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Recognition and reaction mechanisms of the (6-4) photolyase as determined by using a (6-4) photoproduct analog. （6-4）光解酶的识别和反应机制由（6-4）光产物类似物确定。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp111
Junpei Yamamoto, Kenichi Hitomi, Ryosuke Hayashi, Elizabeth D Getzoff, Shigenori Iwai
{"title":"Recognition and reaction mechanisms of the (6-4) photolyase as determined by using a (6-4) photoproduct analog.","authors":"Junpei Yamamoto, Kenichi Hitomi, Ryosuke Hayashi, Elizabeth D Getzoff, Shigenori Iwai","doi":"10.1093/nass/nrp111","DOIUrl":"10.1093/nass/nrp111","url":null,"abstract":"<p><p>The (6-4) photoproduct, which is one of the major UV-induced DNA lesions formed at bipyrimidine sites, causes carcinogenesis at high frequency. The (6-4) photolyases restore the (6-4) photoproducts to their intact bases in a light-dependent manner, but its overall repair mechanism remains obscure. To investigate the light-dependent conversion of the (6-4) photoproduct, we prepared a (6-4) photoproduct analog with modification at 3' pyrimidone ring, in which the carbonyl group was replaced with an imine to apply to the (6-4) photolyase assay. The (6-4) photolyase shows affinity to an oligonucleotide carrying this imine analog of the (6-4) photoproduct, though the imine analog is not repaired by the (6-4) photolyase.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"221-2"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28398867","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 and thermal denaturation studies of covalently linked DNA triplexes. 共价链DNA三联体的合成及热变性研究。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp083
Itaru Okamoto, Shota Ito, Takashi Ono, Akira Ono
{"title":"Synthesis and thermal denaturation studies of covalently linked DNA triplexes.","authors":"Itaru Okamoto,&nbsp;Shota Ito,&nbsp;Takashi Ono,&nbsp;Akira Ono","doi":"10.1093/nass/nrp083","DOIUrl":"https://doi.org/10.1093/nass/nrp083","url":null,"abstract":"<p><p>We report on the synthesis and thermal stability of small covalently linked DNA triplexes. These modified triplexes were found to contain covalently linked T-T pairs at the edges, and thermal denaturation studies revealed that the covalent linking efficiently stabilized triplex formation.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"165-6"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp083","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28396114","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
Regulation of duplex DNA strand displacement by visible light sensitive bis-peptide nucleic acid. 可见光敏感双肽核酸对双链DNA位移的调控。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp096
Shinjiro Sawada, Ichiro Imada, Nobuo Kato, Kunihiro Kaihatsu
{"title":"Regulation of duplex DNA strand displacement by visible light sensitive bis-peptide nucleic acid.","authors":"Shinjiro Sawada,&nbsp;Ichiro Imada,&nbsp;Nobuo Kato,&nbsp;Kunihiro Kaihatsu","doi":"10.1093/nass/nrp096","DOIUrl":"https://doi.org/10.1093/nass/nrp096","url":null,"abstract":"<p><p>A novel visible light sensitive azobenzene (AZO) was synthesized and introduced into bis-peptide nucleic acid (bis-PNA), which consists of two homopyrimidine PNA strands, as a linker. Visible light irradiation of the bis-PNA-AZO conjugate induced photoisomerization of the azobenzene moiety from trans to cis. The cis-form of bis-PNA-AZO displaced the complementary duplex DNA more efficiently than the trans-form.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"191-2"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp096","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28398389","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
Synthesis and anti-HCV activity of 2',5'-deoxy-5'-phenacyladenosine analogs. 2'，5'-脱氧-5'-苯丙基腺苷类似物的合成及抗hcv活性研究
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp052
Masahiro Ikejiri, Takayuki Ohshima, Akemi Fukushima, Kunitada Shimotohno, Tokumi Maruyama
{"title":"Synthesis and anti-HCV activity of 2',5'-deoxy-5'-phenacyladenosine analogs.","authors":"Masahiro Ikejiri,&nbsp;Takayuki Ohshima,&nbsp;Akemi Fukushima,&nbsp;Kunitada Shimotohno,&nbsp;Tokumi Maruyama","doi":"10.1093/nass/nrp052","DOIUrl":"https://doi.org/10.1093/nass/nrp052","url":null,"abstract":"<p><p>Several nucleoside analogs containing a methylene group instead of a 5'-O atom were synthesized to study the effect of the 5'-modification of nucleoside analogs on their anti-HCV activity. Among the analogs, a 5'-phenacyl analog exhibited good anti-HCV activity with an EC(50) of 15.1 muM. This compound is hypothesized to function via a novel type of mechanism that does not involve the conventional 5'-O-triphosphorylation process.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"103-4"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp052","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28397458","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
