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Synthesis and radical reaction of 1'-phenylselenonucleosides. 1'-苯基硒核苷的合成及自由基反应。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.109
T Kodama, M Nomura, S Shuto, A Matsuda
{"title":"Synthesis and radical reaction of 1'-phenylselenonucleosides.","authors":"T Kodama,&nbsp;M Nomura,&nbsp;S Shuto,&nbsp;A Matsuda","doi":"10.1093/nass/44.1.109","DOIUrl":"https://doi.org/10.1093/nass/44.1.109","url":null,"abstract":"<p><p>The 1'alpha-phenylselenouridine derivative (4) was successfully synthesized via enolization at the 1'-position of the 3',5'-O-TIPDS-2'-ketouridine (1). After the introduction of a vinylsilyl tether as an intramolecular radical acceptor at the 2'-hydroxy group of 4, its atom-transfer radical cyclization reaction, followed by the treatment with TBAF gave 1'alpha-vinyluridine derivative (10). Using this procedure, 1'alpha-vinyluridine (11) and -cytidine (14) were successfully synthesized.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.109","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518142","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 oligonucleotides using the 2-(levulinyloxymethyl)-5-nitrobenzoyl group for the 5'-position of nucleoside 3'-H-phosphonate and -H-phosphonothioate derivatives. 利用核苷3′- h -膦酸盐和- h -膦硫酸盐衍生物的5′位2-(乙酰丙基氧甲基)-5-硝基苯甲酰合成寡核苷酸。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.33
K Kamaike, K Hirose, E Kawashima
{"title":"Synthesis of oligonucleotides using the 2-(levulinyloxymethyl)-5-nitrobenzoyl group for the 5'-position of nucleoside 3'-H-phosphonate and -H-phosphonothioate derivatives.","authors":"K Kamaike,&nbsp;K Hirose,&nbsp;E Kawashima","doi":"10.1093/nass/44.1.33","DOIUrl":"https://doi.org/10.1093/nass/44.1.33","url":null,"abstract":"<p><p>Synthetic studies on phosphodiester, phosphorothioate, and phosphorodithioate-linked oligonucleotides in terms of 2-(levulinyloxymethyl)-5-nitrobenzoyl (LMNBz) group as the base-labile protecting group for the 5'-hydroxyl groups of nucleoside 3'-H-phosphonate and -H-phosphonothioate derivatives, are described.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.33","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518387","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
Characterization of RNA structure by bis-pyrene-labeled 2'-O-methyloligonucleotides. 用双芘标记的2'- o -甲基寡核苷酸表征RNA结构。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.199
A Mahara, R Iwase, K Yamana, T Yamaoka, A Murakami
{"title":"Characterization of RNA structure by bis-pyrene-labeled 2'-O-methyloligonucleotides.","authors":"A Mahara,&nbsp;R Iwase,&nbsp;K Yamana,&nbsp;T Yamaoka,&nbsp;A Murakami","doi":"10.1093/nass/44.1.199","DOIUrl":"https://doi.org/10.1093/nass/44.1.199","url":null,"abstract":"<p><p>Properties of 2'-O-methyloligoribonucleotides containing two consecutive 2'-O-(1-pyrenylmethyl)uridine were investigated as a fluorescent probe to search the single strand regions of RNA. The bis-pyrene-labeled 2'-O-methyloligoribonucleotide (OMUpy2) induced the formation of pyrene dimer upon hybridization with the complementary oligoribonucleotides and showed remarkable appearance of broad structureless fluorescence at 480 nm. Contrarily, when OMUpy2 was hybridized with the complementary oligodeoxyribonucleotides, such enhancement of fluorescence was scarcely observed. When various OMUpy2 were applied to E. coli 5S-rRNA, the fluorescence intensity at 480 nm was varied in a sequence specific manner.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.199","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518390","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
Construction of a ribozyme-expression system that effectively transports ribozymes to the cytoplasm. 构建有效将核酶转运到细胞质的核酶表达系统。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.203
M Sano, T Kuwabara, Y Nara, M Warashina, K Taira
