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Immobilization of a naphthalene diimide-DNA complex on the gold through dithiolane moieties. 通过二硫烷基团在金上固定化萘二亚胺- dna复合物。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp074
Shinobu Sato, Keiichi Ohtsuka, Shigeori Takenaka
{"title":"Immobilization of a naphthalene diimide-DNA complex on the gold through dithiolane moieties.","authors":"Shinobu Sato,&nbsp;Keiichi Ohtsuka,&nbsp;Shigeori Takenaka","doi":"10.1093/nass/nrp074","DOIUrl":"https://doi.org/10.1093/nass/nrp074","url":null,"abstract":"<p><p>Naphthalene diimide 1 having two dithiolane moieties at its substituted termini was newly synthesized to immobilize double stranded DNA through dithiolane moieties of 1. Double stranded DNA could be immobilized on the gold surface of a quartz crystal microbalance (QCM) chip after binding 1. Once immobilized, the complex will serve as a hybridization marker based on its frequency decrease. QCM experiments showed that a DNA duplex with a 24-meric single stranded region also could be immobilized on the gold surface of a QCM chip and subsequent frequency decrease was observed after hybridization with a 24-meric complementary DNA, but not with non-complementary DNA, indicating specific hybridization. This result reveals that 1 provides a new immobilization method for intact DNA on gold and that the immobilized DNA can hybridize with target DNA.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"147-8"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp074","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28475059","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
Design and synthesis of the novel cross-linking agent. 新型交联剂的设计与合成。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp085
Shuhei Kusano, Keiichi Hattori, Shuhei Imoto, Fumi Nagatsugi
{"title":"Design and synthesis of the novel cross-linking agent.","authors":"Shuhei Kusano,&nbsp;Keiichi Hattori,&nbsp;Shuhei Imoto,&nbsp;Fumi Nagatsugi","doi":"10.1093/nass/nrp085","DOIUrl":"https://doi.org/10.1093/nass/nrp085","url":null,"abstract":"<p><p>Previously, we have developed a highly efficient and selective cross-linking reaction to the cytosine base at the target site of DNA using the oligodeoxynucleotide (ODN) containing 2-amino-6-vinylpurine derivative (1). Based on these results, we have designed the novel cross-linking agents, which are pyrimidine derivatives having two hydrogen bond sites and vinyl group as a reactive moiety. In this paper, we wish to report the results to investigate on the synthesis of the pyrimidine derivatives having potential as novel cross-linking agents.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"169-70"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp085","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28396116","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
Investigations of the cation binding to nucleotides by monitoring the hairpin-duplex equilibrium of a self-complementary sequence. 通过监测自互补序列的发夹-双工平衡来研究阳离子与核苷酸的结合。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp115
Shu-ichi Nakano, Hidenobu Hirayama, Naoki Sugimoto
{"title":"Investigations of the cation binding to nucleotides by monitoring the hairpin-duplex equilibrium of a self-complementary sequence.","authors":"Shu-ichi Nakano,&nbsp;Hidenobu Hirayama,&nbsp;Naoki Sugimoto","doi":"10.1093/nass/nrp115","DOIUrl":"https://doi.org/10.1093/nass/nrp115","url":null,"abstract":"<p><p>Nucleotide folding accompanies cation binding that shields the electronegative potential of phosphate groups, and metal ions in the condensation layer predominantly associate diffusely with base-paired nucleotides. Although metal ions bound at specific sites have been well studied, information of diffusely bound cations, that usually have a weak binding affinity than those associating at specific sites, have not been thoroughly studied. We explored a convenient experimental system using a self-complementary nucleotide sequence for analyzing cationic ligands diffusely bound to DNA or RNA base pairs. To study the metal ion-nucleotide interaction under a non-homologous aqueous condition, solutions containing a large amount of PEG (polyethylene glycol) were examined. We found that PEG (e.g., 20 wt%) substantially influenced the metal ion binding to nucleotides, suggesting significances of the molecular environment on nucleotide-cation interactions.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"229-30"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp115","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28396478","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 of potent G-quadruplex binders of macrocyclic heptaoxazole and evaluation of their activities. 大环七恶唑强效g -四联体结合物的合成及其活性评价。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp116
Masayuki Tera, Keisuke Iida, Kazuo Shin-ya, Kazuo Nagasawa
