Pub Date : 2003-09-01DOI: 10.2174/1574090054484261
T. Wada, N. Oka, K. Saigo
Stereocontrolled synthesis of oligodeoxyribonucleoside phosphorothioates using nucleoside 3'-O-oxazaphospholidine derivatives as monomer units is described. N-(Cyanomethyl)pyrrolidinium triflate (CMPT) was found to be effective as an activator for the highly diastereoselective internucleotidec bond formation. The present method was applied to the solid-phase synthesis of stereoregulated oligodeoxyribonucleoside phosphorothioates.
{"title":"Stereocontrolled synthesis of phosphorothioate DNA by an oxazaphospholidine approach.","authors":"T. Wada, N. Oka, K. Saigo","doi":"10.2174/1574090054484261","DOIUrl":"https://doi.org/10.2174/1574090054484261","url":null,"abstract":"Stereocontrolled synthesis of oligodeoxyribonucleoside phosphorothioates using nucleoside 3'-O-oxazaphospholidine derivatives as monomer units is described. N-(Cyanomethyl)pyrrolidinium triflate (CMPT) was found to be effective as an activator for the highly diastereoselective internucleotidec bond formation. The present method was applied to the solid-phase synthesis of stereoregulated oligodeoxyribonucleoside phosphorothioates.","PeriodicalId":19724,"journal":{"name":"Nucleic acids research. Supplement","volume":"63 1","pages":"109-10"},"PeriodicalIF":0.0,"publicationDate":"2003-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78248032","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}
T. Sunami, T. Kobuna, J. Kondo, I. Hirao, Kimitsuna Watanabe, K. Miura, A. Takénaka
A DNA fragment d(GCGAAAGCT), known to adopt a stable mini-hairpin structure in solution, has been crystallized under a slightly acidic condition, and its crystal structure has been determined at 2.5A resolution. In the first half of the oligomer, the sequence CGAA forms a parallel duplex with another symmetry-related half through the homo base pairs, C2:C2+ (semi-protonated between the Watson-Crick sites), G3:G3 (between the minor groove sites), A4:A4 (between the major groove sites) and A5:A5 (between the Watson-Crick sites). The second halves of the parallel duplex are split away in the different direction, and extended to form an anti-parallel B-form duplex with another second half.
{"title":"Crystal structure of d(GCGAAAGCT) containing parallel-stranded duplex with homo base pairs and anti-parallel duplex with Watson-Crick base pairs.","authors":"T. Sunami, T. Kobuna, J. Kondo, I. Hirao, Kimitsuna Watanabe, K. Miura, A. Takénaka","doi":"10.1093/NASS/2.1.51","DOIUrl":"https://doi.org/10.1093/NASS/2.1.51","url":null,"abstract":"A DNA fragment d(GCGAAAGCT), known to adopt a stable mini-hairpin structure in solution, has been crystallized under a slightly acidic condition, and its crystal structure has been determined at 2.5A resolution. In the first half of the oligomer, the sequence CGAA forms a parallel duplex with another symmetry-related half through the homo base pairs, C2:C2+ (semi-protonated between the Watson-Crick sites), G3:G3 (between the minor groove sites), A4:A4 (between the major groove sites) and A5:A5 (between the Watson-Crick sites). The second halves of the parallel duplex are split away in the different direction, and extended to form an anti-parallel B-form duplex with another second half.","PeriodicalId":19724,"journal":{"name":"Nucleic acids research. Supplement","volume":"9 1","pages":"51-2"},"PeriodicalIF":0.0,"publicationDate":"2002-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87466159","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}
The modifications of N2,N2-dimethylguanine (m2(2)G) are found in tRNAs and rRNAs from eukarya and archaea. In tRNAs, modification at position G26 is generated by tRNA (m2(2)G26) methyltransferase, which is encoded by the corresponding gene, trm1. This enzyme catalyzes the methyl-transfer from S-adenosyl-L-methionine to the semi-conserved residue, G26, via the intermediate modified base, m2G26. Recent genome sequencing project has been reported that the putative trm1 is encoded in the genome of Aquifex aeolicus, a hyper-thermophilic eubacterium as only one exception among eubacteria. In order to confirm whether this bacterial trm1 gene product is a real tRNA (m2(2)G26) methyltransferase or not, we expressed this protein by wheat germ in vitro cell-free translation system. Our biochemical analysis clearly showed that this gene product possessed tRNA (m2(2)G26) methyltransferase activity.
