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Nucleic acids research. Supplement (2001)最新文献

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Novel strategy for DNA aptamers inhibiting enzymatic activity using algorithm mimicking evolution. 利用模拟进化算法的DNA适体抑制酶活性的新策略。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.205
Kazunori Ikebukuro, Yuji Okumura, Koichi Sumikura, Isao Karube
{"title":"Novel strategy for DNA aptamers inhibiting enzymatic activity using algorithm mimicking evolution.","authors":"Kazunori Ikebukuro,&nbsp;Yuji Okumura,&nbsp;Koichi Sumikura,&nbsp;Isao Karube","doi":"10.1093/nass/3.1.205","DOIUrl":"https://doi.org/10.1093/nass/3.1.205","url":null,"abstract":"<p><p>We screened the DNA aptamer inhibiting thrombin with novel method using algorithm mimicking evolution. For screening, we first randomly designed and synthesized ten 15-mer oligonucleotides supposed to form G-quartet structure and then measured the inhibitory activity for thrombin. The aptamers showing the high activities were selected and we shuffled and mutated those sequences in silico to generate 10 new sequences of aptamers for next generation. After repeating 5 cycles, we successfully obtained the same aptamers reported previously showing high inhibitory activity. In addition, we added 8-mer oligonucleotides to the both 5' and 3' ends of the selected 15-mer aptamer and then repeated evolution in silico. After 2 cycles, we were able to obtain the aptamer showing better inhibitory activity than the 15-mer aptamer.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"205-6"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.205","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40824932","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
Beyond the Watson-Crick double helix: design of functional nucleic acids in silico, in tube, and in cell. 沃森-克里克双螺旋结构之外:在硅片、试管和细胞中设计功能性核酸。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.211
Naoki Sugimoto
{"title":"Beyond the Watson-Crick double helix: design of functional nucleic acids in silico, in tube, and in cell.","authors":"Naoki Sugimoto","doi":"10.1093/nass/3.1.211","DOIUrl":"https://doi.org/10.1093/nass/3.1.211","url":null,"abstract":"<p><p>The structures and thermodynamic properties of non-Watson-Crick structures in RNA and DNA are described. The recent data on dangling ends in RNA, peptide nucleic acid (PNA), triplex, and G-quadruplex have resulted in an understanding of the catalysis, tertiary contact domains, and biological functions associated with these unpaired regions and special helices, and are useful in developing functional nucleic acids in cell.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"211-2"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.211","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40824935","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
An unnatural base pair for efficient incorporation of nucleotide analogs into RNAs. 一种非自然的碱基对，用于将核苷酸类似物有效地结合到rna中。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.215
Ichiro Hirao, Tsuneo Mitsui, Michiko Kimoto, Yoko Harada, Shigeyuki Yokoyama
{"title":"An unnatural base pair for efficient incorporation of nucleotide analogs into RNAs.","authors":"Ichiro Hirao,&nbsp;Tsuneo Mitsui,&nbsp;Michiko Kimoto,&nbsp;Yoko Harada,&nbsp;Shigeyuki Yokoyama","doi":"10.1093/nass/3.1.215","DOIUrl":"https://doi.org/10.1093/nass/3.1.215","url":null,"abstract":"<p><p>An unnatural base, 2-amino-6-(2-thiazolyl)purine (denoted as v), was developed as an efficient complementary base of another unnatural base, 2-oxo(1H)pyridine (denoted as y). The nucleoside derivatives of v and DNA fragments containing v were chemically synthesized. The efficiency and selectivity of the v-y pairing in replication and transcription were examined and compared to those of a previously developed unnatural base pair between 2-amino-6-(2-thienyl)purine (s) and y. The nucleoside 5'-triphosphate of y (dyTP or yTP) was selectively and efficiently incorporated into DNA or RNA opposite v. The efficiency of the v-y pairing was much higher than that of the s-y pairing. The unnatural v-y pair could be useful for large-scale preparations of RNA molecules containing unnatural bases at desired positions for the expansion of the genetic alphabet.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"215-6"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.215","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40824937","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
Design of artificial nucleic acid chaperones for DNA engineering. 用于DNA工程的人工核酸伴侣的设计。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.219
