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Ferroceneacetyl naphthalene diimide as a new electrochemical ligand for DNA sensing. 二茂铁乙酰萘二亚胺作为一种新的DNA传感电化学配体。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.171
S Sato, K Yamashita, M Takagi, S Takenaka
{"title":"Ferroceneacetyl naphthalene diimide as a new electrochemical ligand for DNA sensing.","authors":"S Sato,&nbsp;K Yamashita,&nbsp;M Takagi,&nbsp;S Takenaka","doi":"10.1093/nass/44.1.171","DOIUrl":"https://doi.org/10.1093/nass/44.1.171","url":null,"abstract":"<p><p>New electrochemically active DNA ligand 1 was synthesized by the connection of ferroceneacetic acid at the terminal amino moieties of two imide substituents of naphthalene diimide. Electrochemical experiments in aqueous solution containing DMSO showed that the selectivity for double stranded DNA of 1 has increased from that of ligand 2 previously reported. The peak current of 1 shifted toward the negative side from that of 2, thereby shortening the time required for gene detection.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"171-2"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.171","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517396","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
Preparation of DNA catenanes and observation of their topological structures by atomic force microscopy. DNA链烷的制备及原子力显微镜对其拓扑结构的观察。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.229
H Yamaguchi, K Kubota, A Harada
{"title":"Preparation of DNA catenanes and observation of their topological structures by atomic force microscopy.","authors":"H Yamaguchi,&nbsp;K Kubota,&nbsp;A Harada","doi":"10.1093/nass/44.1.229","DOIUrl":"https://doi.org/10.1093/nass/44.1.229","url":null,"abstract":"<p><p>DNA catenanes have been prepared by the reaction of T4 DNA ligase with linear DNA in the presence of nicked DNA. Single molecular images of DNA catenanes and large circular DNAs have been clearly observed by AFM using a tapping mode at room temperature and in an ambient atmosphere.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"229-30"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.229","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517754","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: 9
Synthesis of non-natural DNA using DNA polymerase. 利用DNA聚合酶合成非天然DNA。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.143
Y Ebara, T Sugiyama, K Kaihatsu, S Ueji
{"title":"Synthesis of non-natural DNA using DNA polymerase.","authors":"Y Ebara,&nbsp;T Sugiyama,&nbsp;K Kaihatsu,&nbsp;S Ueji","doi":"10.1093/nass/44.1.143","DOIUrl":"https://doi.org/10.1093/nass/44.1.143","url":null,"abstract":"<p><p>Nonnatural nucleotide modified by glucose or galactose was synthesized to increase functional diversity of DNA library. These compounds were incorporated in a DNA double strand using Klenow Fragment as well as dTTP. These functional group could be ordered sequentially on a DNA double strand at intervals of few angstroms according to the designed template sequence within a few hours. This method must be useful to constructing nonnatural DNA library or designed supramolecular structures.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"143-4"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.143","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518006","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
Expression mechanism of the allosteric interactions in a ribozyme catalysis. 核酶催化变构相互作用的表达机制。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.205
M Araki, Y Okuno, Y Sugiura
{"title":"Expression mechanism of the allosteric interactions in a ribozyme catalysis.","authors":"M Araki,&nbsp;Y Okuno,&nbsp;Y Sugiura","doi":"10.1093/nass/44.1.205","DOIUrl":"https://doi.org/10.1093/nass/44.1.205","url":null,"abstract":"<p><p>The contribution of substrate binding to cooperative regulation in the rate process of ribozyme catalysis has been investigated using allosteric ribozymes. The high sensitivity to the substrate lengths is attributed to the catalytic core folding which proceeds due to the energetic contribution of the substrate binding. One role of the effector (FMN) is the promotion of the core folding through the stabilization of the aptamer domain. Another role is the inhibition of the cleavage chemistry by perturbing the intermediate state in the rate process. The total effects of these two types of kinetic regulation determine the substrate dependency of the cooperative interaction on the catalytic reaction. An adequate correlation between the type of regulation and the substrate binding is responsible for the cooperative interaction in the kinetic process.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"205-6"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.205","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518393","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
