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Nucleic acids research. Supplement (2001)最新文献

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Towards artificial repair of UV-damaged DNA: studies on drug binding and alkali hydrolysis. 紫外线损伤DNA的人工修复:药物结合和碱水解的研究。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.181
Shigenori Iwai, Aki Inase, Sharif Jafar, Miho Higurashi, Takashi Ohtsuki, Yan Xu, Hiroshi Sugiyama
{"title":"Towards artificial repair of UV-damaged DNA: studies on drug binding and alkali hydrolysis.","authors":"Shigenori Iwai,&nbsp;Aki Inase,&nbsp;Sharif Jafar,&nbsp;Miho Higurashi,&nbsp;Takashi Ohtsuki,&nbsp;Yan Xu,&nbsp;Hiroshi Sugiyama","doi":"10.1093/nass/3.1.181","DOIUrl":"https://doi.org/10.1093/nass/3.1.181","url":null,"abstract":"<p><p>Properties of the DNA containing the (6-4) photoproduct, one of the major UV-induced lesions, were analyzed. Two basic studies towards artificial recognition and repair of this type of damaged DNA are presented here. One is recognition of the UV-damaged DNA by a minor groove-binding drug. It was found by CD spectroscopy that distamycin could bind DNA duplexes containing the (6-4) photoproduct as effectively as the unmodified DNA, whereas a DNA duplex containing the cyclobutane pyrimidine dimer was not recognized by this drug. The other is a mechanistic study on alkali degradation of this photoproduct. HPLC and NMR analyses revealed that hydrolysis between the N3 and C4 positions of the 5' pyrimidine component occurred first. This intermediate was relatively stable, and further degradation to the strand break required severe conditions like the hot piperidine treatment.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"181-2"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.181","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825090","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
Differential transcriptional regulation of two distinct S-adenosylmethionine synthetase genes (SAM1 and SAM2) of Saccharomyces cerevisiae. 酿酒酵母两种不同s -腺苷蛋氨酸合成酶基因(SAM1和SAM2)的差异转录调控
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.303
Tsutomu Kodaki, Shinji Tsuji, Naoko Otani, Daihei Yamamoto, Kota Sreenivasa Rao, Seiya Watanabe, Masahiro Tsukatsune, Keisuke Makino
{"title":"Differential transcriptional regulation of two distinct S-adenosylmethionine synthetase genes (SAM1 and SAM2) of Saccharomyces cerevisiae.","authors":"Tsutomu Kodaki,&nbsp;Shinji Tsuji,&nbsp;Naoko Otani,&nbsp;Daihei Yamamoto,&nbsp;Kota Sreenivasa Rao,&nbsp;Seiya Watanabe,&nbsp;Masahiro Tsukatsune,&nbsp;Keisuke Makino","doi":"10.1093/nass/3.1.303","DOIUrl":"https://doi.org/10.1093/nass/3.1.303","url":null,"abstract":"<p><p>Expression of a number of genes encoding enzymes involved in phospholipid biosynthesis in yeast Saccharomyces cerevisiae is known to be repressed on the addition of myo-inositol and choline to the culture medium (inositol-choline regulation). All genes subject to this inositol-choline regulation have an octamer sequence 5'-CATRTGAA-3' in their upstream regions and those octamer sequences play an important role in this regulation. To confirm the role of the octamer sequence further, we studied the transcriptional regulation of two distinct S-adenosylmethionine synthetase genes (SAM1 and SAM2) of S. cerevisiae. Quantitative RT-PCR analysis showed that only the SAM2 gene was subject to the inositol-choline regulation, consistent with the fact that only the SAM2 gene has two octamer sequences in its upstream region. Furthermore, functional promoter analysis revealed that the proximal octamer sequence of the SAM2 gene has an essential role for this regulation.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"303-4"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.303","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825132","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: 13
Synthesis and properties of telomere-mimic carbocyclic 5'-nor 3'-deoxyoligonucleotide. 端粒模拟碳环5′-nor - 3′-脱氧寡核苷酸的合成及性质。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.53
Masakazu Koga, Toshiyuki Yamamuro, Koichi Tamai, Masao Kanda, Masahiro Shigeta, Takaaki Suzuki, Toshiaki Saeki
