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Molecular design of sequence specific DNA alkylating agents. 序列特异性DNA烷基化剂的分子设计。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp035
Masafumi Minoshima, Toshikazu Bando, Ken-ichi Shinohara, Hiroshi Sugiyama
{"title":"Molecular design of sequence specific DNA alkylating agents.","authors":"Masafumi Minoshima,&nbsp;Toshikazu Bando,&nbsp;Ken-ichi Shinohara,&nbsp;Hiroshi Sugiyama","doi":"10.1093/nass/nrp035","DOIUrl":"https://doi.org/10.1093/nass/nrp035","url":null,"abstract":"<p><p>Sequence-specific DNA alkylating agents have great interest for novel approach to cancer chemotherapy. We designed the conjugates between pyrrole (Py)-imidazole (Im) polyamides and DNA alkylating chlorambucil moiety possessing at different positions. The sequence-specific DNA alkylation by conjugates was investigated by using high-resolution denaturing polyacrylamide gel electrophoresis (PAGE). The results showed that polyamide chlorambucil conjugates alkylate DNA at flanking adenines in recognition sequences of Py-Im polyamides, however, the reactivities and alkylation sites were influenced by the positions of conjugation. In addition, we synthesized conjugate between Py-Im polyamide and another alkylating agent, 1-(chloromethyl)-5-hydroxy-1,2-dihydro-3H-benz[e]indole (seco-CBI). DNA alkylation reactivies by both alkylating polyamides were almost comparable. In contrast, cytotoxicities against cell lines differed greatly. These comparative studies would promote development of appropriate sequence-specific DNA alkylating polyamides against specific cancer cells.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"69-70"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp035","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28398378","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: 12
A photochemical detection of methylcytosine by using hydrophobic interaction. 疏水相互作用光化学检测甲基胞嘧啶。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp102
Takehiro Ami, Masayuki Ogino, Yuuta Taya, Yumiko Takemura, Kenzo Fujimoto
{"title":"A photochemical detection of methylcytosine by using hydrophobic interaction.","authors":"Takehiro Ami,&nbsp;Masayuki Ogino,&nbsp;Yuuta Taya,&nbsp;Yumiko Takemura,&nbsp;Kenzo Fujimoto","doi":"10.1093/nass/nrp102","DOIUrl":"https://doi.org/10.1093/nass/nrp102","url":null,"abstract":"<p><p>In this paper, the nonenzymatic detection of 5-methylcytosine with high selectivity is described. We present a new methylation detection method by using template-directed photoligation through 5-cyanovinyl-2'-deoxyuridine ((C)U). Significantly, the photoligation yield of the 5-methylcytosine case was approximately 9.1-fold higher than that in the case of cytosine.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"203-4"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp102","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28398395","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
Osmium complex binding to mismatched methylcytosine: effect of adjacent bases. 锇配合物与不匹配的甲基胞嘧啶结合:相邻碱基的影响。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp104
Akiko Nomura, Kazuki Tainaka, Akimitsu Okamoto
{"title":"Osmium complex binding to mismatched methylcytosine: effect of adjacent bases.","authors":"Akiko Nomura,&nbsp;Kazuki Tainaka,&nbsp;Akimitsu Okamoto","doi":"10.1093/nass/nrp104","DOIUrl":"https://doi.org/10.1093/nass/nrp104","url":null,"abstract":"<p><p>We investigated the efficiency of osmium complex formation at 5-methylcytosine in mismatched DNA duplexes. Osmium complexation was not observed in fully matched duplexes, whereas the complexation site and efficiency in mismatched duplexes depended on the 5'-neighboring base of the 5-methylcytosine. In particular, when the base adjacent to the 5' side of the mismatched base pair was thymine, a unique side reaction was observed. However, the mismatched base pairs did not influence the selectivity of osmium complexation with methylated DNA.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"207-8"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp104","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28398397","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
The highly stabilized ribosome display selection of metal binding peptide aptamers. 高度稳定的核糖体展示了金属结合肽适配体的选择。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp132
Akira Wada, Yoshihiro Ito
