The Experts below are selected from a list of 132 Experts worldwide ranked by ideXlab platform
Makoto Komiyama - One of the best experts on this subject based on the ideXlab platform.
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artificial restriction dna cutter using Nuclease S1 for site selective scission of genomic dna
Current protocols in human genetics, 2019Co-Authors: Makoto Komiyama, Arivazhagan Rajendran, Narumi Shigi, Jun SumaokaAbstract:: By combining a pair of pseudo-complementary peptide nucleic acids (pcPNAs) with S1 Nuclease, a novel tool to cut DNA at a predetermined site can be obtained. Complementary pcPNAs invade the DNA duplex and base pair to each strand of a target site, creating single-stranded regions that are cleaved by S1 Nuclease. The scission site can be freely modulated by the design of pcPNAs. This method can be used to cleave a single site in the human genome. This protocol presents experimental details for site-selective scission using this versatile new tool. © 2019 by John Wiley & Sons, Inc.
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high throughput snp genotyping by combining exoNuclease iii Nuclease S1 and acridine bearing pna
Nucleic acids symposium series (2004), 2004Co-Authors: Makoto KomiyamaAbstract:: Recently we reported a precise and straightforward method for genotyping of single nucleotide polymorphisms (SNPs) in double-stranded DNA substrates. The substrates were consecutively treated by two enzymes (exoNuclease III and Nuclease S1) in the presence of peptide nucleic acid (PNA) probes, and the resultant DNA fragments were analyzed by mass spectroscopy. Here, the selectivity of DNA scission by Nuclease S1 has been greatly improved by attaching an acridine to the PNA probes. Modification at the C-terminus was especially effective. The number of DNA fragments formed has been greatly decreased so that double-stranded DNA substrates can be genotyped by using the two enzymes still more easily and precisely.
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Straightforward detection of SNPs in double-stranded DNA by using exoNuclease III/Nuclease S1/PNA system.
Nucleic Acids Research, 2004Co-Authors: Jingmin Zhou, Makoto KomiyamaAbstract:Single-nucleotide polymorphisms (SNPs) in double-stranded DNA (dsDNA) have been straightforwardly genotyped by matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry (MALDI-TOF MS). Peptide nucleic acid (PNA), a DNA analog, was used as a probe molecule. In its presence, genomic dsDNA was first treated with exoNuclease III and then with Nuclease S1. By these one-pot reactions, single-stranded DNA fragments including the SNP sites were formed in situ. These fragments were directly analyzed by MALDI-TOF MS, and the identity of the DNA base at the SNP site was determined in terms of mass number. By using two or more PNA probes simultaneously, multiplex analysis was also successful. Various genotypes of apolipoprotein E gene (e2/e2, e3/e3, e4/e4, e2/e3 and e3/e4) were identified from dsDNA obtained by PCR from corresponding patients.
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straightforward detection of snps in double stranded dna by using exoNuclease iii Nuclease S1 pna system
Nucleic Acids Research, 2004Co-Authors: Jingmin Zhou, Makoto KomiyamaAbstract:Single-nucleotide polymorphisms (SNPs) in double-stranded DNA (dsDNA) have been straightforwardly genotyped by matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry (MALDI-TOF MS). Peptide nucleic acid (PNA), a DNA analog, was used as a probe molecule. In its presence, genomic dsDNA was first treated with exoNuclease III and then with Nuclease S1. By these one-pot reactions, single-stranded DNA fragments including the SNP sites were formed in situ. These fragments were directly analyzed by MALDI-TOF MS, and the identity of the DNA base at the SNP site was determined in terms of mass number. By using two or more PNA probes simultaneously, multiplex analysis was also successful. Various genotypes of apolipoprotein E gene (e2/e2, e3/e3, e4/e4, e2/e3 and e3/e4) were identified from dsDNA obtained by PCR from corresponding patients.
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acridine bearing pna for efficient protection of designated site of dna from Nuclease S1
Chemistry Letters, 2003Co-Authors: Sheng Ye, Xingguo Liang, Makoto KomiyamaAbstract:By using peptide nucleic acid (PNA) bearing an acridine at its N-terminus, a predetermined portion of DNA substrate was efficiently protected from Nuclease S1. Promotion of the protecting activity by the acridine is remarkable enough to provide the target DNA fragment in high selectivity and yield.
Peter E Nielsen - One of the best experts on this subject based on the ideXlab platform.
