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Classification of 3D structural character of RNA by hydrogen bond and base stacking. 基于氢键和碱基堆叠的RNA三维结构特征分类。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.227
A Takasu, K Watanabe, G Kawai
{"title":"Classification of 3D structural character of RNA by hydrogen bond and base stacking.","authors":"A Takasu,&nbsp;K Watanabe,&nbsp;G Kawai","doi":"10.1093/nass/44.1.227","DOIUrl":"https://doi.org/10.1093/nass/44.1.227","url":null,"abstract":"<p><p>We are developing a computational system to classify RNA structures by its structural character. Here, an improved grouping algorithm was introduced to the system and the base-stacking pattern (BSP) is used as a criterion for the classification in addition to hydrogen-bond pattern (HBP). 279 conformers of 15 mer RNA hairpin were classified into 89 and 36 groups by HBP and BSP, respectively, suggesting that HBP represents conformational character better than BSP.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"227-8"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.227","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517753","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
Acceleration of DNA strand exchange by polycation comb-type copolymer. 用多阳离子梳型共聚物加速DNA链交换。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.289
W J Kim, T Ishihara, T Akaike, A Maruyama
{"title":"Acceleration of DNA strand exchange by polycation comb-type copolymer.","authors":"W J Kim,&nbsp;T Ishihara,&nbsp;T Akaike,&nbsp;A Maruyama","doi":"10.1093/nass/44.1.289","DOIUrl":"https://doi.org/10.1093/nass/44.1.289","url":null,"abstract":"<p><p>The accelerating effect of cationic substances on DNA strand exchange reaction between 20 bp DNA duplex and its complementary single strand was studied. A comb-type polycationic copolymer which is composed of poly (L-lysine) backbone and dextran graft chain (PLL-g-Dex) and known to stabilize triplex DNA expedites the strand exchange reaction under physiological relevant conditions. Electrostatically small excess of the copolymer increased DNA strand exchange rate by 300-fold while large excess of spermine or cethyltrimethylammonium bromide, cationic detergent known to promote markedly hybridization of complementary DNA strands, showed slight effect. It should be noted that the copolymer promotes the strand exchange reaction while it stabilizes double stranded DNA.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"289-90"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.289","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518606","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
Fluorescent labelling of ribonucleosides at 2'-terminus; comparative fluorescence studies. 2′端核糖核苷的荧光标记比较荧光研究。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.291
A Misra, S Tripathi, K Misra
{"title":"Fluorescent labelling of ribonucleosides at 2'-terminus; comparative fluorescence studies.","authors":"A Misra,&nbsp;S Tripathi,&nbsp;K Misra","doi":"10.1093/nass/44.1.291","DOIUrl":"https://doi.org/10.1093/nass/44.1.291","url":null,"abstract":"<p><p>In case of RNA's, multiple labelling can be achieved by exploiting the available 2'-OH position of sugar moiety of nucleosides. N-protected nucleoside viz. cytidine has been prepared using a selective photolabile group i.e. 2-nitrobenzyloxycarbonyl. After protection of 5',3'-OH with 1,1,3,3,-tetraisopropyl disiloxyl group, 2'-OH was selectively activated by using N,N'-carbonyl diimidazole (CDI) and subsequently condensed with dansyl amide. After usual deprotection step comparative fluorescence studies of the monomer were carried out using different solvents/buffers.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"291-2"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.291","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518607","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
Analysis of aptamer binding site for HCV-NS3 protease by alanine scanning mutagenesis. 丙氨酸扫描诱变HCV-NS3蛋白酶适体结合位点分析。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.253
J Hwang, H Fauzi, K Fukuda, S Sekiya, N Kakiuchi, K Taira, I Kusakabe, S Nishikawa
