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Synthesis of deuterated benzyladenine and its application as a surrogate. 氘化苄基腺嘌呤的合成及其替代应用。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp053
Nkaelang Modutlwa, Hiroyuki Tada, Yoshiki Sugahara, Koichi Shiraki, Nobuyuki Hara, Yoshihiro Deyashiki, Takayuki Ando, Tomohiro Maegawa, Yasunari Monguchi, Hironao Sajiki
{"title":"Synthesis of deuterated benzyladenine and its application as a surrogate.","authors":"Nkaelang Modutlwa,&nbsp;Hiroyuki Tada,&nbsp;Yoshiki Sugahara,&nbsp;Koichi Shiraki,&nbsp;Nobuyuki Hara,&nbsp;Yoshihiro Deyashiki,&nbsp;Takayuki Ando,&nbsp;Tomohiro Maegawa,&nbsp;Yasunari Monguchi,&nbsp;Hironao Sajiki","doi":"10.1093/nass/nrp053","DOIUrl":"https://doi.org/10.1093/nass/nrp053","url":null,"abstract":"<p><p>Palladium on carbon-ethylenediamine complex [Pd/C(en)] catalyzed deuteration of N(6)-benzyladenine-d(5), which is a plant growth regulator, to introduce 5 deuterium atoms, while use of Pd/C as a catalyst led to a complete removal of N(6)-benzyl group. The corresponding deuterated N(6)-benzyladenine was successfully used as a surrogate compound for the quantitative analysis of residual benzyladenine in crops using LC/MS/MS.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"105-6"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp053","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28397459","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
Release of DNA binary complexes from the ternary complexes by carboxymethyl poly(L-histidine). 羧甲基聚l -组氨酸从三元配合物中释放DNA二元配合物。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp127
Shoichiro Asayama, Miyuki Sudo, Hiroyoshi Kawakami
{"title":"Release of DNA binary complexes from the ternary complexes by carboxymethyl poly(L-histidine).","authors":"Shoichiro Asayama,&nbsp;Miyuki Sudo,&nbsp;Hiroyoshi Kawakami","doi":"10.1093/nass/nrp127","DOIUrl":"https://doi.org/10.1093/nass/nrp127","url":null,"abstract":"<p><p>The DNA ternary complexes with carboxymethyl poly(L-histidine) (CM-PLH) and poly(ethylenimine) (PEI) have released the DNA binary complexes with PEI by the protonation of CM-PLH at endosomal/lysosomal pH. The dissociation of the CM-PLH from the CM-PLH/PEI/DNA ternary complexes is proved by the fluorescence resonance energy transfer (FRET) analysis between the CM-PLH and PEI. The resulting PEI/DNA binary complexes easily released DNA, as compared with the CM-PLH/PEI/DNA ternary complexes, which was examined by competitive exchange with dextran sulfate. The release of the DNA binary complexes from the ternary complexes is promising mechanism for higher transfection activity by the CM-PLH/PEI/DNA ternary complexes.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"253-4"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp127","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28397573","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
Reaction of the 4'-benzenesulfonyl derivatives of thymidine with organosilicon and organoaluminum reagents. 胸腺嘧啶的4′-苯磺酰衍生物与有机硅和有机铝试剂的反应。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp001
Hisashi Shimada, Satoshi Kikuchi, Saori Okuda, Kazuhiro Haraguchi, Hiromichi Tanaka
{"title":"Reaction of the 4'-benzenesulfonyl derivatives of thymidine with organosilicon and organoaluminum reagents.","authors":"Hisashi Shimada,&nbsp;Satoshi Kikuchi,&nbsp;Saori Okuda,&nbsp;Kazuhiro Haraguchi,&nbsp;Hiromichi Tanaka","doi":"10.1093/nass/nrp001","DOIUrl":"https://doi.org/10.1093/nass/nrp001","url":null,"abstract":"<p><p>With an aim to develop a new approach to synthesize 4'-substituted nucleosides, reactions of thymidine derivatives having a benzenesulfonyl leaving group at the 4'-position with organosilicon and organoaluminum reagents were investigated. Two substrates 4alpha (alpha-L-isomer) and 4 beta (beta-D-isomer) were prepared for this purpose. Although reaction of 4alpha with organosilicon reagents gave preferentially the 4'-substituted (allyl and N(3)) beta-D-nucleoside, its reaction with AlMe(3) gave the 4'-methyl-alpha-L-thymidine as the major product. On the other hand, the substrate 4beta, upon reacting with AlMe(3), furnished the desired 4'-methylthymidine exclusively in high yield.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"1-2"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28470937","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
Stereocontrolled synthesis of oligodeoxyribonucleoside boranophosphates via stereodefined H-phosphonate intermediates. 通过立体定义的h -膦酸盐中间体立体控制合成硼磷酸寡脱氧核糖核苷。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp005
Naoki Iwamoto, Natsuhisa Oka, Takeshi Wada