Triplex formation using ODN conjugates with polycation comb-type copolymer. 用ODN与聚阳离子共轭梳型共聚物形成三聚体。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.209
M Ueda, M Saito, T Ishihara, T Akaike, A Maruyama
{"title":"Triplex formation using ODN conjugates with polycation comb-type copolymer.","authors":"M Ueda,&nbsp;M Saito,&nbsp;T Ishihara,&nbsp;T Akaike,&nbsp;A Maruyama","doi":"10.1093/nass/44.1.209","DOIUrl":"https://doi.org/10.1093/nass/44.1.209","url":null,"abstract":"<p><p>Polycation comb-type copolymer that is composed of polylysine backbone and dextran side chains (PLL-g-Dex) has previously been shown to stabilize duplex and triplex DNAs quite effectively. In this study, we have conjugated PLL-g-Dex with oligonucleotides (ODN) aiming to increase the triplex stabilizing efficiency of the copolymer. Here we have demonstrated that the copolymer-TFO conjugates selectively stabilize triplex DNA. Also its potential to form triplex DNA was found to be greater than PLL-g-Dex/ODN mixture.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"209-10"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.209","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518395","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
Genome structure of Ri plasmid (3). Sequencing analysis of the vir region of pRi1724 in Japanese Agrobacterium rhizogenes. Ri质粒的基因组结构(3).日本根农杆菌pRi1724 vir区序列分析。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.95
N Satuti, K Moriguchi, M Sato, M Kataoka, Y Maeda, N Tanaka, K Yoshida
{"title":"Genome structure of Ri plasmid (3). Sequencing analysis of the vir region of pRi1724 in Japanese Agrobacterium rhizogenes.","authors":"N Satuti,&nbsp;K Moriguchi,&nbsp;M Sato,&nbsp;M Kataoka,&nbsp;Y Maeda,&nbsp;N Tanaka,&nbsp;K Yoshida","doi":"10.1093/nass/44.1.95","DOIUrl":"https://doi.org/10.1093/nass/44.1.95","url":null,"abstract":"<p><p>The entire genome of the pRi1724 (217.6-kb) in the mikimopine type Agrobacterium rhizogenes strain MAFF03-01724 has been completely sequenced. The vir region covering 30.2-kb has found to be composed of 21 genes resembling virH1, virA, virB1-11, virG, virC1-2, and virD1-5. The structural organization of the pRi1724 vir operons in this study is exactly the same as that of the previously reported vir operons of other Ri or Ti plasmids, although the size of some ORFs showed little variations among the plasmids. We also found virE3 gene in the pRi1724 (1), but different from Ti plasmids, virE1 and virE2 that are also important for the virulence do not exist in the vir region of pRi1724.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"95-6"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.95","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518710","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
Improvement of IGCR technique using FRET. 利用FRET技术改进IGCR技术。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.159
T Yasukochi, A Ooyama, H Kumazawa, J Kawanabe, K Ozawa, Y Shibanaka
{"title":"Improvement of IGCR technique using FRET.","authors":"T Yasukochi,&nbsp;A Ooyama,&nbsp;H Kumazawa,&nbsp;J Kawanabe,&nbsp;K Ozawa,&nbsp;Y Shibanaka","doi":"10.1093/nass/44.1.159","DOIUrl":"https://doi.org/10.1093/nass/44.1.159","url":null,"abstract":"<p><p>The fluorescent detection system has been introduced into the study on denaturation/reassociation process of DNA fragments in gel, for improving In-Gel Competitive Reassociation technique, one of genome subtraction methods. The annealing behaviour of the mixture of 3'-Fluorescein-labelled and 5'-Cy5-labelled DNA fragments was analysed by Fluorescence Resonance Energy Transfer (FRET) technique from donor Fluorescein to acceptor Cy5. We showed that two fluorescent dyes labelled at 3' and 5' ends of DNA fragments caused FRET in both the solution and the gel. The characterisation of fluorescence-labelled fragments in gel and the changes of their fluorescence intensity will be reported.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"159-60"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.159","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517390","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