{"title":"The highly stabilized ribosome display selection of metal binding peptide aptamers.","authors":"Akira Wada,&nbsp;Yoshihiro Ito","doi":"10.1093/nass/nrp132","DOIUrl":"https://doi.org/10.1093/nass/nrp132","url":null,"abstract":"<p><p>Development of methods for in vitro selection of peptide aptamers with target binding affinities have been expected to construct biocatalysts, biosensors, and molecular targeted drugs in leading-edge fields of biotechnology and medical therapies. Therefore, a highly stabilized ribosome display method has been devised for efficient selection of various peptide aptamers from an artificial peptide library (APL). This ribosome display selection is performed by using a ribosomal conjugate consisted of APL, Cv RNA-associating protein (Cvap), and mRNA having Cv RNA motif at 5' terminus. The conjugate generated by in vitro translation can automatically link a peptide as phenotype and its mRNA as genotype, which can be stabilized by a high affinity association between Cv motif and Cvap. Here, in order to demonstrate the utility of this ribosome display method, we performed in vitro selection of peptide aptamers against a metal complex, and succeeded in identification and characterization of peptide aptamers with specific metal binding affinity. These results validate the concept to design APL in DNA level and indicate the versatility of the highly stabilized ribosome display selection.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"263-4"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp132","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28397467","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: 3
Interaction between tetraplex structure of mouse telomeric DNA and telomeric DNA binding domains of mouse telomere binding protein Pot1. 小鼠端粒DNA四复体结构与端粒结合蛋白Pot1端粒DNA结合域的相互作用。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp123
Kaoru Kaneda, Hidetaka Torigoe
{"title":"Interaction between tetraplex structure of mouse telomeric DNA and telomeric DNA binding domains of mouse telomere binding protein Pot1.","authors":"Kaoru Kaneda,&nbsp;Hidetaka Torigoe","doi":"10.1093/nass/nrp123","DOIUrl":"https://doi.org/10.1093/nass/nrp123","url":null,"abstract":"<p><p>Mouse telomeric DNA sequence, Tel3.5: 5'-AGGG(T TAGGG)(3)-3', has the ability to form antiparallel tetraplex structure in the presence of Na(+). We examined the interaction between the antiparallel tetraplex structure of Tel3.5 and each of two single-stranded telomeric DNA-binding domains of mouse telomere binding protein Pot1, mPot1OB1 and mPot1OB2. The antiparallel tetraplex of Tel3.5 became unfolded upon the interaction with mPot1OB1. On the other hand, no significant structural change of the antiparallel tetraplex of Tel3.5 was observed upon the interaction with mPot1OB2. Considering that the antiparallel tetraplex inhibits telomerase-mediated telomere elongation, we conclude that the ability of mPot1OB1 to unfold the antiparallel tetraplex of the mouse telomeric DNA is required for telomerase-mediated telomere elongation.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"245-6"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp123","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28397569","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
Biochemical dissection of RISC assembly and function. RISC组装与功能的生化剖析。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp008
Yukihide Tomari
{"title":"Biochemical dissection of RISC assembly and function.","authors":"Yukihide Tomari","doi":"10.1093/nass/nrp008","DOIUrl":"https://doi.org/10.1093/nass/nrp008","url":null,"abstract":"<p><p>Small silencing RNAs, including small interfering RNAs (siRNAs) and microRNAs (miRNAs), regulate expression of their target genes via RNA-induced silencing complex (RISC). RISC assembly follows complex, ordered pathways, and RISC function is as diverse as cleavage, translational repression, and deadenylation of the target. We have recently shown how siRNAs and miRNAs are assembled into distinct types of RISC, and how differently they function, using Drosophila as a model organism.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"15"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28470944","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: 4
Synthesis and characterization of deoxyuridine triphosphates labeled with pyrene. 芘标记的三磷酸脱氧尿苷的合成与表征。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp066
Yosuke Tanimizu, Tadao Takada, Mitsunobu Nakamura, Kazushige Yamana
{"title":"Synthesis and characterization of deoxyuridine triphosphates labeled with pyrene.","authors":"Yosuke Tanimizu,&nbsp;Tadao Takada,&nbsp;Mitsunobu Nakamura,&nbsp;Kazushige Yamana","doi":"10.1093/nass/nrp066","DOIUrl":"https://doi.org/10.1093/nass/nrp066","url":null,"abstract":"<p><p>Deoxyuridine triphosphate derivatives modified with pyrene was synthesized to functionalize DNA with fluorescent molecules based on the template DNA sequence. Incorporation of pyrene-labeled deoxyuridine triphosphates into DNA by DNA polymerase was investigated by using reverse-phase HPLC and polyacrylamide gel electrophoresis. The fluorescent properties of functionalized DNA were characterized by the steady-state fluorescence measurements.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"131-2"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp066","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28470954","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