One-electron oxidation of DNA: mechanism and consequences. DNA的单电子氧化:机制和后果。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp043
Gary B Schuster
{"title":"One-electron oxidation of DNA: mechanism and consequences.","authors":"Gary B Schuster","doi":"10.1093/nass/nrp043","DOIUrl":"https://doi.org/10.1093/nass/nrp043","url":null,"abstract":"<p><p>All living organisms store the information necessary to maintain life in their DNA. Any process that damages DNA and causes loss or corruption of that information threatens the viability of the organism. One-electron oxidation is such a process. Loss of an electron from DNA generates a radical cation that is located primarily on its nucleobases. The radical cation migrates reversibly through duplex DNA by hopping until it is eventually trapped in an irreversible chemical reaction. The particular sequence of nucleobases in a DNA oligomer determines both the efficiency of hopping and the specific location and nature of the damaging chemical reaction. In its normal aqueous solutions, DNA is a polyanion because of the negative charge carried by its phosphate groups. Counter ions (typically Na(+)) to the phosphate groups play an important role in facilitating both the migration of the radical cation and in its eventual reaction with H(2)O. Irreversible reaction of a radical cation with H(2)O in duplex DNA occurs preferentially at the most reactive site. In normal DNA that is comprised of the four common DNA nucleobases, reaction occurs most commonly at a guanine and results in its conversion primarily to 8-oxo-7,8-dihydroguanine (8-OxoG). Both electronic and steric effects control the outcome of this process. If the DNA oligomer does not contain a suitable guanine, then reaction of the radical cation occurs at the thymine of a TT step primarily by a tandem process. The general outcomes revealed in the one-electron oxidation of DNA oligomers in solution appear to be generally valid also for more complex DNA structures and for the cellular DNA of living organisms.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"85-6"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp043","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28397560","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
Synthesis of 4'-substituted cordycepins via benzenesulfenylation at the 4'-position as a key step. 以4′位苯磺酰化为关键步骤合成4′取代虫草素。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp050
Yutaka Kubota, Mariko Ehara, Hiroki Kumamoto, Hisashi Shimada, Kazuhiro Haraguchi, Hiromichi Tanaka
{"title":"Synthesis of 4'-substituted cordycepins via benzenesulfenylation at the 4'-position as a key step.","authors":"Yutaka Kubota,&nbsp;Mariko Ehara,&nbsp;Hiroki Kumamoto,&nbsp;Hisashi Shimada,&nbsp;Kazuhiro Haraguchi,&nbsp;Hiromichi Tanaka","doi":"10.1093/nass/nrp050","DOIUrl":"https://doi.org/10.1093/nass/nrp050","url":null,"abstract":"<p><p>With an aim to synthesize 4'-substituted cordycepins, the 4'-phenylthio precursor 4 was prepared from adenosine through an electrophilic addition to the 3',4'-unsaturated derivative 2 by using NIS/PhSH system. Nucleophilic substitution of 4 with a series of alcohols in the presence of NBS gave the respective 4'-alpha-alkoxy cordycepins 6 as the major stereoisomer. Use of DAST, in stead of alcohol in this reaction, gave the 4'-fluoro analogue 7. The 4'-sulfone derivative 8 obtained by m-CPBA oxidation of 4 was employed for the reaction with organoaluminum reagents. These reactions furnished various types of the 4'-carbon-substituted cordycepins 9.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"99-100"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp050","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28397567","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
Synthesis and properties of terminally modified oligonucleotides capable of short-RNA selective hybridization. 短rna选择性杂交末端修饰寡核苷酸的合成及其性质。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp007
Kohji Seio, Kazuya Miyazaki, Sayako Kurohagi, Yoshiaki Masaki, Hirosuke Tsunoda, Akihiro Ohkubo, Mitsuo Sekine
{"title":"Synthesis and properties of terminally modified oligonucleotides capable of short-RNA selective hybridization.","authors":"Kohji Seio,&nbsp;Kazuya Miyazaki,&nbsp;Sayako Kurohagi,&nbsp;Yoshiaki Masaki,&nbsp;Hirosuke Tsunoda,&nbsp;Akihiro Ohkubo,&nbsp;Mitsuo Sekine","doi":"10.1093/nass/nrp007","DOIUrl":"https://doi.org/10.1093/nass/nrp007","url":null,"abstract":"<p><p>We have developed 2'-O-methyl-RNAs having phosphorylated cyclohexane at the 5' and/or 3'-terminal adenine. These 2'-O-methyl-RNAs formed less stable duplex with the longer target RNA than that with the short target RNA. We tried to improve the short-RNA selective hybridization property by the synthesis of 2'-O-methyl-RNAs having terminal guanine modifications.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"13-4"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28470943","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
