Nucleic acids research. Supplement (2001)最新文献

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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
Synthesis of 3'-fluoro analogue of Cl-IB-MECA as adenosine A3 receptor ligand. Cl-IB-MECA 3'-氟类似物作为腺苷A3受体配体的合成。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.19
Moon Woo Chun, Moo Hong Lim, Hyung Ryong Moon, Hea Ok Kim, Kenneth A Jacobson, Lak Shin Jeong
{"title":"Synthesis of 3'-fluoro analogue of Cl-IB-MECA as adenosine A3 receptor ligand.","authors":"Moon Woo Chun, Moo Hong Lim, Hyung Ryong Moon, Hea Ok Kim, Kenneth A Jacobson, Lak Shin Jeong","doi":"10.1093/nass/3.1.19","DOIUrl":"10.1093/nass/3.1.19","url":null,"abstract":"<p><p>3'-Fluoro analogue 1 of selective and potent adenosine A3 receptor agonist, Cl-IB-MECA was synthesized from D-xylose via highly regioselective opening of lyxo-epoxide 4 with fluoride anion. Compared to the high binding affinity of Cl-IB-MECA to the A3 adenosine receptor, the corresponding 3'-fluoro derivative showed remarkably decreased binding affinity, indicating that 3'-hydroxyl group acts as hydrogen bonding donor, not hydrogen bonding acceptor like fluorine atom in binding to the A3 adenosine receptor.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"19-20"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40824176","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
A new synthetic approach to cyclic bis(3'-->5')diguanylic acid. 环双胍酸(3′->5′)的新合成方法。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.103
Rie Kawai, Reiko Nagata, Akiyoshi Hirata, Yoshihiro Hayakawa
{"title":"A new synthetic approach to cyclic bis(3'-->5')diguanylic acid.","authors":"Rie Kawai,&nbsp;Reiko Nagata,&nbsp;Akiyoshi Hirata,&nbsp;Yoshihiro Hayakawa","doi":"10.1093/nass/3.1.103","DOIUrl":"https://doi.org/10.1093/nass/3.1.103","url":null,"abstract":"<p><p>We developed a novel synthesis of biologically important cyclic bis(3'-->5')diguanylic acid (cGpGp). The present synthesis includes two strategies different from those employed in an existing synthesis. They are the phosphoramidite method for the preparation of a guanylyl(3'-->5')guanylic acid intermediate and allyl protection for guanine bases and internucleotide linkages. These distinctive strategies have allowed the new synthesis to provide the target compound in a higher yield than that of the existing synthesis.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"103-4"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.103","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825073","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
trans-3',4'-BNAs, novel nucleic acid analogues with an S-type conformation: synthesis and incorporation into oligonucleotides. 反式3′,4′-BNAs,具有s型构象的新型核酸类似物:合成和整合到寡核苷酸中。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.111
Mitsuaki Sekiguchi, Tomohisa Osaki, Yasuki Harada, Satoshi Obika, Takeshi Imanishi
{"title":"trans-3',4'-BNAs, novel nucleic acid analogues with an S-type conformation: synthesis and incorporation into oligonucleotides.","authors":"Mitsuaki Sekiguchi,&nbsp;Tomohisa Osaki,&nbsp;Yasuki Harada,&nbsp;Satoshi Obika,&nbsp;Takeshi Imanishi","doi":"10.1093/nass/3.1.111","DOIUrl":"https://doi.org/10.1093/nass/3.1.111","url":null,"abstract":"<p><p>We designed and successfully synthesized novel nucleic acid analogues with a C3'-C4' trans-fused six-membered ring, trans-3',4'-BNAs from D-glucose. A 1H-NMR experiment and X-ray crystallographic analysis demonstrated that the sugar puckering of trans-3',4'-BNA was restricted in an S-type conformation. We also achieved its incorporation into oligonucleotides using automated DNA synthesizer.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"111-2"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.111","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825077","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: 2
Design and evaluation of novel nucleoside analogs (WNA) for specific formation of non-natural type triplexes containing a TA or CG interrupting site. 新型核苷类似物(WNA)的设计和评价,用于含有TA或CG中断位点的非天然型三联体的特定形成。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.113
Yosuke Taniguchi, Yusuke Senko, Kelichi Kodama, Ayako Nakamura, Shigeki Sasaki
{"title":"Design and evaluation of novel nucleoside analogs (WNA) for specific formation of non-natural type triplexes containing a TA or CG interrupting site.","authors":"Yosuke Taniguchi,&nbsp;Yusuke Senko,&nbsp;Kelichi Kodama,&nbsp;Ayako Nakamura,&nbsp;Shigeki Sasaki","doi":"10.1093/nass/3.1.113","DOIUrl":"https://doi.org/10.1093/nass/3.1.113","url":null,"abstract":"<p><p>In a search of suitable recognition molecules for the formation of stable non-natural triplex DNA, we have developed the new nucleoside analogs (WNA, W-shape nucleoside analog) bearing an aromatic ring, a recognition base and a bicyclic skeleton to hold them. A successful result with WNA-betaT that recognizes a TA base pair selectively has suggested that the basic structure of the WNA is useful as a scaffold for search of other candidates for the formation of triplex containing a TA or a CG interrupting site. In this study, we have synthesized and investigated binding property of a variety of WNA candidates. As a result, we have determined new potential analog, WNA-betaC for a CG interrupting site. It should be noted that the triplexes containing a WNA-betaT:TA or a WNA-betaC:CG base triplet have exhibited higher stability than the natural anti-parallel triplexes constructed of A:AT and G:GC triplets. The results that H-WNA-betaT lacking a benzene ring did not show stabilization effect to any base pairs have clearly indicated that a benzene ring plays a key role in stability of triplexes.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"113-4"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.113","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825078","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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