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sequence selective double strand dna cleavage by peptide nucleic acid pna targeting using Nuclease S1
Nucleic Acids Research, 1993Co-Authors: Vadim V Demidov, Maxim D Frankkamenetskii, Michael Egholm, Ole Buchardt, Peter E NielsenAbstract:Abstract A novel method for sequence specific double strand DNA cleavage using PNA (peptide nucleic acid) targeting is described. Nuclease S1 digestion of double stranded DNA gives rise to double strand cleavage at an occupied PNA strand displacement binding site, and under optimized conditions complete cleavage can be obtained. The efficiency of this cleavage is more than 10 fold enhanced when a tandem PNA site is targeted, and additionally enhanced if this site is in trans rather than in cis orientation. Thus in effect, the PNA targeting makes the single strand specific Nuclease S1 behave like a pseudo restriction endoNuclease.
Jingmin Zhou - One of the best experts on this subject based on the ideXlab platform.
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Straightforward detection of SNPs in double-stranded DNA by using exoNuclease III/Nuclease S1/PNA system.
Nucleic Acids Research, 2004Co-Authors: Jingmin Zhou, Makoto KomiyamaAbstract:Single-nucleotide polymorphisms (SNPs) in double-stranded DNA (dsDNA) have been straightforwardly genotyped by matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry (MALDI-TOF MS). Peptide nucleic acid (PNA), a DNA analog, was used as a probe molecule. In its presence, genomic dsDNA was first treated with exoNuclease III and then with Nuclease S1. By these one-pot reactions, single-stranded DNA fragments including the SNP sites were formed in situ. These fragments were directly analyzed by MALDI-TOF MS, and the identity of the DNA base at the SNP site was determined in terms of mass number. By using two or more PNA probes simultaneously, multiplex analysis was also successful. Various genotypes of apolipoprotein E gene (e2/e2, e3/e3, e4/e4, e2/e3 and e3/e4) were identified from dsDNA obtained by PCR from corresponding patients.
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straightforward detection of snps in double stranded dna by using exoNuclease iii Nuclease S1 pna system
Nucleic Acids Research, 2004Co-Authors: Jingmin Zhou, Makoto KomiyamaAbstract:Single-nucleotide polymorphisms (SNPs) in double-stranded DNA (dsDNA) have been straightforwardly genotyped by matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry (MALDI-TOF MS). Peptide nucleic acid (PNA), a DNA analog, was used as a probe molecule. In its presence, genomic dsDNA was first treated with exoNuclease III and then with Nuclease S1. By these one-pot reactions, single-stranded DNA fragments including the SNP sites were formed in situ. These fragments were directly analyzed by MALDI-TOF MS, and the identity of the DNA base at the SNP site was determined in terms of mass number. By using two or more PNA probes simultaneously, multiplex analysis was also successful. Various genotypes of apolipoprotein E gene (e2/e2, e3/e3, e4/e4, e2/e3 and e3/e4) were identified from dsDNA obtained by PCR from corresponding patients.
Fumio Sakiyama - One of the best experts on this subject based on the ideXlab platform.
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amino acid sequence of Nuclease S1 from aspergillus oryzae
Journal of Biochemistry, 1991Co-Authors: Akihiro Iwamatsu, Hideyuki Aoyama, Gabor Dibo, Susumu Tsunasawa, Fumio SakiyamaAbstract:: The amino acid sequence of Nuclease S1, a Nuclease which cleaves both single-stranded DNA and RNA, from Aspergillus oryzae was determined. Reduced and S-carboxymethylated or S-aminoethylated Nuclease S1 was digested with Achromobacter protease I, Staphylococcus aureus V8 protease, or endoproteinase Asp-N. Peptides thus obtained were purified by reverse-phase high-performance liquid chromatography and sequenced, and the complete primary structure was established. Nuclease S1 consists of a single peptide chain of 267 amino acid residues bearing N-glycosylated Asns 92 and 228. Five half-cystine residues are present at positions 25, 72, 80, 85, and 216, and the latter four residues are implicated in the formation of disulfide bonds by analogy with those in Nuclease P1. Two short stretches of sequences involving His 60 and His 125 are shown to be identical with those involving active site His 119 in bovine riboNuclease A and active-site His 134 in porcine deoxyriboNuclease I, respectively.
Vadim V Demidov - One of the best experts on this subject based on the ideXlab platform.
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sequence selective double strand dna cleavage by peptide nucleic acid pna targeting using Nuclease S1
Nucleic Acids Research, 1993Co-Authors: Vadim V Demidov, Maxim D Frankkamenetskii, Michael Egholm, Ole Buchardt, Peter E NielsenAbstract:Abstract A novel method for sequence specific double strand DNA cleavage using PNA (peptide nucleic acid) targeting is described. Nuclease S1 digestion of double stranded DNA gives rise to double strand cleavage at an occupied PNA strand displacement binding site, and under optimized conditions complete cleavage can be obtained. The efficiency of this cleavage is more than 10 fold enhanced when a tandem PNA site is targeted, and additionally enhanced if this site is in trans rather than in cis orientation. Thus in effect, the PNA targeting makes the single strand specific Nuclease S1 behave like a pseudo restriction endoNuclease.