{"title":"Analysis of aptamer binding site for HCV-NS3 protease by alanine scanning mutagenesis.","authors":"J Hwang,&nbsp;H Fauzi,&nbsp;K Fukuda,&nbsp;S Sekiya,&nbsp;N Kakiuchi,&nbsp;K Taira,&nbsp;I Kusakabe,&nbsp;S Nishikawa","doi":"10.1093/nass/44.1.253","DOIUrl":"https://doi.org/10.1093/nass/44.1.253","url":null,"abstract":"<p><p>Nonstructural protein 3 (NS3) of Hepatitis C virus (HCV) is a multifunctional protein and possesses protease, nucleotide triphosphatase and helicase activities. The N-terminal domain of NS3 (amino acids 1027-1218; delta NS3) has a trypsin-like protease activity and is essential for processing of viral polyprotein. Accordingly it is a potential target for anti-HCV drugs and we isolated RNA aptamers (Kd = 10 nM, Ki = 100 nM) using in vitro selection strategy. To study the interaction between delta NS3 and its aptamer, we applied alanine scanning mutagenesis and constructed seven mutant proteins at positive amino acid residues on the surface of delta NS3. Binding and inhibitory activities of the NS3 aptamer against mutant proteins were kinetically analyzed. These results clarified that especially Arg161 and Arg130 are important for interaction with the NS3 aptamer.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"253-4"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.253","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517659","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
Efficient cross-linking to cytidine using substituted phenylsulfide derivatives of 2-amino-6-vinylpurine nucleoside via synchronous activation within duplex. 通过双相内同步激活，利用取代的2-氨基-6-乙烯基嘌呤核苷的苯基硫化物衍生物与胞苷进行高效交联。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.129
T Kawasaki, F Nagatsugi, M Maeda, S Sasaki
{"title":"Efficient cross-linking to cytidine using substituted phenylsulfide derivatives of 2-amino-6-vinylpurine nucleoside via synchronous activation within duplex.","authors":"T Kawasaki,&nbsp;F Nagatsugi,&nbsp;M Maeda,&nbsp;S Sasaki","doi":"10.1093/nass/44.1.129","DOIUrl":"https://doi.org/10.1093/nass/44.1.129","url":null,"abstract":"<p><p>We have previously described that oligonucleotides containing phenylsulfoxide derivative of 2-amino-6-vinyulpurine nucleoside analog (1) are activated within duplex to form cross-link toward cytidine selectively at the target site. The new cross-linking motif with phenylsulfoxide structure (2) is characteristic in that the stable precursor may be transformed automatically within duplex to a reactive species. To search for more stable precursor susceptible for activation, we designed a series of substituted phenylsulfide analogs of 1. It has been demonstrated that introduction of an electron-donating group on the phenyl ring improved the cross-linking reaction. Particularly, 2-carboxyphenyl sulfide derivative exhibited cross-linking as effectively as phenylsulfoxide derivative without chemical oxidation prior to cross-linking.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"129-30"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.129","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517999","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
DNA binding of a basic leucine-zipper protein with novel folding domain. 一种新型折叠结构域的碱性亮氨酸拉链蛋白的DNA结合。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.13
S Sato, K Makino, T Morii
{"title":"DNA binding of a basic leucine-zipper protein with novel folding domain.","authors":"S Sato,&nbsp;K Makino,&nbsp;T Morii","doi":"10.1093/nass/44.1.13","DOIUrl":"https://doi.org/10.1093/nass/44.1.13","url":null,"abstract":"<p><p>DNA-binding proteins frequently utilize short alpha-helices as their critical DNA recognition elements. In this research, we have employed the structure-based design to construct a small domain that could target the specific DNA sequences recognized by the yeast transcriptional activator GCN4. The new DNA binding motif recognizes specific DNA sequences as a dimer with high affinity and specificity under the physiological conditions.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"13-4"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.13","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518378","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
Crystallization of the most active RNA-cleaving deoxyribozyme. 最活跃的rna切割脱氧核酶的结晶。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.201
J Kondo, A Takénaka
