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Nucleic acids research. Supplement (2001)最新文献

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Utilization efficiency of the oxidized purine nucleotide analogs by DNA polymerase eta. DNA聚合酶对氧化嘌呤核苷酸类似物的利用效率。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.299
Naomi Nishimoto, Hiroyuki Kamiya, Hideyoshi Harashima, Shunji Izuta
{"title":"Utilization efficiency of the oxidized purine nucleotide analogs by DNA polymerase eta.","authors":"Naomi Nishimoto,&nbsp;Hiroyuki Kamiya,&nbsp;Hideyoshi Harashima,&nbsp;Shunji Izuta","doi":"10.1093/nass/3.1.299","DOIUrl":"https://doi.org/10.1093/nass/3.1.299","url":null,"abstract":"<p><p>To elucidate the behavior of DNA polymerase eta against the oxidized purine nucleotides, we determined the utilization efficiency of 2-hydroxy-dATP and 8-hydroxy-dGTP by the recombinant yeast DNA polymerase eta using the primer extension assay with the synthetic oligonucleotide template-primers, and compared those by DNA polymerase alpha. Results indicate that DNA polymerase eta incorporates 2-hydroxy-dATP opposite template G in addition to template T and 8-hydroxy-dGTP opposite A in addition to C, respectively. Kinetic analysis revealed that the rate of mutation caused by 2-OH-dATP and 8-OH-dGTP with DNA polymerase eta should be much higher than those with DNA polymerase alpha.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"299-300"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.299","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A novel approach of cell-free peptide synthesis and SNPs detection using nano-circular single-stranded DNA. 一种利用纳米环状单链DNA进行无细胞肽合成和snp检测的新方法。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.311
Tatsuo Ohmichi, Aki Takashima, Naoki Sugimoto
{"title":"A novel approach of cell-free peptide synthesis and SNPs detection using nano-circular single-stranded DNA.","authors":"Tatsuo Ohmichi,&nbsp;Aki Takashima,&nbsp;Naoki Sugimoto","doi":"10.1093/nass/3.1.311","DOIUrl":"https://doi.org/10.1093/nass/3.1.311","url":null,"abstract":"<p><p>Development of peptide/protein synthesis is very important for investigating the functions of peptides and proteins. The advantages of cell-free synthesis, which has been extensively developed, include the ability to synthesize toxic proteins, aggregated proteins and proteins containing unnatural amino acids. However, this promising approach does not have a high reaction yield. In this study, we examine whether the rolling synchronization system, which produces long RNAs with a repeated sequence encoded by very small circular ssDNAs without the promoter sequence for RNA polymerase, can be used for cell-free peptide synthesis to improve the reaction yield. As a result, we have found that rolling synchronization is useful for large-scale cell-free peptide/protein synthesis.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"311-2"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.311","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Directed evolution of xylanase J from alkaliphilic Bacillus sp. strain 41M-1: restore of alkaliphily of a mutant with an acidic pH optimum. 嗜碱芽孢杆菌菌株41M-1木聚糖酶J的定向进化:最适酸性条件下突变体嗜碱性的恢复
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.315
Mayuko Inami, Chihiro Morokuma, Akiko Sugio, Hidenori Tamanoi, Rie Yatsunami, Satoshi Nakamura
{"title":"Directed evolution of xylanase J from alkaliphilic Bacillus sp. strain 41M-1: restore of alkaliphily of a mutant with an acidic pH optimum.","authors":"Mayuko Inami,&nbsp;Chihiro Morokuma,&nbsp;Akiko Sugio,&nbsp;Hidenori Tamanoi,&nbsp;Rie Yatsunami,&nbsp;Satoshi Nakamura","doi":"10.1093/nass/3.1.315","DOIUrl":"https://doi.org/10.1093/nass/3.1.315","url":null,"abstract":"<p><p>Alkaliphilic Bacillus sp. strain 41M-1 produces an alkaliphilic xylanase (xylanase J). The newly constructed mutant E177Q deltaJC had an acidic pH optimum and showed almost no activity at pH 8.0. The alkaliphily of the enzyme was restored by directed evolution. The evolved mutants, Y176S/E177Q deltaJC and G32V/Y176D/E177Q deltaJC, retained about 30% and 43% activity of their maximal activities at pH 6.0, respectively.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"315-6"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.315","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 14
Palladium-catalyzed H-D exchange into nucleic acids in deuterium oxide. 钯催化H-D在氧化氘中交换成核酸。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.55