Thermodynamic analyses of triplex formation with homopurine oligonucleotide. 同嘌呤寡核苷酸形成三络合物的热力学分析。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.61
H Torigoe, R Shimizume
{"title":"Thermodynamic analyses of triplex formation with homopurine oligonucleotide.","authors":"H Torigoe,&nbsp;R Shimizume","doi":"10.1093/nass/44.1.61","DOIUrl":"https://doi.org/10.1093/nass/44.1.61","url":null,"abstract":"<p><p>We analyzed the thermodynamics of purine motif triplex formation by isothermal titration calorimetry. The signs of calorimetric enthalpy change, delta Hcal, and entropy change, delta S, of the triplex formation were negative in the temperature range between 15 and 35 degrees C. Since an observed negative delta S was unfavorable for the triplex formation, the triplex formation was driven by a large negative delta Hcal. delta Hcal decreased with increasing temperature, yielding a negative heat capacity change, delta Cp, of approximately -1.2 kcal mol-1 K-1. We found that the binding constant, Ka, increased with increasing temperature, leading to an apparent positive van't Hoff enthalpy change, delta Hvh, which was in sharp contrast with the large negative delta Hcal. The analyses of the observed temperature dependence of Ka and delta Hcal and the negative delta Cp suggest that the purine motif triplex formation near room temperature is not a simple two-state binding process but exhibits multiple states, which was previously observed for the pyrimidine motif triplex formation near room temperature.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"61-2"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.61","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517642","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
X-ray analyses of two DNA dodecamers containing N4-methoxy-cytosine paired with adenine or guanine. 含有n4 -甲氧基胞嘧啶与腺嘌呤或鸟嘌呤配对的两个DNA十二聚体的x射线分析。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.239
M T Hossain, T Hikima, M Tsunoda, T Chatake, Y Ueno, A Matsuda, A Takénaka
{"title":"X-ray analyses of two DNA dodecamers containing N4-methoxy-cytosine paired with adenine or guanine.","authors":"M T Hossain,&nbsp;T Hikima,&nbsp;M Tsunoda,&nbsp;T Chatake,&nbsp;Y Ueno,&nbsp;A Matsuda,&nbsp;A Takénaka","doi":"10.1093/nass/44.1.239","DOIUrl":"https://doi.org/10.1093/nass/44.1.239","url":null,"abstract":"<p><p>To investigate mismatch of base-pairings in relation to mutagenesis by oxyamines, crystal structures of two DNA dodecamers with the sequence d(CGCZAA TTmo4CGCG) (Z = A or G), containing N4-methoxy-cytosine (mo4C), have been determined by X-ray analysis. These dodecamers essentially form right-handed B-form duplexes, respectively. In the dodecamer with Z = A, the two mo4C residues are adapted in imino form with the anti methoxyl group to form pairs with A on the opposite strand in a manner of Watson-Crick fashion. While in the dodecamer with Z = G, one mo4C in amino form with the anti methoxyl group forms a normal Watson-Crick pair with G, but the other one in imino form with syn methoxyl conformation wobbles with G. Based on these results, possible mutation mechanism has been proposed.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"239-40"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.239","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517652","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 selection by using mutated GCN4-bZIP peptides for analysis of peptide-DNA interactions. 利用突变GCN4-bZIP肽进行体外筛选，分析肽与dna的相互作用。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.245
H Furusawa, T Morii, Y Okahata
{"title":"In vitro selection by using mutated GCN4-bZIP peptides for analysis of peptide-DNA interactions.","authors":"H Furusawa,&nbsp;T Morii,&nbsp;Y Okahata","doi":"10.1093/nass/44.1.245","DOIUrl":"https://doi.org/10.1093/nass/44.1.245","url":null,"abstract":"<p><p>In vitro selection has been used as a method to determine the optimal binding site for DNA-binding proteins. We report here in vitro selection of dsDNA sequences that bind to mutated-GCN4-bZIP peptides. The GCN4-bZIP peptide mutated from alanine to histidine on a position-14 that contacts with DNA bound to different sequence from a binding site of wild type peptide.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"245-6"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.245","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517655","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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