{"title":"Construction of a ribozyme-expression system that effectively transports ribozymes to the cytoplasm.","authors":"M Sano,&nbsp;T Kuwabara,&nbsp;Y Nara,&nbsp;M Warashina,&nbsp;K Taira","doi":"10.1093/nass/44.1.203","DOIUrl":"https://doi.org/10.1093/nass/44.1.203","url":null,"abstract":"<p><p>In our previous studies, it was demonstrated that the activity of a ribozyme in vivo was governed by several parameters, which include a high level-expression of ribozyme, the intracellular stability of the ribozyme and colocalization of the ribozyme with its target RNA in the same cellular compartment. To generate ribozymes with significant activity in vivo, we have developed a ribozyme-expression system based on a human tRNA(Val) promoter. Our tRNA-embedded ribozymes produced by our ribozyme-expression system remain relatively stable in cultured cells with half-lives longer than 30 min. Moreover, tRNA-ribozymes with a cloverleaf structure were efficiently exported from the nucleus to the cytoplasm, where they would effectively cleave target RNAs. In the present study, we investigated the relationship between the secondary structure of the tRNA-ribozymes and the transport efficacy of them in mammalian cells by using a screening system in vivo. Furthermore, we also investigated the mechanism of the export of tRNA-embedded ribozymes both in mammalian cells and in Xenopus oocytes.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.203","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518392","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
Salt-dependent folding of long duplex DNA by histone H1. 组蛋白H1对长双工DNA的盐依赖性折叠。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.293
Y Yoshikawa, T Kanbe
{"title":"Salt-dependent folding of long duplex DNA by histone H1.","authors":"Y Yoshikawa,&nbsp;T Kanbe","doi":"10.1093/nass/44.1.293","DOIUrl":"https://doi.org/10.1093/nass/44.1.293","url":null,"abstract":"<p><p>It is found that T4 phage DNA complexed with histone H1 assembled into a string-of-bead structure, when the complex is prepared by a gentle diluting procedure from a high salt solution (2 M NaCl) to a low salt solution (50 mM NaCl). We used fluorescence microscopy to perform the real-time observation on formation and motion of a string-of-bead structure. Spatial histone H1 distribution on the DNA-H1 complex is observed by immuno-fluorescence microscopy.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.293","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518608","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
Smart probe: a novel fluorescence quenching-based oligonucleotide probe carrying a fluorophore and an intercalator. 智能探针:一种基于荧光猝灭的新型寡核苷酸探针，携带荧光团和插层器。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.297
A Yamane
{"title":"Smart probe: a novel fluorescence quenching-based oligonucleotide probe carrying a fluorophore and an intercalator.","authors":"A Yamane","doi":"10.1093/nass/44.1.297","DOIUrl":"https://doi.org/10.1093/nass/44.1.297","url":null,"abstract":"<p><p>A novel probe (Smart probe) has been developed for nucleic acid detection. The smart probe is an oligodeoxyribonucleotide carrying a fluorophore and an intercalator internally. Fluorescence of the smart probe is quenched by the intercalator in the absence of target sequence. While upon hybridization the probe emits greater fluorescence due to the interference of quenching by intercalation. The smart probe has been shown to recognize a single base mismatch in the double-stranded form without utilizing thermal stability difference of hybrids.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.297","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518610","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
Toward structural and functional genomics of Agrobacterium tumefaciens: linkage map of the left region of linear chromosome. 农杆菌结构与功能基因组学研究:线性染色体左区连锁图谱。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.97
D M De Costa, K Suzuki, K Yoshida
{"title":"Toward structural and functional genomics of Agrobacterium tumefaciens: linkage map of the left region of linear chromosome.","authors":"D M De Costa,&nbsp;K Suzuki,&nbsp;K Yoshida","doi":"10.1093/nass/44.1.97","DOIUrl":"https://doi.org/10.1093/nass/44.1.97","url":null,"abstract":"<p><p>Genome of A. tumefaciens contains a linear and a circular chromosome. As an initial step of elucidating the structural and functional genomics of this bacterium, linkage map of the left region of its linear chromosome was constructed. Total genomic libraries of A. tumefaciens MAFF301001 were constructed in BAC vectors namely, pFOS1 and pBeloBAC11. Upon construction of sub-libraries, minimum overlapping clones needed to cover the left region was determined. So far, four contigs have been assembled with a total of 19 overlapping clones. Detailed EcoRI physical map of contig III was constructed and it covers a 110 kb region of the Pme5 fragment of the linear chromosome. Seven end regions of the linking clones were partially sequenced but no gene existence was determined due to low homology.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.97","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518711","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