{"title":"Identification of Aquifex aeolicus tRNA (m2(2G26) methyltransferase gene.","authors":"H. Takeda, H. Hori, Y. Endo","doi":"10.1093/NASS/2.1.229","DOIUrl":"https://doi.org/10.1093/NASS/2.1.229","url":null,"abstract":"The modifications of N2,N2-dimethylguanine (m2(2)G) are found in tRNAs and rRNAs from eukarya and archaea. In tRNAs, modification at position G26 is generated by tRNA (m2(2)G26) methyltransferase, which is encoded by the corresponding gene, trm1. This enzyme catalyzes the methyl-transfer from S-adenosyl-L-methionine to the semi-conserved residue, G26, via the intermediate modified base, m2G26. Recent genome sequencing project has been reported that the putative trm1 is encoded in the genome of Aquifex aeolicus, a hyper-thermophilic eubacterium as only one exception among eubacteria. In order to confirm whether this bacterial trm1 gene product is a real tRNA (m2(2)G26) methyltransferase or not, we expressed this protein by wheat germ in vitro cell-free translation system. Our biochemical analysis clearly showed that this gene product possessed tRNA (m2(2)G26) methyltransferase activity.","PeriodicalId":19724,"journal":{"name":"Nucleic acids research. Supplement","volume":"37 1","pages":"229-30"},"PeriodicalIF":0.0,"publicationDate":"2002-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77362079","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}
Pub Date : 2002-08-06DOI: 10.1107/S0108767302095892
T. Sunami, J. Kondo, M. Tsunoda, T. Sekiguchi, I. Hirao, Kimitsuna Watanabe, K. Miura, A. Takénaka
Crystal structure of a DNA fragment d(GCGAAGC), known to adopt a stable mini-hairpin structure in solution, has been determined at 1.6A resolution. Two heptamers are associated to form a duplex with a molecular two-fold symmetry. Three duplexes in the asymmetric unit have a similar structure. At the both ends of each duplexes, two Watson-Crick G:C pairs constitute the stem region. In the central part, two sheared pairs of G:A and A:G are formed, the two G bases being stacked as well as the two A bases. At this point, the two strands are crossed between the two base-stacked columns. The adenine moiety of the bulged A5 residue, which intercalates between the A4 and G6 residues, makes a small bending of the duplex at the two sites. The difference between the bulge-in structure of d(GCGAAGC) and the zipper-like duplex of d(GCGAAAGC) is ascribed to switching the partner of the sheared G:A pairs.