{"title":"Stereocontrolled synthesis of oligodeoxyribonucleoside boranophosphates via stereodefined H-phosphonate intermediates.","authors":"Naoki Iwamoto,&nbsp;Natsuhisa Oka,&nbsp;Takeshi Wada","doi":"10.1093/nass/nrp005","DOIUrl":"https://doi.org/10.1093/nass/nrp005","url":null,"abstract":"P-Stereodefined oligodeoxyribonucleoside boranophosphates (PB-ODNs) were successfully synthesized by the conversion of diastereopure H-phosphonate intermediates. Thermal denaturation studies clearly showed that the duplex stability of PB-ODNs with the complementary DNA and RNA depends on the stereochemistry of the boranophosphate linkages.","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"9-10"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28470941","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
Metal ion binding of modified pyrimidine-base pairs in DNA duplexes. DNA双链中修饰嘧啶碱基对的金属离子结合。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp009
Akira Ono, Kenji Iwamoto, Kumiko Sugiyama, Itaru Okamoto
{"title":"Metal ion binding of modified pyrimidine-base pairs in DNA duplexes.","authors":"Akira Ono,&nbsp;Kenji Iwamoto,&nbsp;Kumiko Sugiyama,&nbsp;Itaru Okamoto","doi":"10.1093/nass/nrp009","DOIUrl":"https://doi.org/10.1093/nass/nrp009","url":null,"abstract":"<p><p>We report the synthesis and metal ion-binding properties of DNA duplexes containing 5-substituted uracil ((X)U) pairs, such as 5-bromouracil, 5-fluorouracil and 5-cyanouracil pairs. Thermal denaturation studies of these modified DNA duplexes revealed that the DNA duplexes were stabilized in the presence of Hg(II) ions in acidic and neutral solutions. On the other hand, the duplexes were stabilized in the presence of Hg(II) and Ag(I) ions. These results indicated that (X)U-Hg(II)-(X)U complex was formed in the acidic and neutral solutions, then, in the basic solutions (X)U-Ag(I)-(X)U complex as well as the (X)U-Hg(II)-(X)U complex were formed. ESI-TOF MS analysis also indicated formation of the metal ion-DNA complexes.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"17-8"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28470945","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
Introduction of 8-methyladenosine into 2', 5'-oligoadenylate (2-5A) 2'-terminus induces dramatic shift in binding site of RNase L. 将8-甲基腺苷引入2'，5'-寡聚腺苷酸(2- 5a) 2'端可引起RNase L结合位点的剧烈移位。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp062
Kumi Nagaoka, Seiya Kito, Yoshiaki Kitamura, Yoshihito Ueno, Yukio Kitade
{"title":"Introduction of 8-methyladenosine into 2', 5'-oligoadenylate (2-5A) 2'-terminus induces dramatic shift in binding site of RNase L.","authors":"Kumi Nagaoka,&nbsp;Seiya Kito,&nbsp;Yoshiaki Kitamura,&nbsp;Yoshihito Ueno,&nbsp;Yukio Kitade","doi":"10.1093/nass/nrp062","DOIUrl":"https://doi.org/10.1093/nass/nrp062","url":null,"abstract":"<p><p>The 2',5'-oligoadenylate (2-5A) system is an interferon (IFN)-regulated RNA decay pathway that provides innate immunity against viral infections. The biological action of the 2-5A system is mediated by RNase L, an endoribonuclease that becomes enzymatically active after binding to 2-5A. It has been reported that the 5'-phosphoryl group of 2-5A is required for RNase L activation. However, we have found that 5'-O-dephosphorylated 2-5A tetramer analogs with 8-methyladenosine at the 2'-terminus were more effective as an activator of RNase L than the parent 2-5A (p5'A2'p5'A2'p5'A2'p5'A2'). Introduction of 8-methyladenosine is thought to induce a dramatic shift in the binding site of RNase L.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"123-4"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp062","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28470950","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 imidazopyridopyrimidine:naphthyridine base pairs: selective incorporation and extension reaction by DNA polymerases. 非天然咪唑吡啶嘧啶:萘啶碱基对:DNA聚合酶的选择性掺入和延伸反应。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp063
Noriaki Minakawa, Shintaro Ogata, Mayumi Takahashi, Akira Matsuda
{"title":"Unnatural imidazopyridopyrimidine:naphthyridine base pairs: selective incorporation and extension reaction by DNA polymerases.","authors":"Noriaki Minakawa,&nbsp;Shintaro Ogata,&nbsp;Mayumi Takahashi,&nbsp;Akira Matsuda","doi":"10.1093/nass/nrp063","DOIUrl":"https://doi.org/10.1093/nass/nrp063","url":null,"abstract":"<p><p>We describe herein the results of (i) enzymatic recognition for imidazopyridopyrimidine (Im):naphthyridine (Na) base pairs and (ii) further primer extension reactions after the Im:Na base pairs by DNA polymerases. Among the base pairs examined, ImN(O):NaO(N) base pair was rather selectively recognized by Klenow fragment exo(-) [F(exo(-))]as complementary base. However, this DNA polymerase did not catalyze primer extension reactions after the ImN(O):NaO(N) base pair. Therefore, we carried out a screening of DNA polymerases to promote the primer extension reaction as well as to improve the selectivity of base pair recognition. As a result, a family B DNA polymerase, especially Deep Vent (exo(-)), seemed most promising for this purpose.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"125-6"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp063","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28470951","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 base recognition abilities of 2'-deoxynucleoside N-oxide derivatives by polymerase reactions. 用聚合酶反应评价2'-脱氧核苷n -氧化物衍生物的碱基识别能力。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp064