Posttranscriptional modification of transfer RNA in the submarine hyperthermophile Pyrolobus fumarii. 海底超嗜热菌富马氏焦叶菌转移RNA的转录后修饰。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.267
J A McCloskey, X H Liu, P F Crain, E Bruenger, R Guymon, T Hashizume, K O Stetter
{"title":"Posttranscriptional modification of transfer RNA in the submarine hyperthermophile Pyrolobus fumarii.","authors":"J A McCloskey,&nbsp;X H Liu,&nbsp;P F Crain,&nbsp;E Bruenger,&nbsp;R Guymon,&nbsp;T Hashizume,&nbsp;K O Stetter","doi":"10.1093/nass/44.1.267","DOIUrl":"https://doi.org/10.1093/nass/44.1.267","url":null,"abstract":"<p><p>In the RNA of hyperthermophiles, which grow optimally between 80 degrees C and 106 degrees C, posttranscriptional modification has been identified as a leading mechanism of structural stabilization. Particularly in the Archaeal evolutionary domain these modifications are expressed as a structurally diverse array of modification motifs, many of which include ribose methylation. Using mass spectrometric techniques we have examined the posttranscriptional modifications in unfractionated tRNA from the remarkable organism Pyrolobus fumarii, which grows optimally at 106 degrees C, but up to 113 degrees C (Blöchl et al. (1997), Extremophiles, 1, 14-21). Twenty-six modified nucleosides were detected, 11 of which are methylated in ribose. A new RNA nucleoside, 1,2'-O-dimethylguanosine (m1Gm) was characterized and the structure confirmed by chemical synthesis.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.267","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518719","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: 25
Photo-regulation of DNA/RNA duplex formation by azobenzene-tethered DNA towards antisense strategy. 偶氮苯拴链DNA对反义策略下DNA/RNA双链形成的光调控。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.277
X Liang, T Yoshida, H Asanuma, M Komiyama
{"title":"Photo-regulation of DNA/RNA duplex formation by azobenzene-tethered DNA towards antisense strategy.","authors":"X Liang,&nbsp;T Yoshida,&nbsp;H Asanuma,&nbsp;M Komiyama","doi":"10.1093/nass/44.1.277","DOIUrl":"https://doi.org/10.1093/nass/44.1.277","url":null,"abstract":"<p><p>Modified DNA carrying an azobenzene was successfully applied to the photo-regulation of DNA/RNA hybridization. When the azobenzene was isomerized from trans- to cis-form on UV-irradiation, the melting temperature of the duplex was significantly lowered. This process was totally reversible so that the Tm increased by cis-->trans isomerization induced by visible light irradiation.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.277","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518724","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: 6
Quantification analysis of translation initiation signal in vertebrate mRNAs: effect of nucleotides at positions +4(-)+6 upon efficiency of translation initiation. 脊椎动物mrna翻译起始信号的定量分析:+4(-)+6位点核苷酸对翻译起始效率的影响。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.77
Y Iida, D Kanagu
{"title":"Quantification analysis of translation initiation signal in vertebrate mRNAs: effect of nucleotides at positions +4(-)+6 upon efficiency of translation initiation.","authors":"Y Iida,&nbsp;D Kanagu","doi":"10.1093/nass/44.1.77","DOIUrl":"https://doi.org/10.1093/nass/44.1.77","url":null,"abstract":"Concerning the translation initiation signal in vertebrate mRNAs, a consensus, sequence, (GCC)GCC(A or G) CCATGG, has been proposed, but actual initiation sequences differ from it in a greater or lesser degree. Kozak monitored selection by ribosomes of the first versus second ATG codons as a function of mutations introduced at positions +4, and +6 of the first ATG codon. Codons possessing G at +4 strongly enhanced selection of the first ATG codon. However, ATG codon recognition was unaffected by most mutations in positions and +6. These data were well understood by our quantification analysis.","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.77","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517650","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
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