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Escherichia coli proline tRNA: structure and recognition sites for prolyl-tRNA synthetase. 大肠杆菌脯氨酸tRNA:脯氨酸tRNA合成酶的结构和识别位点。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.7
T Hasegawa, T Yokogawa
{"title":"Escherichia coli proline tRNA: structure and recognition sites for prolyl-tRNA synthetase.","authors":"T Hasegawa,&nbsp;T Yokogawa","doi":"10.1093/nass/44.1.7","DOIUrl":"https://doi.org/10.1093/nass/44.1.7","url":null,"abstract":"<p><p>A major proline tRNA was purified from bulk Escherichia coli A19 tRNA by affinity chromatography with a biotinylated DNA probe. Its nucleotide sequence including modified nucleotides was determined by the post-labelling technique. In order to study the recognition sites of this proline tRNA for prolyl-tRNA synthetase, various mutant transcripts were prepared using an in vitro transcription system with T7 RNA polymerase. Based on the results of in vitro kinetic analyses of mutant transcripts, it was concluded that the second and third letters, G35 and G36, of the anticodon, G37 of the anticodon loop, the discriminator base A73, G72 of the acceptor stem, G49 and U17A that existed in the corner of an L-shaped structure are the recognition sites of proline tRNA for prolyl-tRNA synthetase.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"7-8"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517913","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: 10
Synthesis and evaluation of novel bioconjugates as antiviral agents. 新型生物偶联物抗病毒药物的合成与评价。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.179
G Watal, V Shukla, K Misra
{"title":"Synthesis and evaluation of novel bioconjugates as antiviral agents.","authors":"G Watal,&nbsp;V Shukla,&nbsp;K Misra","doi":"10.1093/nass/44.1.179","DOIUrl":"https://doi.org/10.1093/nass/44.1.179","url":null,"abstract":"<p><p>Novel lipid (mannito-stearate) antiviral nucleoside and oligonucleotide conjugates were prepared with improved lipophilic and membrane associating properties of drugs. Potential advantages of these liponucleotide prodrugs are lower toxicity, increased cellular uptake, nuclease resistivity and antiviral activity. Oligonucleotide conjugate complementary to a unique segment of viral genome may selectively disrupt the processes dependent on the segment by hybridisation.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"179-80"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.179","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517918","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
A graphic tool for circular genome maps. 用于绘制环形基因组图谱的图形工具。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.189
T Tsudzuki
{"title":"A graphic tool for circular genome maps.","authors":"T Tsudzuki","doi":"10.1093/nass/44.1.189","DOIUrl":"10.1093/nass/44.1.189","url":null,"abstract":"<p><p>A program has been developed for drawing map of circular DNA such as organelle or plasmid genome. Total size of the genome, gene names and positions, and other details, if required, should be prepared in a simple format text file then the program process it to a PostScript(R) (PS) file with which you can print a image of the map on suitable device(s). The final touch on the map can be given through editing the PS file.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"189-90"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.189","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517923","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 triplex forming ability of conformationally locked oligonucleotides containing unnatural nucleobases: efficient recognition of a C.G interruption. 含有非自然核碱基的构象锁定寡核苷酸的合成和三联体形成能力:有效识别C.G中断。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.131
S Obika, Y Hari, M Sekiguchi, T Imanishi
{"title":"Synthesis and triplex forming ability of conformationally locked oligonucleotides containing unnatural nucleobases: efficient recognition of a C.G interruption.","authors":"S Obika,&nbsp;Y Hari,&nbsp;M Sekiguchi,&nbsp;T Imanishi","doi":"10.1093/nass/44.1.131","DOIUrl":"https://doi.org/10.1093/nass/44.1.131","url":null,"abstract":"<p><p>In order to develop a novel nucleoside analogue which recognizes C.G interruption in homopurine.homopyrimidine DNA, we designed and synthesized a conformationally locked nucleoside analogue, 1-(2-O,4-C-methylene-beta-D-ribofuranosyl)pyridin-2-one (4), and introduced it into a triplex-forming oligonucleotide (TFO). On melting temperature (Tm) measurements, the unprecedented C.G base recognition ability of 4 was observed.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"131-2"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.131","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518000","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
New thermodynamic characterization and transition mechanism of DNA duplex formation. DNA双链形成的新的热力学表征和过渡机制。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.15
P Wu, N Sugimoto
{"title":"New thermodynamic characterization and transition mechanism of DNA duplex formation.","authors":"P Wu,&nbsp;N Sugimoto","doi":"10.1093/nass/44.1.15","DOIUrl":"https://doi.org/10.1093/nass/44.1.15","url":null,"abstract":"<p><p>A new transition mechanism of DNA duplex association was proposed and a segregated transition model (STM) was further derived. The experimental results in various molar ratios showed that the duplex association transition is imperfect and the thermodynamic properties and self-transition behavior of single strands exert a significant influence on DNA duplex formation.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"15-6"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.15","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518379","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 2'-O-deuteriomethyl ribonucleosides Gm-d3, Am-d3, Um-d3 and Cm-d3. 2'- o -氘甲基核糖核苷Gm-d3, Am-d3, Um-d3和Cm-d3的合成。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.23
T Hashizume