Hironao Sajiki, Fumiyo Aoki, Hiroyoshi Esaki, Tomohiro Maegawa, Kosaku Hirota
{"title":"Palladium-catalyzed H-D exchange into nucleic acids in deuterium oxide.","authors":"Hironao Sajiki,&nbsp;Fumiyo Aoki,&nbsp;Hiroyoshi Esaki,&nbsp;Tomohiro Maegawa,&nbsp;Kosaku Hirota","doi":"10.1093/nass/3.1.55","DOIUrl":"https://doi.org/10.1093/nass/3.1.55","url":null,"abstract":"<p><p>We have developed an efficient and extensive deuterium incorporation method using a heterogeneous Pd/C-D2O-H2 system into the base moiety of nucleic acids. The results presented here provide a deuterium gas-free, totally catalytic and post-synthetic deuterium labeling method in D2O media.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"55-6"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.55","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Extracellular DNA and RNA produced by a marine photosynthetic bacterium Rhodovulum sulfidophilum. 一种海洋光合细菌硫红Rhodovulum sulfidophilum产生的细胞外DNA和RNA。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.279
Seiichiro Nishimura, Terumichi Tanaka, Kyoko Fujita, Mitsuhiro Itaya, Akira Hiraishi, Yo Kikuchi
{"title":"Extracellular DNA and RNA produced by a marine photosynthetic bacterium Rhodovulum sulfidophilum.","authors":"Seiichiro Nishimura,&nbsp;Terumichi Tanaka,&nbsp;Kyoko Fujita,&nbsp;Mitsuhiro Itaya,&nbsp;Akira Hiraishi,&nbsp;Yo Kikuchi","doi":"10.1093/nass/3.1.279","DOIUrl":"https://doi.org/10.1093/nass/3.1.279","url":null,"abstract":"<p><p>A marine photosynthetic bacterium Rhodovulum sulfidophilum secretes nucleic acids that are involved in flocculating ability. These extracellular nucleic acids have not been well characterized. Here, we have analyzed these nucleic acids and revealed that the extracellular nucleic acids are a mixture of double-stranded DNAs and single-stranded RNAs. The DNAs have sizes of more than 30 kbp and at least a part of these DNAs is probably an amplified portion of genomic DNA. The RNAs seems to be tRNA like molecules from size estimation.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"279-80"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.279","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 16
Synthesis and properties of oligodeoxyribonucleotides containing the new base pairs, Im-N(O):Na-O(N) and Im-O(N):Na-N(O), with the ability to form four hydrogen bonds. 含有新碱基对Im-N(O):Na-O(N)和Im-O(N):Na-N(O)，并能形成四个氢键的寡脱氧核糖核苷酸的合成与性质
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.35
Sadao Hikishima, Yuki Fujisawa, Maki Ogawa, Noriaki Minakawa, Akira Matsuda
{"title":"Synthesis and properties of oligodeoxyribonucleotides containing the new base pairs, Im-N(O):Na-O(N) and Im-O(N):Na-N(O), with the ability to form four hydrogen bonds.","authors":"Sadao Hikishima,&nbsp;Yuki Fujisawa,&nbsp;Maki Ogawa,&nbsp;Noriaki Minakawa,&nbsp;Akira Matsuda","doi":"10.1093/nass/3.1.35","DOIUrl":"https://doi.org/10.1093/nass/3.1.35","url":null,"abstract":"<p><p>Previously, we synthesized oligodeoxyribonucleotides (ODNs) containing novel base pairing motif consisting of tricyclic nucleosides, Im-N(O) and Im-O(N), with the ability to form four hydrogen bonds (H-bonds). When the base pair, Im-N(O):Im-O(N) pair, was incorporated into the duplex, thermal stability of the duplex depended on the sequence context. In this time, on the basis of previous results, we designed two new bicyclic nucleosides, Na-N(O) and Na-O(N) as complementary nucleobase of the tricyclic nucleobases. These nucleosides were synthesized via a Pd-mediated cross coupling reaction as a key step. When the new Im-O(N):Na-N(O) pair was incorporated into the duplex, it was remarkably stabilized independent of the sequence context.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"35-6"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.35","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40903178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Highly selective binding of metal ions to thymine-thymine and cytosine-cytosine base pairs in DNA duplexes. 金属离子与DNA双链中胸腺嘧啶-胸腺嘧啶和胞嘧啶-胞嘧啶碱基对的高度选择性结合。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.227
Akira Ono, Yoko Miyake