{"title":"X-ray structure of d(GCGAAGC); switching of partner for G:A pair in duplex form.","authors":"T. Sunami, J. Kondo, M. Tsunoda, T. Sekiguchi, I. Hirao, Kimitsuna Watanabe, K. Miura, A. Takénaka","doi":"10.1107/S0108767302095892","DOIUrl":"https://doi.org/10.1107/S0108767302095892","url":null,"abstract":"Crystal structure of a DNA fragment d(GCGAAGC), known to adopt a stable mini-hairpin structure in solution, has been determined at 1.6A resolution. Two heptamers are associated to form a duplex with a molecular two-fold symmetry. Three duplexes in the asymmetric unit have a similar structure. At the both ends of each duplexes, two Watson-Crick G:C pairs constitute the stem region. In the central part, two sheared pairs of G:A and A:G are formed, the two G bases being stacked as well as the two A bases. At this point, the two strands are crossed between the two base-stacked columns. The adenine moiety of the bulged A5 residue, which intercalates between the A4 and G6 residues, makes a small bending of the duplex at the two sites. The difference between the bulge-in structure of d(GCGAAGC) and the zipper-like duplex of d(GCGAAAGC) is ascribed to switching the partner of the sheared G:A pairs.","PeriodicalId":19724,"journal":{"name":"Nucleic acids research. Supplement","volume":"53 1","pages":"181-2"},"PeriodicalIF":0.0,"publicationDate":"2002-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82169571","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}
K. Haraguchi, M. Delaney, C. Wiederholt, A. Sambandam, Z. Hantosi, M. Greenberg
The preparation of oligonucleotides containing Fapy.dA (N4-(2-Deoxy-alpha,beta-D-erythro-pentofuranosyl)-4,6-diamino- 5-formamidopyrimidine) and Fapy.dG (N6-(2-Deoxy-alpha,beta-D-erythro-pento-furanosyl)-2,6- diamino-4-hydroxy-5-formamido-pyrimidine) at defined sites was achieved by introducing the lesions as dinucleotide phosphoramidites. Oligonucleotides as composed of as many as 36-nucleotides were prepared by solid-phase synthesis and/or a combination of chemical synthesis and enzymatic ligation. Oligonucleotides containing non-hydrolyzable analogues were also prepared. Oligonucleotides containing these modified nucleotides were characterized by a variety of chemical and biochemical methods.
含fpy寡核苷酸的制备。dA (N4-(2-脱氧- α， β -d -红-戊呋喃基)-4,6-二氨基- 5-甲脒嘧啶)和Fapy。dG (N6-(2- deoxy - α， β - d - red -戊-呋喃基)-2,6-二氨基-4-羟基-5-甲脒-嘧啶)是通过将病变引入二核苷酸磷酰胺而获得的。通过固相合成和/或化学合成和酶连接相结合的方法制备了由多达36个核苷酸组成的寡核苷酸。还制备了含有不可水解类似物的寡核苷酸。含有这些修饰的核苷酸的寡核苷酸通过各种化学和生化方法进行了表征。
{"title":"Synthesis and characterization of oligonucleotides containing formamidopyrimidine lesions (Fapy.dA, Fapy.dG) at defined sites.","authors":"K. Haraguchi, M. Delaney, C. Wiederholt, A. Sambandam, Z. Hantosi, M. Greenberg","doi":"10.1093/NASS/1.1.129","DOIUrl":"https://doi.org/10.1093/NASS/1.1.129","url":null,"abstract":"The preparation of oligonucleotides containing Fapy.dA (N4-(2-Deoxy-alpha,beta-D-erythro-pentofuranosyl)-4,6-diamino- 5-formamidopyrimidine) and Fapy.dG (N6-(2-Deoxy-alpha,beta-D-erythro-pento-furanosyl)-2,6- diamino-4-hydroxy-5-formamido-pyrimidine) at defined sites was achieved by introducing the lesions as dinucleotide phosphoramidites. Oligonucleotides as composed of as many as 36-nucleotides were prepared by solid-phase synthesis and/or a combination of chemical synthesis and enzymatic ligation. Oligonucleotides containing non-hydrolyzable analogues were also prepared. Oligonucleotides containing these modified nucleotides were characterized by a variety of chemical and biochemical methods.","PeriodicalId":19724,"journal":{"name":"Nucleic acids research. Supplement","volume":"23 1","pages":"129-30"},"PeriodicalIF":0.0,"publicationDate":"2001-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80831170","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}
Pub Date : 2001-11-01DOI: 10.14891/ANALSCISP.17ICAS.0.I1449.0
T. Nojima, Yasumitsu Kondoh, S. Takenaka, Teruhisa Ichihara, Makoto Takagi, Hideo Tashiro, Kazuko Matsumoto
Toward development of a DNA microarray system in which neither labeling nor amplification of the nucleic acids from living cell is required, we have developed a new method for the detection and quantification of target DNA hybridized with probe DNA fixed on a solid surface. This method utilizes a fluorescent intercalator: naphthalene diimide derivative carrying two fluorescent tetradentate beta-diketone-Eu3+ chelates. This compound selectively binds to double stranded DNA (dsDNA) fixed on a plastic assay plate. The amount of the compound bound to single stranded DNA (ssDNA) is negligible. The fluorescent intensity of Eu3+ was in proportion to the amount of the fixed DNA, showing that the compound quantitatively binds to dsDNA. Therefore, this method can be used not only to detect dsDNA, but also to measure the amount of DNA on a solid surface.