{"title":"Synthesis and properties of telomere-mimic carbocyclic 5'-nor 3'-deoxyoligonucleotide.","authors":"Masakazu Koga,&nbsp;Toshiyuki Yamamuro,&nbsp;Koichi Tamai,&nbsp;Masao Kanda,&nbsp;Masahiro Shigeta,&nbsp;Takaaki Suzuki,&nbsp;Toshiaki Saeki","doi":"10.1093/nass/3.1.53","DOIUrl":"https://doi.org/10.1093/nass/3.1.53","url":null,"abstract":"<p><p>Telomere-mimic carbocyclic 5'-nor 3'-deoxyoligonucleotide was synthesized. And it's selectivity to RNA was shown.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"53-4"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.53","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825183","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
Photochemistry of bromouracil containing Z-DNA. 含Z-DNA溴酸的光化学性质。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.69
Ryu Tashiro, Hiroshi Sugiyama
{"title":"Photochemistry of bromouracil containing Z-DNA.","authors":"Ryu Tashiro,&nbsp;Hiroshi Sugiyama","doi":"10.1093/nass/3.1.69","DOIUrl":"https://doi.org/10.1093/nass/3.1.69","url":null,"abstract":"<p><p>To investigate the mechanism underlying the photoreaction of bromouracil in DNA, a detailed analysis of photoirradiated 5'-d(CGCG(Br)UGCG)-3'/5'-d(C(8MeO)GCAC(m)GCG)-3' was undertaken. We found that rG- and 2-aminoimidazolone-containing octanucleotides are formed efficiently in Z-form DNA. These results suggest that interstrand electron transfer initiates the photoreaction of bromouracil in Z-DNA.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"69-70"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.69","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825191","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
Analysis of processing-defective variants of human tRNA(Val). 人类tRNA加工缺陷变异(Val)的分析。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.283
Yoshio Kato, Masayuki Sano, Kazunari Taira
{"title":"Analysis of processing-defective variants of human tRNA(Val).","authors":"Yoshio Kato,&nbsp;Masayuki Sano,&nbsp;Kazunari Taira","doi":"10.1093/nass/3.1.283","DOIUrl":"https://doi.org/10.1093/nass/3.1.283","url":null,"abstract":"<p><p>Eukaryotic tRNAs are transcribed, processed and exported from the nucleus to the cytoplasm to participate in protein biosynthesis. A variant of human gene for tRNA(Val), HtV4, is not processed neither its 5'- nor its 3'-flanking sequences. By RT-PCR analysis and in situ hybridization, we demonstrated that the HtV4 was constitutively expressed without processing, and localized in the nucleus in HeLa cells.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"283-4"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.283","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825196","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
Application of recombination transfer to the cognate Bacillus subtilis genome. 同源枯草芽孢杆菌基因组重组转移的应用。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.295
Satoshi Tomita, Kenji Tsuge, Yo Kikuchi, Mitsuhiro Itaya
{"title":"Application of recombination transfer to the cognate Bacillus subtilis genome.","authors":"Satoshi Tomita,&nbsp;Kenji Tsuge,&nbsp;Yo Kikuchi,&nbsp;Mitsuhiro Itaya","doi":"10.1093/nass/3.1.295","DOIUrl":"https://doi.org/10.1093/nass/3.1.295","url":null,"abstract":"<p><p>Isolation of the designated genome region of Bacillus subtilis was investigated using a B. subtilis recombinational transfer (BReT) system. Two DNA sequences flanking the precise genome region are cloned in the BReT vector. The BReT plasmid recovered the predicted genome sequence as large as 100 kb with high fidelity. The result indicates that the BReT system originally developed to recover the non-cognate segments cloned in the B. subtilis genome vector can be applied to the cognate sequence.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"295-6"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.295","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825202","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
Effective photo-regulation of transcription reaction by SP6 RNA polymerase with modified DNA tethering multiple azobenzenes. 修饰DNA系住多个偶氮苯的SP6 RNA聚合酶对转录反应的有效光调控。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.265
