragment. This fragment having blunt ends at both termini was ligated with the gene of enhanced green fluorescent protein (EGFP) prepared by PCR. The resultant recombinant vector was translated and the fluorescent protein was successfully expressed in cells. Throughout the manipulation, neither natural restriction enzymes nor homologous recombination was employed. Thus, this strategy has promising applicability to construction of still larger vectors.

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Recent Studies of Nucleophilic, General-Acid, and Metal Ion Catalysis of Phosphate Diester Hydrolysis

Cited by 136 publications

References 32 publications

Zn(II) Coordination by Open-chain Polyamine Ligands Containing Dipyridine Units. Highly Active Dinuclear Zn(II) Complexes in Phosphate Ester Hydrolysis

Zn(II) Coordination by Open-chain Polyamine Ligands Containing Dipyridine Units. Highly Active Dinuclear Zn(II) Complexes in Phosphate Ester Hydrolysis

Artificial site-selective DNA cutters to manipulate single-stranded DNA

Site-specific gene cassette insertion by combining artificial restriction DNA cutter and single-stranded DNA specific endonuclease

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