{"title":"Crystallization of the most active RNA-cleaving deoxyribozyme.","authors":"J Kondo,&nbsp;A Takénaka","doi":"10.1093/nass/44.1.201","DOIUrl":"https://doi.org/10.1093/nass/44.1.201","url":null,"abstract":"<p><p>The structural compositions of the most active deoxyribozyme and its derivatives have been examined by electrophoresis, and their crystallization conditions were surveyed for X-ray analysis. It has been found that Mg2+ ion is essential to form the active binary complex between the catalytic DNA and the substrate, and that heat-treatment is effective to prevent formation of the inactive quaternary complex between the two enzymes and the two substrates. Crystals obtained by the hanging drop vapor diffusion method are composed of the active binary complex.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"201-2"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.201","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518391","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
Development of a novel functional biosensor with a short Ca(2+)-dependent deoxyribozyme. 一种具有短Ca(2+)依赖性脱氧核酶的新型功能性生物传感器的研制。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.79
Y Okumoto, N Sugimoto
{"title":"Development of a novel functional biosensor with a short Ca(2+)-dependent deoxyribozyme.","authors":"Y Okumoto,&nbsp;N Sugimoto","doi":"10.1093/nass/44.1.79","DOIUrl":"https://doi.org/10.1093/nass/44.1.79","url":null,"abstract":"<p><p>We develop a novel functional biosensor on a deoxyribozyme. A 5'-end-immobilized short Ca(2+)-dependent deoxyribozyme (dCGCTGGCAGGCTACAACGAGTCTTC) binds to a target RNA substrate (rGAAGACA decrease UGCCAGCG; decrease denotes an RNA cleavage site), and acts as an enzyme in the presence of Ca2+. It cleaves the target RNA substrate at one site of rAp decrease U in the asymmetric internal loop.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"79-80"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.79","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518702","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
Unnatural base pairs between 2-amino-6-(2-thienyl)purine and the complementary bases. 2-氨基-6-(2-噻吩基)嘌呤与互补碱基之间的非自然碱基对。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.261
I Hirao, T Fujiwara, M Kimoto, T Mitsui, T Okuni, T Ohtsuki, S Yokoyama
{"title":"Unnatural base pairs between 2-amino-6-(2-thienyl)purine and the complementary bases.","authors":"I Hirao,&nbsp;T Fujiwara,&nbsp;M Kimoto,&nbsp;T Mitsui,&nbsp;T Okuni,&nbsp;T Ohtsuki,&nbsp;S Yokoyama","doi":"10.1093/nass/44.1.261","DOIUrl":"https://doi.org/10.1093/nass/44.1.261","url":null,"abstract":"<p><p>The unnatural base, 2-amino-6-(2-thienyl)purine (designated as s), instead of 2-amino-6-(N,N-dimethylamino)purine (designated as x), was designed in order to improve the specificity and efficiency of the base pairing with pyridin-2-one (designated as y). DNA fragments containing s were chemically synthesized, and the thermal stability and the enzymatic reactions involving the s-y pairing were examined. Thermal denaturation experiments showed that the DNA duplex (12-mer) containing the s-y pair was more stable than that containing the x-y pair. The incorporation of dyTP was also more advantageous to the s-y pairing than the x-y pairing in single-nucleotide insertion experiments using the Klenow fragment of Escherichia coli DNA polymerase I.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"261-2"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.261","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518716","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
Functional analysis of the pro-apoptotic factor Bax using hammerhead ribozymes. 用锤头核酶分析促凋亡因子Bax的功能。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.169
H Takeda, H Kawasaki, K Taira
{"title":"Functional analysis of the pro-apoptotic factor Bax using hammerhead ribozymes.","authors":"H Takeda,&nbsp;H Kawasaki,&nbsp;K Taira","doi":"10.1093/nass/44.1.169","DOIUrl":"https://doi.org/10.1093/nass/44.1.169","url":null,"abstract":"<p><p>A pro-apoptotic protein Bax is a Bcl-2 family member and forms homodimers and also heterodimerizes with death antagonists, Bcl-2 and Bcl-XL. To elucidate the detail of function of Bax in cells, we constructed a hammerhead ribozyme targeted to the Bax mRNA. The level of Bax protein in Hela-K cells expressing Bax-ribozyme was decreased compared with that of wild type Hela-K cells. Therefore, the Bax-ribozyme should be useful for the future investigations of the details of apoptosis pathway.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"169-70"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.169","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517395","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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