{"title":"Highly selective binding of metal ions to thymine-thymine and cytosine-cytosine base pairs in DNA duplexes.","authors":"Akira Ono,&nbsp;Yoko Miyake","doi":"10.1093/nass/3.1.227","DOIUrl":"https://doi.org/10.1093/nass/3.1.227","url":null,"abstract":"<p><p>Very specific binding of of Hg(II) and Ag(I) cations unexpectedly and significantly stabilizes the naturally occurring miss-base pairs, thymine-thymine and cytosine-cytosine, in DNA duplexes.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"227-8"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.227","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40824275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Optimization of an ATP-binding ribonucleopeptide receptor. atp结合核糖核肽受体的优化。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.239
Shin-ichi Sato, Tetsuya Hasegawa, Masaki Hagihara, Masatora Fukuda, Katsutoshi Ohkubo, Takashi Morii
{"title":"Optimization of an ATP-binding ribonucleopeptide receptor.","authors":"Shin-ichi Sato,&nbsp;Tetsuya Hasegawa,&nbsp;Masaki Hagihara,&nbsp;Masatora Fukuda,&nbsp;Katsutoshi Ohkubo,&nbsp;Takashi Morii","doi":"10.1093/nass/3.1.239","DOIUrl":"https://doi.org/10.1093/nass/3.1.239","url":null,"abstract":"<p><p>We describe here a new strategy for the selection and evolution of functional RNA-peptide complexes. An ATP-binding ribonucleopeptide was obtained by means of a structure-based design of ribonucleopeptide domain and by in vitro selection of the RNA subunit of the ribonucleopeptide. Approaches to optimize the ligand-binding selectivity of ribonucleopeptide will be discussed.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"239-40"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.239","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40824281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Helix formation of oligodeoxyribonucleotides containing base-aromatic ring conjugates. 含有碱基-芳香环共轭物的寡脱氧核糖核苷酸的螺旋形成。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.77
Mio Kubota, Momo Kosuge, Akira Ono
{"title":"Helix formation of oligodeoxyribonucleotides containing base-aromatic ring conjugates.","authors":"Mio Kubota,&nbsp;Momo Kosuge,&nbsp;Akira Ono","doi":"10.1093/nass/3.1.77","DOIUrl":"https://doi.org/10.1093/nass/3.1.77","url":null,"abstract":"<p><p>Novel nucleoside analogues with base moieties containing pyrene groups have been synthesized and incorporated into oligodeoxyribonucleotides (ODNs). ODNs containing tandem pyrene residues at the 5'-end gave fluorescence spectra characteristic of eximers that were diminished by duplex formation of the ODNs with complementary strands.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"77-8"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.77","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40824644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Photo-induced DNA cleavage reaction characteristics of propargylic sulfones possessing an anthraquinone chromophore. 具有蒽醌发色团的丙炔砜的光诱导DNA裂解反应特性。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.81
Ken-ichi Haruna, Atsushi Ishii, Kazuhito Tanabe, Wei-Min Dai, Hiroshi Hatta, Sei-ichi Nishimoto
{"title":"Photo-induced DNA cleavage reaction characteristics of propargylic sulfones possessing an anthraquinone chromophore.","authors":"Ken-ichi Haruna,&nbsp;Atsushi Ishii,&nbsp;Kazuhito Tanabe,&nbsp;Wei-Min Dai,&nbsp;Hiroshi Hatta,&nbsp;Sei-ichi Nishimoto","doi":"10.1093/nass/3.1.81","DOIUrl":"https://doi.org/10.1093/nass/3.1.81","url":null,"abstract":"<p><p>Propargylic sulfones (PS) are known as pH dependent DNA cleaver. DNA cleavage by PS was considered to proceed by alkylation of G base to allenic sulfones formed from PS in basic condition. We designed PS posessing naphthalene and anthraquinone (AQ) unit and investigated DNA cleavage characteristics. Although these compounds showed high intercalating abilities, this high intercalating ability did not lead to DNA cleaving activity. This result indicates that spatial arrangement of activated allene against guanine base is very important in DNA cleavage by PS. In addition, UV-irradiation to PS possessing AQ unit leads to efficient DNA cleavage at 5'-G of GG sequence. This cleavage pattern exhibited typical cleavage of one-electron oxidation of B-form DNA. Therefore, this result suggests that PS possessing AQ unit cleave DNA by both the alkylation mechanism and the photooxidaization mechanism.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"81-2"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.81","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40824646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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