Atsushi Maruyama, Satoru Inoue, Kaori Tajima, Yuichi Sato, Won Jong Kim, Toshihiro Akaike
{"title":"Design of artificial nucleic acid chaperones for DNA engineering.","authors":"Atsushi Maruyama,&nbsp;Satoru Inoue,&nbsp;Kaori Tajima,&nbsp;Yuichi Sato,&nbsp;Won Jong Kim,&nbsp;Toshihiro Akaike","doi":"10.1093/nass/3.1.219","DOIUrl":"https://doi.org/10.1093/nass/3.1.219","url":null,"abstract":"<p><p>We have shown that the comb-type copolymer consisting of a polycation backbone and hydrophilic side chains stabilizes DNA hybrids. Furthermore, the copolymers showed the activity to accelerate DNA strand exchange reactions between double helical DNA and its complementary DNA. The copolymer was considered to stimulate breakage and reassociation of base pairing and act as an artificial nucleic acid chaperone. The polymer's chaperoning activity was elaborated for rapid and precise judging of a subtle difference in DNA sequences. One base alternation out of 20mer DNA was quickly detected by the strand exchange assay employing the copolymer. From these, we conclude that the copolymer would be a useful material in DNA engineering that employs rapid and precise DNA folding.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"219-20"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.219","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40824939","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
RNA interference and chemically modified siRNAs. RNA干扰和化学修饰sirna。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.115
Muthiah Manoharan
{"title":"RNA interference and chemically modified siRNAs.","authors":"Muthiah Manoharan","doi":"10.1093/nass/3.1.115","DOIUrl":"https://doi.org/10.1093/nass/3.1.115","url":null,"abstract":"<p><p>RNA interference (RNAi) represents one of the most promising new frontiers in drug discovery. Short double-stranded RNA molecules are able to sequence-specifically inhibit expression of genes. This young technology offers both opportunities and challenges to nucleic acid chemists.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"115-6"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.115","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825079","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: 17
Evaluating the immune responses stimulated by CpG oligodeoxynucleotides. 评估CpG寡脱氧核苷酸刺激的免疫反应。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.323
Mieko Hayashi, Makoto Kuwahara, Miwa Ogata, Naoko Miyao-Kurosaki, Takayuki Abel, Ryouji Ueki, Mayuka Yano, Masayuki Fujii, Gunther Hartmann, Hiroshi Takaku
{"title":"Evaluating the immune responses stimulated by CpG oligodeoxynucleotides.","authors":"Mieko Hayashi,&nbsp;Makoto Kuwahara,&nbsp;Miwa Ogata,&nbsp;Naoko Miyao-Kurosaki,&nbsp;Takayuki Abel,&nbsp;Ryouji Ueki,&nbsp;Mayuka Yano,&nbsp;Masayuki Fujii,&nbsp;Gunther Hartmann,&nbsp;Hiroshi Takaku","doi":"10.1093/nass/3.1.323","DOIUrl":"https://doi.org/10.1093/nass/3.1.323","url":null,"abstract":"<p><p>CpG oligonucleotides have recently been highlighted as an immunomodulator that biases toward a Th1-dominant phenotype. To substantiate the synergism between CpG-ODNs and Ag, we introduced a linked conjugate between CpG-ODNs and Ag and the antiviral effect of antigen-conjugated CpG-ODNs therapy following an infection of mice with the influenza virus A. We found that the conjugate inhibited the influenza virus infection more efficiently than the coadministration of the unconjugated CpG-ODNs and the Ag mixture. CpG-ODNs is effective in immunity induction and will be useful in treating virus infections.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"323-4"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.323","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825094","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: 7
Staurosporine stimulates insulin gene expression via CRE dependent manner. Staurosporine通过CRE依赖方式刺激胰岛素基因表达。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.301
Yoriko Shinozuka, Masayuki Okada, Nobuyuki Yasuda, Kazunari K Yokoyama