Interaction of silver ion with CG.C+ base triplets in DNA triplex. DNA三联体中银离子与cg +碱基三联体的相互作用。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp010
Toshihiro Ihara, Tatsuaki Ishii, Akinori Jyo
{"title":"Interaction of silver ion with CG.C+ base triplets in DNA triplex.","authors":"Toshihiro Ihara,&nbsp;Tatsuaki Ishii,&nbsp;Akinori Jyo","doi":"10.1093/nass/nrp010","DOIUrl":"https://doi.org/10.1093/nass/nrp010","url":null,"abstract":"<p><p>When designing ligands for specific sequences in DNA duplexes, triple helix formation is a useful recognition motif, because base triplet formation is based on the simple rule of complementary Hoogsteen hydrogen bonding, CG.C(+) and TA.T. However the triplexes containing CG.C(+) triplets form only in a weak acidic solution, because cytosines in third strand need to be protonated to satisfy its complementarity to CG base-pairs. A simple and easy method to stabilize the DNA triplex using Ag(+) was reported. A silver ion displaces the N3 proton of cytosine in Hoogsteen base-pairing to form a base triplet, CG.CAg(+). By the addition of an equimolar amount of Ag(+), the third strand 15 mer sequence containing five cytosines was stabilized by ca. 30 degrees C in melting temperature at pH 7. The triplex structure was stable even under weak basic conditions.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"19-20"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28470946","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
Evaluation of mobility of 2-N-tert-butylaminoxyladenosine incorporated into oligodeoxynucleotides. 低聚脱氧核苷酸中2- n -叔丁基氨基氧化腺苷迁移率的评价。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp076
Yoshitaka Higuchi, Mariko Aso, Ryouko Harada, Noboru Koga, Hiroshi Suemune
{"title":"Evaluation of mobility of 2-N-tert-butylaminoxyladenosine incorporated into oligodeoxynucleotides.","authors":"Yoshitaka Higuchi,&nbsp;Mariko Aso,&nbsp;Ryouko Harada,&nbsp;Noboru Koga,&nbsp;Hiroshi Suemune","doi":"10.1093/nass/nrp076","DOIUrl":"https://doi.org/10.1093/nass/nrp076","url":null,"abstract":"<p><p>We synthesized oligodeoxynucleotide (ODN, 3) containing 2-N-tert-butylaminoxyladenosine (1) and studied EPR spectra of 3 and its duplexes. The h(+)/h(0) values in the EPR spectra of duplexes between 3 and 5-8 well correlated with Tm values. We also synthesized ODN 4 containing 2, which has a cyclic aminoxyl via a linker, to compare with ODN 3. The h(+)/h(0) values in the EPR spectra of duplexes between 4 and 5-8 did not correlate with Tm values. These results indicate that 1 has a potential to monitor of motion of the nucleobase.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"151-2"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp076","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28475061","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
Molecular basis of human telomere DNA/RNA structure and its potential application. 人端粒DNA/RNA结构的分子基础及其潜在应用。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp032
Yan Xu, Yuta Suzuki, Kuniyuki Kaminaga, Makoto Komiyama
{"title":"Molecular basis of human telomere DNA/RNA structure and its potential application.","authors":"Yan Xu,&nbsp;Yuta Suzuki,&nbsp;Kuniyuki Kaminaga,&nbsp;Makoto Komiyama","doi":"10.1093/nass/nrp032","DOIUrl":"https://doi.org/10.1093/nass/nrp032","url":null,"abstract":"<p><p>Telomeric repeat-containing RNA is a non-coding RNA molecule newly found in mammalian cells. However, structure and function of the telomeric RNA in chromosome ends have not yet been elucidated. Using a combination of NMR, CD and MALDI-TOFMS experiments, we have demonstrated that human telomere RNA can form a parallel G-quadruplex structure. Furthermore, we successfully found for the first time that human telomere DNA and RNA sequence can form a DNA-RNA hybrid type G-quadruplex structure based on click chemistry approach. Telomerase or its telomere DNA substrate is also known to present a specific target in discovering anticancer agents. Recently, we developed a structure-based approach to sequence-specific cleaving of human telomeric DNA by G-quadruplex formation. These results not only provide valuable information to allow understanding of the roles of human telomeric RNA in telomere biology, but also serve as a start step for developing new anti-cancer reagent.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"63-4"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp032","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28398375","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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