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Structure and affinity of DNA binding peptides. DNA结合肽的结构和亲和力。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.49
T Kubo, K Yokoyama, R Ueki, S Abe, K Goto, T Niidome, H Aoyagi, K Iwakuma, S Ando, S Ono, M Fujii
{"title":"Structure and affinity of DNA binding peptides.","authors":"T Kubo,&nbsp;K Yokoyama,&nbsp;R Ueki,&nbsp;S Abe,&nbsp;K Goto,&nbsp;T Niidome,&nbsp;H Aoyagi,&nbsp;K Iwakuma,&nbsp;S Ando,&nbsp;S Ono,&nbsp;M Fujii","doi":"10.1093/nass/44.1.49","DOIUrl":"https://doi.org/10.1093/nass/44.1.49","url":null,"abstract":"<p><p>Artificial peptides designed to form alpha-helical, beta-turn, antiparallel beta-sheet and beta-hairpin structures which are among the motifs most frequently found in natural DNA/RNA binding proteins were synthesized and their characteristic features were examined in the presence or absence of double or triple stranded DNA by means of UV melting experiments, CD spectra, SPR measurements. It was revealed that amphiphilic character arising from the specific secondary structures and positive charge in the hydrophobic face of peptides played an important role in the interaction with DNA, and that hybrid duplex and triplex were intensively stabilized by the cationic amphiphilic peptides. It was also found that these peptides could protect dsDNA against DNase 1 digestion. These results indicate that structurally designed amphiphilic peptides synthesized in the present study can be powerful tools for antisense and antigene strategies.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"49-50"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.49","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517740","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
DNA binding properties of DAPI (4',6-diamidino-2-phenylindole) analogs having an imidazoline ring or a tetrahydropyrimidine ring: groove-binding and intercalation. 具有咪唑啉环或四氢嘧啶环的DAPI(4′，6-二氨基-2-苯基吲哚)类似物的DNA结合特性:凹槽结合和插层。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.53
Y Kubota, K Kubota, S Tani
{"title":"DNA binding properties of DAPI (4',6-diamidino-2-phenylindole) analogs having an imidazoline ring or a tetrahydropyrimidine ring: groove-binding and intercalation.","authors":"Y Kubota,&nbsp;K Kubota,&nbsp;S Tani","doi":"10.1093/nass/44.1.53","DOIUrl":"https://doi.org/10.1093/nass/44.1.53","url":null,"abstract":"<p><p>DAPI analogs containing an imidazoline ring or a tetrahydropyrimidine ring have been synthesized to study DNA binding properties. Spectroscopic (absorption, CD, flow dichroism and fluorescence) and viscosity measurements indicate that DAPI analogs interact with DNA both by intercalation and by groove binding. The solution structures of complexes between DAPI analog and DNA oligomers have been characterized by proton NMR spectroscopy.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"53-4"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.53","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517742","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: 21
Lithiation study on D4T. D4T的锂化研究。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.107
H Kumamoto, H Tanaka
{"title":"Lithiation study on D4T.","authors":"H Kumamoto,&nbsp;H Tanaka","doi":"10.1093/nass/44.1.107","DOIUrl":"https://doi.org/10.1093/nass/44.1.107","url":null,"abstract":"<p><p>Upon treatment with LTMP, 5'-O-protected D4T undergoes deprotonation of the vinylic proton (H-3' or H-2'): when 5'-O-silyl derivative was used, the 3'-C-silylated product was formed as a result of C3'-lithiation and subsequent O-->C silyl migration, while deprotonation at the 2'-position led to the formation of an allene derivative. A stannyl version of this reaction was also examined to develop a method for C3'-functionalization of D4T.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"107-8"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.107","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518141","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 carbocyclic nucleosides and their SAH hydrolase inhibitory activities. 碳环核苷的合成及其对SAH水解酶的抑制作用。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.111
Y Kitade, A Kozaki, T Miwa, M Nakanishi, C Yatome
{"title":"Synthesis of carbocyclic nucleosides and their SAH hydrolase inhibitory activities.","authors":"Y Kitade,&nbsp;A Kozaki,&nbsp;T Miwa,&nbsp;M Nakanishi,&nbsp;C Yatome","doi":"10.1093/nass/44.1.111","DOIUrl":"https://doi.org/10.1093/nass/44.1.111","url":null,"abstract":"<p><p>The cellular enzyme S-adenosyl-L-homocysteine (SAH) hydrolase has emerged as a target enzyme for the molecular design of anti-viral agents. Recently, SAH hydrolase has been considered as an attractive target in parasite chemotherapy for malaria. We report synthesis of several carbocyclic purine nucleosides and their inhibitory activities against human and malaria recombinant SAH hydrolases.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"111-2"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.111","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518143","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
Chemical synthesis of hydroxymethylphosphonate alpha-DNA. 羟甲基膦酸α - dna的化学合成。
Nucleic acids symposium series Pub Date : 2000-01-01
Y Sato, G Tateno, T Wada, K Seio, M Sekine
{"title":"Chemical synthesis of hydroxymethylphosphonate alpha-DNA.","authors":"Y Sato,&nbsp;G Tateno,&nbsp;T Wada,&nbsp;K Seio,&nbsp;M Sekine","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>In this paper, we report the synthesis of hydroxymethylphosphonate alpha-DNAs and related compounds by use of the H-phosphonate method. These modified alpha-DNAs were designed to improve the inherent poor solubility of well-known methylphosphonate alpha-DNAs by introduction of a more hydrophilic hydroxymethylphosphonate function. The hybridization ability of hydroxymethylphosphonate alpha-DNAs was studied. We also report a novel strategy for the synthesis of alpha-thymidine by use of C1'-epimerization. The details of the neighboring effect of various 5'- and 3'-hydroxyl protective groups such as carbamoyl groups on the beta-->alpha conversion will be described.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"31-2"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518386","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 the P7 region within the catalytic core of the Tetrahymena ribozyme by employing in vitro selection. 四膜酶核酶催化核心P7区域的体外筛选分析。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.197