{"title":"Synthesis of potent G-quadruplex binders of macrocyclic heptaoxazole and evaluation of their activities.","authors":"Masayuki Tera,&nbsp;Keisuke Iida,&nbsp;Kazuo Shin-ya,&nbsp;Kazuo Nagasawa","doi":"10.1093/nass/nrp116","DOIUrl":"https://doi.org/10.1093/nass/nrp116","url":null,"abstract":"<p><p>Guanine-rich DNA sequences form unique three-dimensional conformation known as G-quadruplexes (G-q). G-q structures have been found in telomere and in some oncogene promoter. Recently, it was suggested that G-q showed some biological activities including telomere shortening and transcriptional regulation. In this paper, we synthesized selective G-q binders and evaluated of their biological activities.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"231-2"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp116","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28396479","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
G-quadruplex recognition by macrocyclic hexaoxazole (6OTD) dimer. 大环六恶唑(6OTD)二聚体对g -四联体的识别。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp117
Keisuke Iida, Masayuki Tera, Kazuo Shin-Ya, Kazuo Nagasawa
{"title":"G-quadruplex recognition by macrocyclic hexaoxazole (6OTD) dimer.","authors":"Keisuke Iida,&nbsp;Masayuki Tera,&nbsp;Kazuo Shin-Ya,&nbsp;Kazuo Nagasawa","doi":"10.1093/nass/nrp117","DOIUrl":"https://doi.org/10.1093/nass/nrp117","url":null,"abstract":"<p><p>Telomestatin (TMS: 1) is as a potent and selective telomeric G-quadruplex binder. Two molecules of TMS were suggested to be intercalated to one telomeric G-quadruplex according to docking study. In this paper, we designed and synthesized hexaoxazole TMS derivative (6OTD) dimer, and evaluated its G-quadruplex stabilizing ability.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"233-4"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp117","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28396480","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: 5
Tetraplex structure of budding yeast telomeric DNA. 出芽酵母端粒DNA的四联体结构。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp118
Hidetaka Torigoe, Eugene Horio, Takashi Takehara, Kaoru Kaneda, Tetsuo Kozasa
{"title":"Tetraplex structure of budding yeast telomeric DNA.","authors":"Hidetaka Torigoe,&nbsp;Eugene Horio,&nbsp;Takashi Takehara,&nbsp;Kaoru Kaneda,&nbsp;Tetsuo Kozasa","doi":"10.1093/nass/nrp118","DOIUrl":"https://doi.org/10.1093/nass/nrp118","url":null,"abstract":"<p><p>We examined the structural properties of budding yeast telomeric DNA sequences, SCTELG4: 5'-(TGGG TGTG)(4)-3' and SCTELGG4: 5'-(TGGGTGTGG)(4)-3', in the presence of Na(+) or K(+). The conformation of SCTELG4 with Na(+) was a mixture of parallel tetraplex DNA and unstructured single-stranded DNA. On the other hand, the conformation of SCTELGG4 with Na(+) was a mixture of parallel and antiparallel tetraplex DNA. The ratio of the amount of parallel tetraplex to that of unstructured single-strand was increased for SCTELG4 by the presence of K(+). The conformation of almost all of SCTELGG4 was changed into parallel tetraplex by the presence of K(+). These results indicate that structural change of SCTELG4 and SCTELGG4 may be induced by the type of cation. We conclude that the conformation of budding yeast telomeric DNA sequences depends on the base sequence and the type of cation.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"235-6"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp118","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28396481","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
The use of conformationally rigid nucleoside probes to study the role of sugar pucker and nucleobase orientation in the thrombin binding aptamer. 利用构象刚性核苷探针研究糖皱缩和核碱基取向在凝血酶结合适体中的作用。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp055
Hisao Saneyoshi, Stefania Mazzini, Anna Aviñó, Guillem Portella, Carlos González, Modesto Orozco, Victor E Marquez, Ramon Eritja
{"title":"The use of conformationally rigid nucleoside probes to study the role of sugar pucker and nucleobase orientation in the thrombin binding aptamer.","authors":"Hisao Saneyoshi,&nbsp;Stefania Mazzini,&nbsp;Anna Aviñó,&nbsp;Guillem Portella,&nbsp;Carlos González,&nbsp;Modesto Orozco,&nbsp;Victor E Marquez,&nbsp;Ramon Eritja","doi":"10.1093/nass/nrp055","DOIUrl":"https://doi.org/10.1093/nass/nrp055","url":null,"abstract":"<p><p>Thrombin binding aptamers (TBAs) incorporating North-/South-deoxyguanosines built on the rigid bicyclo[3.1.0]hexane template were synthesized. Individual 2'-deoxyguanosines at positions dG14 and dG15 of the aptamer were replaced by these analogues where the North/anti and South/syn conformational states were confined. The substitution at position 14 with a locked South/syn-dG nucleoside produced an aptamer with the same stability and global structure as the innate, unmodified one. Replacing position 15 with the same South/syndG nucleoside induced a strong destabilization of the aptamer, while the antipodal North/anti-dG nucleoside was less destabilizing. Remarkably, the insertion of a North/anti-dG nucleoside at position 14, where both pseudosugar conformation and glycosyl torsion angle are opposite with respect to the native structure, led to the complete disruption of the G-tetraplex structure as detected by NMR and confirmed by extensive molecular dynamics simulations.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"109-10"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp055","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28397461","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