The NEXT-A (N-terminal EXtension with Transferase and ARS) reaction. NEXT-A (n端扩展与转移酶和ARS)反应。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp019
Masumi Taki, Hiroyuki Kuroiwa, Masahiko Sisido
{"title":"The NEXT-A (N-terminal EXtension with Transferase and ARS) reaction.","authors":"Masumi Taki,&nbsp;Hiroyuki Kuroiwa,&nbsp;Masahiko Sisido","doi":"10.1093/nass/nrp019","DOIUrl":"https://doi.org/10.1093/nass/nrp019","url":null,"abstract":"<p><p>L/F-transferase is known to catalyze transfer of hydrophobic amino acids from aminoacyl tRNA to the N-terminus of a protein possessing lysine or arginine as the N-terminus. Combining L/F-transferase with E. coli phenylalanyl-tRNA synthetase (ARS), we achieved non-ribosomal N-terminal-specific introduction of various kinds of nonnatural amino acids to a protein. A nonnatural amino acid is once charged onto an E. coli tRNA(Phe) by a mutant ARS in situ, and successively transferred from the tRNA to a target protein, namely the NEXT-A reaction. Besides alphaA294G mutation on the ARS, alphaT251A, betaG318W, or betaA356W double-mutation were effective to increase the introduction efficiency through the NEXT-A reaction. Protein specific fluorescence labelling via the NEXT-A reaction followed by Huisgen cycloaddition was also demonstrated.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"37-8"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp019","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28475053","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: 5
Protein detection using oligonucleotide probes. 用寡核苷酸探针检测蛋白质。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp079
Aya Shibata, Hiroshi Abe, Kazuhiro Furukawa, Satoshi Tsuneda, Yoshihiro Ito
{"title":"Protein detection using oligonucleotide probes.","authors":"Aya Shibata,&nbsp;Hiroshi Abe,&nbsp;Kazuhiro Furukawa,&nbsp;Satoshi Tsuneda,&nbsp;Yoshihiro Ito","doi":"10.1093/nass/nrp079","DOIUrl":"https://doi.org/10.1093/nass/nrp079","url":null,"abstract":"<p><p>We developed a new nucleic acid-based fluorescence probe for protein detection. The method is based on the scission of an aptamer into two probes, which are then attached with a chemically reactive fluorogenic compound. The protein-dependent association of the two probes accelerates a chemical reaction and indicates the presence of the target protein, which is detected using a fluorescence readout. The arginine-rich motif peptide was targeted by this type of probe. In presence of the peptide, the fluorescence signal at 450 nm increased, and no significant increase in fluorescence was observed in the absence of the peptide. An oligonucleotide-based fluorescence probe was successfully applied to the detection of the ARM peptide in solution.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"157-8"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp079","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28475064","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: 3
Promotion of triplex formation by 3'-amino-2'-O,4'-C-methylene bridged nucleic acid modification. 3'-氨基-2'-O,4'- c -亚甲基桥接核酸修饰促进三联体形成。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp080
Kiyomi Sasaki, S M Abdur Rahman, Norihiro Sato, Satoshi Obika, Takeshi Imanishi, Hidetaka Torigoe
{"title":"Promotion of triplex formation by 3'-amino-2'-O,4'-C-methylene bridged nucleic acid modification.","authors":"Kiyomi Sasaki,&nbsp;S M Abdur Rahman,&nbsp;Norihiro Sato,&nbsp;Satoshi Obika,&nbsp;Takeshi Imanishi,&nbsp;Hidetaka Torigoe","doi":"10.1093/nass/nrp080","DOIUrl":"https://doi.org/10.1093/nass/nrp080","url":null,"abstract":"<p><p>We examined the effect of 3'-amino-2'-O,4'-C-methylene bridged nucleic acid (3'-amino-2',4'-BNA) backbone modification of triplex-forming oligonucleotide (TFO) on the pyrimidine motif triplex formation at neutral pH, a condition where pyrimidine motif triplexes are unstable. The melting temperature of the pyrimidine motif triplex at pH 6.8 with 3'-amino-2',4'-BNA modified TFO was significantly higher than that observed with unmodified TFO. The 3'-amino-2',4'-BNA modification of TFO increased the thermal stability of the pyrimidine motif triplex at neutral pH. The present results certainly support the idea that the 3'-amino-2',4'-BNA modification of TFO could be a key chemical modification and may eventually lead to progress in therapeutic applications of the antigene strategy in vivo.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"159-60"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp080","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28475065","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
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