{"title":"Staurosporine stimulates insulin gene expression via CRE dependent manner.","authors":"Yoriko Shinozuka,&nbsp;Masayuki Okada,&nbsp;Nobuyuki Yasuda,&nbsp;Kazunari K Yokoyama","doi":"10.1093/nass/3.1.301","DOIUrl":"https://doi.org/10.1093/nass/3.1.301","url":null,"abstract":"<p><p>We examined various compounds to stimulate the transcription of promoter-reporter construct in pancreatic HIT-T15 cells, that had been stably transfected with the rat insulin I promoter-PLAP reporter gene, and found staurosporine at dose of nanomole enhanced insulin promoter activity significantly. Northern blotting analysis and ELISA (enzyme linked immunosorbent assay) showed that the promoter activity of insulin gene was well correlated with the endogenous level of insulin mRNA and protein in HIT-T15, indicating that staurosporine stimulated the biosynthesis of insulin at levels of transcription and translation. The deletion and point mutation of cAMP response element (CRE) in the promoter region of insulin gene lost the promoter activity of reporter gene induced by staurosporine. These results suggested that insulin promoter activity stimulated by staurosporine is CRE-dependent.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"301-2"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.301","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825131","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
Synthesis of antisense oligonucleotides containing photocleavable protecting groups on the thymine bases and their photoinduced duplex formation. 胸腺嘧啶碱基上含有光可切割保护基团的反义寡核苷酸的合成及其光诱导双相形成。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.61
Reiko Iwase, Aki Kitani, Tetsuji Yamaoka, Akira Murakami
{"title":"Synthesis of antisense oligonucleotides containing photocleavable protecting groups on the thymine bases and their photoinduced duplex formation.","authors":"Reiko Iwase,&nbsp;Aki Kitani,&nbsp;Tetsuji Yamaoka,&nbsp;Akira Murakami","doi":"10.1093/nass/3.1.61","DOIUrl":"https://doi.org/10.1093/nass/3.1.61","url":null,"abstract":"<p><p>Oligonucleotides containing photocleavable protecting groups at thymine bases were synthesized to induce the duplex formation by photo-irradiation. 6-Nitroveratryloxycarbonyl (NVOC) group was used for the photocleavable protecting group at N3 position of thymidine. An oligonucleotide containing NVOC groups (NVOC-ODN2:5'-dATG CAC CAT(NVOC) TCT(NVOC)GTC TGT-3') was synthesized by phosphoramidite method. The NVOC groups were found to be removable by UV irradiation at wavelength of 365 nm for 5 h. UV-melting temperature (Tm value) analysis indicated that the duplex of NVOC-ODN2 with the complementary RNA was significantly unstable compared with the unmodified DNA/RNA duplex (delta Tm=-13 degrees C). After UV irradiation at 365 nm, the Tm value of the mixture increased to the almost same as that of the unmodified duplex. These results suggest that the RNA binding ability of the NVOC-ODN2 can be induced by photocleavage of the NVOC groups.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"61-2"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.61","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825187","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
Photoreactivity of 5-iodouracil-containing telomeric DNA. 含5-碘嘧啶端粒DNA的光反应性。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.71
Yan Xu, Hiroshi Sugiyama
{"title":"Photoreactivity of 5-iodouracil-containing telomeric DNA.","authors":"Yan Xu,&nbsp;Hiroshi Sugiyama","doi":"10.1093/nass/3.1.71","DOIUrl":"https://doi.org/10.1093/nass/3.1.71","url":null,"abstract":"<p><p>The photoreaction of 5-iodouracil-((I)U)-containing telomeric oligonucleotides in parallel or antiparallel structures, generated in the presence of K+ or Na+ ions, was investigated. It was found that the photoreactivity of telomeric DNA depends on the differences in the quadruplex conformations in the presence of K+ or Na+ ions.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"71-2"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.71","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825192","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
In vitro analysis of the initial steps of trans-translation. 反译初始步骤的体外分析。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.287
Kazuma Takada, Chie Hori-Takemoto, Masahito Kawazoe, SungGa Lee, Mikako Shirouzu, Shigeyuki Yokoyama, Akira Muto, Hyouta Himeno
{"title":"In vitro analysis of the initial steps of trans-translation.","authors":"Kazuma Takada,&nbsp;Chie Hori-Takemoto,&nbsp;Masahito Kawazoe,&nbsp;SungGa Lee,&nbsp;Mikako Shirouzu,&nbsp;Shigeyuki Yokoyama,&nbsp;Akira Muto,&nbsp;Hyouta Himeno","doi":"10.1093/nass/3.1.287","DOIUrl":"https://doi.org/10.1093/nass/3.1.287","url":null,"abstract":"<p><p>tmRNA has a dual function both as tRNA and mRNA and facilitates trans-translation. We observed the tagging derived from tmRNA from Bacillus subtilis in vivo and in vitro. Our studies give progressive suggestions on the mechanism of trans-translation.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"287-8"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.287","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825198","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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