{"title":"Synthesis of 2'-O-deuteriomethyl ribonucleosides Gm-d3, Am-d3, Um-d3 and Cm-d3.","authors":"T Hashizume","doi":"10.1093/nass/44.1.23","DOIUrl":"https://doi.org/10.1093/nass/44.1.23","url":null,"abstract":"<p><p>The synthesis of 2'-O-deuteriomethyl ribonucleosides by iodomethane-d3 (99.5 + atom % D) deuteriomethylation of 3',5'-O-tetra(isopropyldisiloxane)-diyl nucleosides, followed by deprotection, is described.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"23-4"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.23","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518382","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
Suppression of BCR-ABL mRNA by various ribozymes in HeLa cells. 不同核酶对HeLa细胞BCR-ABL mRNA的抑制作用。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.283
Y Kato, T Kuwabara, H Toda, M Warashina, K Taira
{"title":"Suppression of BCR-ABL mRNA by various ribozymes in HeLa cells.","authors":"Y Kato,&nbsp;T Kuwabara,&nbsp;H Toda,&nbsp;M Warashina,&nbsp;K Taira","doi":"10.1093/nass/44.1.283","DOIUrl":"https://doi.org/10.1093/nass/44.1.283","url":null,"abstract":"<p><p>Ribozymes are RNA molecules with enzymatic activity that can cleave target RNA molecules in a sequence specific manner. To date, various types of ribozyme have been constructed to cleave other RNAs and such trans-acting ribozymes include hammerhead, hairpin and HDV ribozymes. External guide sequence (EGS) can also induce the suppression of a gene-expression by taking advantage of cellular RNase P. Here we compared the activities of various functional RNA cleavers both in vitro and in vivo. The first purpose of this comparison was intended to determine the best ribozyme motif with the highest activity in cells. The second purpose is to know the correlation between the activities of ribozymes in vitro and in vivo. Our results indicated that the intrinsic cleavage activity of ribozymes is not the sole determinant that is responsible for the activity of a ribozyme in cultured cells.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"283-4"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.283","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518603","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
The engineering, structure, and DNA binding properties of a novel His4-type zinc finger peptide. 一种新型his4型锌指肽的工程、结构和DNA结合特性。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.295
Y Hori, K Suzuki, Y Okuno, M Nagaoka, S Futaki, Y Sugiura
{"title":"The engineering, structure, and DNA binding properties of a novel His4-type zinc finger peptide.","authors":"Y Hori,&nbsp;K Suzuki,&nbsp;Y Okuno,&nbsp;M Nagaoka,&nbsp;S Futaki,&nbsp;Y Sugiura","doi":"10.1093/nass/44.1.295","DOIUrl":"https://doi.org/10.1093/nass/44.1.295","url":null,"abstract":"<p><p>We have created a novel His4-type zinc finger protein (H4Sp1) engineered by Cys-->His mutations of the Cys2His2-type zinc finger in transcription factor Sp1. The CD and NMR studies reveal that the His4 domain has Zn(II)-dependent folding properties and similar secondary structures to wild-type Cys2His2 domain. The DNA binding experiments demonstrate that H4Sp1 can bind DNA in a specific way. The present artificial peptide H4Sp1 will provide valuable information about the interaction between a metallopeptide and DNA.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"295-6"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.295","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518609","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
Two-terpyridine.Cu(II) complexes-containing antisense systems for rapid and highly site-specific RNA cleavage. 2 -三联吡啶。cu (II)配合物-用于快速和高度位点特异性RNA切割的含反义系统。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.279
H Inoue, T Furukawa, T Tamura, Y Komatsu, E Ohtsuka
{"title":"Two-terpyridine.Cu(II) complexes-containing antisense systems for rapid and highly site-specific RNA cleavage.","authors":"H Inoue,&nbsp;T Furukawa,&nbsp;T Tamura,&nbsp;Y Komatsu,&nbsp;E Ohtsuka","doi":"10.1093/nass/44.1.279","DOIUrl":"https://doi.org/10.1093/nass/44.1.279","url":null,"abstract":"<p><p>In an approach toward artificial ribonucleases, novel RNA cleaving systems were constructed that contained two terpyridine.Cu(II) residues. The first antisense system used tandem Cu(II) complex--2'-O-methyloligonucleotide 5'- and 3'-conjugates to cleave an RNA substrate. The second system, which will be described in a future paper, contained two contiguous Cu(II) complex residues at an internal site of a 2'-O-methyloligonucleotide. We found that the first system rapidly cleaved RNA with high site-specificity. Based on these results, we expect the second system to also show efficient RNA cleavage.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"279-80"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.279","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518725","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
Automated in vitro selection to obtain functional oligonucleotides. 自动体外选择获得功能性寡核苷酸。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.219
H Zhang, A Hamasaki, E Toshiro, Y Aoyama, Y Ito
{"title":"Automated in vitro selection to obtain functional oligonucleotides.","authors":"H Zhang,&nbsp;A Hamasaki,&nbsp;E Toshiro,&nbsp;Y Aoyama,&nbsp;Y Ito","doi":"10.1093/nass/44.1.219","DOIUrl":"https://doi.org/10.1093/nass/44.1.219","url":null,"abstract":"<p><p>In vitro selection or systematic evolution of ligand by exponential enrichment (SELEX) has been devised for the identification of high-affinity oligonucleotide aptamers to target molecules. However, the selection process is repetitive and time-consuming. We have developed an automatic for in vitro selection by assembling an affinity chromato-column, a PCR thermal cycler, a HPLC and a sample operation system. Several molecular biology methods were optimized for the machine. Automated selection was used to generate nucleic acid aptamers interacting specifically with an environmental contaminant.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"219-20"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.219","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517749","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: 8
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