Y Oe, Y Ikawa, H Shiraishi, T Inoue
{"title":"Analysis of the P7 region within the catalytic core of the Tetrahymena ribozyme by employing in vitro selection.","authors":"Y Oe,&nbsp;Y Ikawa,&nbsp;H Shiraishi,&nbsp;T Inoue","doi":"10.1093/nass/44.1.197","DOIUrl":"https://doi.org/10.1093/nass/44.1.197","url":null,"abstract":"<p><p>The highly conserved P7 region is generally believed to act as a major portion of the catalytic site in the Group I intron ribozyme. However, its functions have not been elucidated except for the fact that it specifically binds a cofactor guanosine required for self-splicing reaction. We attempted an in vitro selection experiment to determine the sequence requirements of this region in the mechanism of catalysis by using the Tetrahymena ribozyme. We found that the selected active clones have the secondary structure similar to that of the wild type with few exceptions. However, their primary sequences were not conserved except G264 and C311 that are the major elements of the binding site for the guanosine. Our results suggest that the unique secondary structure of the P7 region is a primary requisite for the catalytic function of this class of ribozymes.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"197-8"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.197","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518389","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
An efficient synthesis of nucleotides via the phosphoramidite method using a triflic acid salt of an imidazole-related compound as a promoter. 利用咪唑相关化合物的三羧酸盐作为启动子，通过磷酰胺法有效地合成核苷酸。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.137
A Sakakura, M Kataoka, R Kawai, Y Hayakawa
{"title":"An efficient synthesis of nucleotides via the phosphoramidite method using a triflic acid salt of an imidazole-related compound as a promoter.","authors":"A Sakakura,&nbsp;M Kataoka,&nbsp;R Kawai,&nbsp;Y Hayakawa","doi":"10.1093/nass/44.1.137","DOIUrl":"https://doi.org/10.1093/nass/44.1.137","url":null,"abstract":"<p><p>N-Phenylimidazolium triflate and N-methylbenzimidazolium triflate, new imidazole-related compound/triflic acid-complex type of promoters in the phosphoramidite method, has been developed. These reagents are, particularly, useful for internucleotide-bond formation with lowly reactive reactants and have allowed an efficient, high-yield synthesis of oligodeoxyribonucleotides both in a solution phase and on a solid supports.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"137-8"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.137","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518003","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
Mutagenicity of 5-formyluracil in mammalian cells. 5-甲酰基尿嘧啶在哺乳动物细胞中的致突变性。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.81
H Kamiya, N Murata-Kamiya, N Karino, Y Ueno, A Matsuda, H Kasai
{"title":"Mutagenicity of 5-formyluracil in mammalian cells.","authors":"H Kamiya,&nbsp;N Murata-Kamiya,&nbsp;N Karino,&nbsp;Y Ueno,&nbsp;A Matsuda,&nbsp;H Kasai","doi":"10.1093/nass/44.1.81","DOIUrl":"https://doi.org/10.1093/nass/44.1.81","url":null,"abstract":"<p><p>5-Formyluracil, a major oxidized form of thymine, was incorporated into a predetermined site of one of the leading and lagging template strands of a double-stranded vector, and the DNA replication efficiency and the mutation frequency of 5-formyluracil in simian COS-7 cells were investigated. 5-Formyluracil did not block DNA replication and was weakly mutagenic in simian cells. 5-Formyluracil primarily elicited base substitutions at the modified positions.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"81-2"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.81","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518703","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
Advances in gene technology: DNA, RNA and Cancer. Miami Bio/Technology Winter Symposium. February 5-9, 2000. Abstracts. 基因技术的进展:DNA、RNA和癌症。迈阿密生物/技术冬季研讨会。2000年2月5日至9日。摘要。
Nucleic acids symposium series Pub Date : 2000-01-01
{"title":"Advances in gene technology: DNA, RNA and Cancer. Miami Bio/Technology Winter Symposium. February 5-9, 2000. Abstracts.","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 43","pages":"1-94"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21748133","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
Atomic force microscope of drug-DNA interaction. 药物- dna相互作用的原子力显微镜。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.63
K Masuda, T Nakata, K Tamagake
{"title":"Atomic force microscope of drug-DNA interaction.","authors":"K Masuda,&nbsp;T Nakata,&nbsp;K Tamagake","doi":"10.1093/nass/44.1.63","DOIUrl":"https://doi.org/10.1093/nass/44.1.63","url":null,"abstract":"<p><p>We have been investigated the possibility of B-Z transition in ZnTMPyP-DNA interaction based on the observation of spectroscopic data. In this study, we found drastic change in the AFM image of supercoiled plasmid DNA when it was interacted with TMPyPs indicating that the considerable amount of unwinding of double helix or B-Z transition is induced by the drug-DNA interaction. Such phenomena were not observed for other cationic drugs examined.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"63-4"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.63","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517643","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
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