Synthesis and hybridization properties of oligonucleotides having 4-N-(pyrrol-2-ylcarbonyl)deoxycytidine. 含4-N-(吡咯-2-羰基)脱氧胞苷寡核苷酸的合成及杂化性质。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp058
Ken Yamada, Hirosuke Tsunoda, Akihiro Ohkubo, Kohji Seio, Mitsuo Sekine
{"title":"Synthesis and hybridization properties of oligonucleotides having 4-N-(pyrrol-2-ylcarbonyl)deoxycytidine.","authors":"Ken Yamada,&nbsp;Hirosuke Tsunoda,&nbsp;Akihiro Ohkubo,&nbsp;Kohji Seio,&nbsp;Mitsuo Sekine","doi":"10.1093/nass/nrp058","DOIUrl":"https://doi.org/10.1093/nass/nrp058","url":null,"abstract":"<p><p>A new 4-N-acylated deoxycytidine derivative, 4-N-(1H-pyrrol-2-ylcarbonyl)deoxycytidine, was synthesized and found to be stable under rather basic conditions. Oligodeoxynucleotides (ODNs) incorporating this modified deoxynucleoside at various positions were successfully synthesized by using a pivaloyloxymethyl (POM) group for protection of the pyrrole residue. The POM group was removed by treatment with 1.5 M NaOMe/MeOH. ODNs containing modified deoxycytidines exhibited hybridization properties superior to those of the unmodified ODNs. We found the acylation of the cytosine base with an aromatic acyl-type substituent led to significant increase of the thermo stability of DNA duplexes. This is the first noteworthy observation in this kind of modification. The synthesis and hybridization properties of 4-N-(1H-pyrrol-2-ylcarbonyl)deoxycytidine derivatives will be also reported.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"115-6"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp058","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28397464","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
Structural analysis of ribonucleopeptide aptamer against ATP. 抗ATP核糖核肽适配体的结构分析。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp134
Tsukasa Mashima, Akimasa Matsugami, Shun Nakano, Masafumi Inoue, Masatora Fukuda, Takashi Morii, Masato Katahira
{"title":"Structural analysis of ribonucleopeptide aptamer against ATP.","authors":"Tsukasa Mashima,&nbsp;Akimasa Matsugami,&nbsp;Shun Nakano,&nbsp;Masafumi Inoue,&nbsp;Masatora Fukuda,&nbsp;Takashi Morii,&nbsp;Masato Katahira","doi":"10.1093/nass/nrp134","DOIUrl":"https://doi.org/10.1093/nass/nrp134","url":null,"abstract":"<p><p>A ribonucleopeptide aptamer against ATP was obtained by the in vitro selection method. This ribonucleopeptide aptamer comprises a randomized and selected RNA linked to the Rev-responsive element (RRE) in complex with a peptide derived from an HIV Rev protein. The ribonucleopeptide aptamer selectively binds ATP in the presence of the Rev-derived peptide, exclusively. Here, we present the structural analysis of the ribonucleopeptide aptamer with NMR. The secondary structure of the RNA part of the aptamer, the selected RNA region linked to RRE, in the presence of the Rev-derived peptide was determined in an Ado-bound form. G:A and G:G base pairs, together with canonical base pairs, are formed in a duplex of RRE. The selected RNA region plays a crucial role in target binding. It has been found that the two U residues located in the selected RNA region trap Ado through the formation of the U:A:U base triple. This was directly confirmed by the HNN-COSY experiment through the detection of spin-spin couplings across the hydrogen bonds for Watson-Crick and Hoogsteen A:U base pairs in the U:A:U base triple.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"267-8"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp134","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28397469","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
Preparations of hammerhead ribozymes for investigations of their cleavable sequences. 锤头核酶的制备及其可切割序列的研究。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp139
Hisaaki Tateoka, Ikumi Kawahara, Satomi Hasegawa, Kaichiro Haruta, Yoshinori Kondo, Chojiro Kojima, Yoshiyuki Tanaka
{"title":"Preparations of hammerhead ribozymes for investigations of their cleavable sequences.","authors":"Hisaaki Tateoka,&nbsp;Ikumi Kawahara,&nbsp;Satomi Hasegawa,&nbsp;Kaichiro Haruta,&nbsp;Yoshinori Kondo,&nbsp;Chojiro Kojima,&nbsp;Yoshiyuki Tanaka","doi":"10.1093/nass/nrp139","DOIUrl":"https://doi.org/10.1093/nass/nrp139","url":null,"abstract":"<p><p>Recently, in hammerhead ribozymes, newly identified loop-loop interaction was found to be important for their activation. Therefore, we chemically synthesized a hammerhead ribozyme with this extra loop sequences and its mutant ribozymes, as well as their substrate RNA strands in order to clarify their cleavable sequences. After purification with an anion exchange column chromatography, we were able to obtain 44mer and 20mer RNA.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"277-8"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp139","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28397474","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
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