Mingzhe Liu, Hiroyuki Asanuma, Makoto Komiyama
{"title":"Effective photo-regulation of transcription reaction by SP6 RNA polymerase with modified DNA tethering multiple azobenzenes.","authors":"Mingzhe Liu,&nbsp;Hiroyuki Asanuma,&nbsp;Makoto Komiyama","doi":"10.1093/nass/3.1.265","DOIUrl":"https://doi.org/10.1093/nass/3.1.265","url":null,"abstract":"<p><p>Effective photo-regulation of transcription reaction by SP6 RNA polymerase (RNAP) was achieved with photo-responsive SP6 promoter tethering two azobenzenes. With one azobenzene in either TATA or RNAP binding region of the SP6 promoter, photo-regulation activity was very small. But when two azobenzenes were introduced into both regions, efficient photo-regulation of transcription was attained: transcription proceeded 3.5 fold faster under UV irradiation than under dark.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"265-6"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.265","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40903187","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
Repair of oxidative cytosine damage by DNA glycosylases. DNA糖基化酶修复氧化胞嘧啶损伤。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.269
Atsushi Katafuchi, Aya Matsuo, Hiroaki Terato, Yoshihiko Ohyama, Hiroshi Ide
{"title":"Repair of oxidative cytosine damage by DNA glycosylases.","authors":"Atsushi Katafuchi,&nbsp;Aya Matsuo,&nbsp;Hiroaki Terato,&nbsp;Yoshihiko Ohyama,&nbsp;Hiroshi Ide","doi":"10.1093/nass/3.1.269","DOIUrl":"https://doi.org/10.1093/nass/3.1.269","url":null,"abstract":"<p><p>5-Hydroxyuracil (HOU) and 5-hydroxycytosine (HOC) are major oxidative lesions of cytosine with mutagenic potentials. Therefore, HOU and HOC need to be removed from DNA to avoid mutation. In this study, oligonucleotide substrates containing HOU and HOC were synthesized by DNA polymerase reactions and tested for DNA glycosylases. Ung exhibited an extremely low activity for HOU as compared to uracil (U). In contrast, hSMUG1 excised HOU and U with a comparable efficiency. Ung and hSMUG1 did not excise HOC.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"269-70"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.269","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40903189","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
Revisiting the substrate recognition of bacterial ribonuclease P: in the view of the recognition of the base N73 in the substrate. 重新审视细菌核糖核酸酶P的底物识别:从底物中碱基N73的识别来看。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.275
Terumichi Tanaka, Tomoaki Ando, Yo Kikuchi
{"title":"Revisiting the substrate recognition of bacterial ribonuclease P: in the view of the recognition of the base N73 in the substrate.","authors":"Terumichi Tanaka,&nbsp;Tomoaki Ando,&nbsp;Yo Kikuchi","doi":"10.1093/nass/3.1.275","DOIUrl":"https://doi.org/10.1093/nass/3.1.275","url":null,"abstract":"<p><p>The RNA subunit of bacterial ribonuclease P (RNase P) is a ribozyme which can cleave a canonical cloverleaf tRNA precursor and a hairpin RNA with a CCA-3' tag sequence as its substrate. At high concentration of Mg ion, the substrate shape preference of the ribozyme becomes broader to accept a hairpin shape RNA. In hairpin RNA cleavage reactions, we found that the base interaction between the base U294 of E. coli ribozyme and the base N73 of the substrate RNA did not obey the response according to the Watson-Crick type interaction which is usually observed in the interaction between the base U294 of ribozyme and the base N73 of tRNA precursor.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"275-6"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.275","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40903192","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,&nbsp;Moo Hong Lim,&nbsp;Hyung Ryong Moon,&nbsp;Hea Ok Kim,&nbsp;Kenneth A Jacobson,&nbsp;Lak Shin Jeong","doi":"10.1093/nass/3.1.19","DOIUrl":"https://doi.org/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":"https://sci-hub-pdf.com/10.1093/nass/3.1.19","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
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