Extended x-ray absorption fine structure study on the cerium(IV)-induced DNA hydrolysis: Implication to the roles of 4f orbitals in the catalysis

Shigekawa, Hidemi; Ishida, Masahiko; Miyake, Koji; Shioda, R.; Iijima, Yoshitoki; Imai, Takamitsu; Takahashi, Hideyuki; Sumaoka, Jun; Komiyama, Makoto

doi:10.1063/1.123036

Cited by 29 publications

(28 citation statements)

References 10 publications

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“…In order to quantify further and evaluate any role of the 4f orbitals of Ce(IV) in substantial rate enhancements, Komiyama's group [67,68] has carried out elegant core-level photoelectron spectroscopy, EXAFS, and XANES experiments using diphenyl phosphate as the substrate. The electron withdrawal by the metal ions from the phosphodiester linkage (and thus away from the P-O bond) is observed as an increase in the binding energy.…”

Section: Mechanistic Aspects Of Dna Cleavagementioning

confidence: 99%

Catalytic hydrolysis of DNA by metal ions and complexes

Sreedhara

Cowan

2001

J. Biol. Inorg. Chem.

256

148

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Biomimetic hydrolysis of DNA or RNA is of increasing importance in biotechnology and medicine. Most natural nuclease enzymes that mediate such reactions utilize metal ion cofactors. Recent progress in the design of synthetic metallonucleases has included complexes of antibiotics, peptides, nucleic acids, and other organic ligands. In this article, we review a number of synthetic catalyst systems that have been developed to achieve efficient DNA hydrolysis. Methods to evaluate their catalytic efficiencies are critically discussed, and a prognosis for future work in this area is presented.

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Section: Mechanistic Aspects Of Dna Cleavagementioning

confidence: 99%

Catalytic hydrolysis of DNA by metal ions and complexes

Sreedhara

Cowan

2001

J. Biol. Inorg. Chem.

256

148

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“…The distance between the two Ce(IV) atoms is 3.848 Å. This value is fairly in accord with the Ce-Ce distance (3.6 Å) in the 2:1 Ce(IV) complex of diphenyl phosphate, which was evaluated by EXAFS study [21]. …”

Section: Quantum-chemical Studies On the Catalytically Active [Ce IV mentioning

confidence: 94%

Artificial Restriction DNA Cutters (ARCUT) for Future Biotechnology.

Sumaoka¹,

Yamamoto

Kitamura

et al. 2007

COC

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Recent chemical approaches towards artificial restriction DNA cutters (ARCUT) are reviewed. New tools to cut either single-stranded DNA or double-stranded DNA at predetermined sites have been prepared. As molecular scissors, these cutters employ Ce(IV)/EDTA complex that preferentially hydrolyzes single-stranded DNA over double-stranded DNA. Hot-spots for site-selective scission are prepared at predetermined site with the use of appropriate DNA or peptide nucleic acid (PNA) additives. Thus, gap-structures are formed in single-stranded DNA using two oligonucleotide additives, whereas invasion of a pair of PNAs is used for the scission of double-stranded DNA. These single-stranded portions are hydrolyzed by Ce(IV)/EDTA, resulting in the site-selective scission. The DNA scission proceeds totally via hydrolysis of phosphodiester linkages. Both linear DNA and supercoiled DNA are selectively cut at the target site by these restriction DNA cutters, and the fragments are efficiently combined with foreign DNA by using ligase. The recombinant DNA is successfully expressed in cells and produces the target protein (e.g., green fluorescent protein and other fusion proteins). No undesired side-reactions concurrently take place during the DNA manipulation. The length and the sequence of the recognition sites of these man-made DNA cutters are freely chosen, and thus, in principle, even huge DNA of higher animals and higher plants can be selectively cut and manipulated.

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“…7 This conclusion was further supported by physicochemical analyses such as extended X-ray absorption fine structure study and core level photoelectron spectroscopy. 10,11 The DNA hydrolysis was accompanied by a notable…”

Section: Significance Of Site-selective Scission Of Dnamentioning

confidence: 99%

Design and Applications of Artificial Restriction DNA Cutters for Site-Selective Scission of Genomes

Komiyama

Sumaoka

2012

Bulletin of the Chemical Society of Japan

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By combining Ce(IV)/EDTA complex and pseudo-complementary peptide nucleic acid (pcPNA), an artificial restriction DNA cutter which hydrolyzes targeted phosphodiester linkages in double-stranded DNA has been developed. The targeted site in the DNA is activated by two strands of pcPNA and selectively hydrolyzed by the Ce(IV) complex. The DNA cutter required for aimed manipulation can be straightforwardly designed and obtained in terms of (i) the sequence of targeted selective scission, (ii) size of DNA substrate, and (iii) magnitude of desired site-specificity. The sitespecificity can be high enough to cut the whole genome of human beings (3 © 10 9 base-pairs) at one predetermined site. Off-target scissions at the sites of analogous sequences hardly take place. With the use of this specificity, targeted gene can be engineered in human cells through homologous recombination. Other potential applications of this cutter, as well as recent attempts to improve its activity and specificity, are also discussed. Significance of Site-Selective Scission of DNASite-selective scission of DNA is a key step in biotechnology and molecular biology. For a long time, target DNA for our manipulation has been restricted to small DNA such as plasmids which are composed of 30005000 base-pairs (bp). In order to cut them at a desired site, naturally occurring restriction enzymes, which recognize 4-or 6-bp sequence, have been used. The resultant scission fragments are combined with other fragments with the use of another enzyme ligase. With outstanding developments in relevant fields, however, target DNA of our manipulation is gradually shifting from plasmids to genomes which are directly responsible for the memory of genetic information. Unfortunately, the site-specificity of naturally occurring restriction enzymes is too low to manipulate genomes which are by several orders of magnitude larger than plasmids. For example, human genome is composed of 3 © 10 9 bp. If this DNA of enormous size is treated with a restriction enzyme recognizing a 6-bp sequence, the scission occurs at too many sites (statistically, the scission site of this enzyme should appear at every 4 6 (= 4096) bp, and the number of scission sites in this genome should be larger than half million). Precise manipulation is impossible under these conditions. In order to cut genomes selectively at a desired site, we apparently need artificial cutters which recognize a longer sequence. If one should like to cut human genomes at one site and manipulate them precisely, the length of recognition site of the cutter should be at least 16 bp (note that 4 16 > 3 © 10 9). The importance of these artificial DNA cutters having higher and tunable site-specificity has been widely recognized for a long time, and many researchers have devoted efforts to this subject.1 As a result, remarkable progress has already been accomplished, especially in the design of non-protein molecules which selectively bind to target site in doublestranded DNA. Peptide nucleic acids (PNAs) developed by Nielsen 2...

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Extended x-ray absorption fine structure study on the cerium(IV)-induced DNA hydrolysis: Implication to the roles of 4f orbitals in the catalysis

Abstract: Extended X-ray absorption fine structure spectroscopy of selenium-hyperdoped silicon

Cited by 29 publications

References 10 publications

Catalytic hydrolysis of DNA by metal ions and complexes

Catalytic hydrolysis of DNA by metal ions and complexes

Artificial Restriction DNA Cutters (ARCUT) for Future Biotechnology.

Design and Applications of Artificial Restriction DNA Cutters for Site-Selective Scission of Genomes

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