Hirosuke Tsunoda, Akihiro Ohkubo, Kohji Seio, Mitsuo Sekine
{"title":"Evaluation of base recognition abilities of 2'-deoxynucleoside N-oxide derivatives by polymerase reactions.","authors":"Hirosuke Tsunoda,&nbsp;Akihiro Ohkubo,&nbsp;Kohji Seio,&nbsp;Mitsuo Sekine","doi":"10.1093/nass/nrp064","DOIUrl":"https://doi.org/10.1093/nass/nrp064","url":null,"abstract":"The main products obtained by oxidation of cytosine and adenine bases with hydrogen peroxide are cytosine and adenine N-oxide derivatives. There is a possibility that these N-oxide derivatives are mutagenic in genomic DNA like 8-oxoguanine or thymine glycol. Although the chemical synthesis and properties of 2'-deoxynucleoside N-oxide derivatives have been well established, little has been reported about the chemical and biochemical behavior of oligodeoxynucleotides (ODNs) containing these modified 2'-deoxynucleoside. In this study, we examined their base recognition ability by DNA polymerase reactions. It was found that these modified derivatives were incorporated into the 3'-terminal site of an ODN by DNA polymerase selecting accurately the complementary G or T base on a template ODN. In the incorporation reaction using template ODNs containing 2'-deoxynucleoside N-oxide bases, their N-oxide bases were selectively recognized by the complementary 5'-triphosphate (dGTP or dTTP).","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"127-8"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp064","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28470952","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
Duplex formation of multiple pyrene-modified RNAs. 多个芘修饰rna的双工形成。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp067
Minoru Fukuda, Mitsunobu Nakamura, Tadao Takada, Kazushige Yamana
{"title":"Duplex formation of multiple pyrene-modified RNAs.","authors":"Minoru Fukuda,&nbsp;Mitsunobu Nakamura,&nbsp;Tadao Takada,&nbsp;Kazushige Yamana","doi":"10.1093/nass/nrp067","DOIUrl":"https://doi.org/10.1093/nass/nrp067","url":null,"abstract":"<p><p>We synthesized multiple pyrene-modified RNA sequences having two kinds of consecutive sequences, U(Py)U(Py) and A(Py)A(Py), and investigated their duplex formations and the pyrene associations.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"133-4"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp067","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28470955","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
Multiple-turnover cleavage of double-stranded DNA by sandwiched zinc-finger nuclease. 夹锌指核酸酶对双链DNA的多重翻转切割。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp140
Yusuke Mineta, Tomoyuki Okamoto, Kosuke Takenaka, Norio Doi, Yasuhiro Aoyama, Takashi Sera
{"title":"Multiple-turnover cleavage of double-stranded DNA by sandwiched zinc-finger nuclease.","authors":"Yusuke Mineta,&nbsp;Tomoyuki Okamoto,&nbsp;Kosuke Takenaka,&nbsp;Norio Doi,&nbsp;Yasuhiro Aoyama,&nbsp;Takashi Sera","doi":"10.1093/nass/nrp140","DOIUrl":"https://doi.org/10.1093/nass/nrp140","url":null,"abstract":"<p><p>To refine zinc-finger nuclease (ZFN) technology, we constructed a sandwiched ZFN, in which a DNA cleavage enzyme was sandwiched with two artificial zinc-finger proteins (AZPs). Because the sandwiched ZFN is designed to cleave the DNA between the two AZP-binding sites, the sandwiched ZFN is expected to bind preferentially to a DNA substrate rather than to cleavage products and thereby cleave it with multiple turnovers. To prove the concept, we sandwiched a staphylococcal nuclease (SNase), which cleaves DNA as a monomer, between two 3-finger AZPs. The AZP-sandwiched SNase cleaved large amounts of dsDNA site-specifically. Such multiple-turnover cleavage was not observed with control nucleases that possess a single AZP.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"279-80"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp140","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28470959","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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