{"title":"Detection of DNA hybridization by use of a lanthanide fluorescent intercalator that specifically binds to double stranded DNA.","authors":"T. Nojima, Yasumitsu Kondoh, S. Takenaka, Teruhisa Ichihara, Makoto Takagi, Hideo Tashiro, Kazuko Matsumoto","doi":"10.14891/ANALSCISP.17ICAS.0.I1449.0","DOIUrl":"https://doi.org/10.14891/ANALSCISP.17ICAS.0.I1449.0","url":null,"abstract":"Toward development of a DNA microarray system in which neither labeling nor amplification of the nucleic acids from living cell is required, we have developed a new method for the detection and quantification of target DNA hybridized with probe DNA fixed on a solid surface. This method utilizes a fluorescent intercalator: naphthalene diimide derivative carrying two fluorescent tetradentate beta-diketone-Eu3+ chelates. This compound selectively binds to double stranded DNA (dsDNA) fixed on a plastic assay plate. The amount of the compound bound to single stranded DNA (ssDNA) is negligible. The fluorescent intensity of Eu3+ was in proportion to the amount of the fixed DNA, showing that the compound quantitatively binds to dsDNA. Therefore, this method can be used not only to detect dsDNA, but also to measure the amount of DNA on a solid surface.","PeriodicalId":19724,"journal":{"name":"Nucleic acids research. Supplement","volume":"144 1","pages":"105-6"},"PeriodicalIF":0.0,"publicationDate":"2001-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89028176","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}
Theophylline was converted to 7-(2-phenyl-2-methanesulfonyloxy)ethyl congener and the product was treated with ammonia or primary amines in a mixture solution of water and organic solvents. Two products were proven to be the styrene analogue and 7-(2-amino-2-phenylethyl)theophylline. The structure of the third product was elucidated as the 1,2,3,6-tetrahydro-6-imino-2-oxo-7H-purine derivatives by spectroscopic analysis including HMBC correlation and X-ray crystallography.
{"title":"Reaction of 7-(2-mesyloxy-2-phenylethyl)theophylline with amines: Synthesis of 1,2,3,6-tetrahydro-6-imino-2-oxo-7H-purine derivatives.","authors":"S. Kozai, K. Ogimoto, H. Okamoto, T. Maruyama","doi":"10.1093/NASS/1.1.27","DOIUrl":"https://doi.org/10.1093/NASS/1.1.27","url":null,"abstract":"Theophylline was converted to 7-(2-phenyl-2-methanesulfonyloxy)ethyl congener and the product was treated with ammonia or primary amines in a mixture solution of water and organic solvents. Two products were proven to be the styrene analogue and 7-(2-amino-2-phenylethyl)theophylline. The structure of the third product was elucidated as the 1,2,3,6-tetrahydro-6-imino-2-oxo-7H-purine derivatives by spectroscopic analysis including HMBC correlation and X-ray crystallography.","PeriodicalId":19724,"journal":{"name":"Nucleic acids research. Supplement","volume":"22 1","pages":"27-8"},"PeriodicalIF":0.0,"publicationDate":"2000-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72744461","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}
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