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Nucleic acids research. Supplement (2001)最新文献

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DNA nanomotor using duplex-quadruplex conformational transition. 利用双-四重构象跃迁的DNA纳米马达。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.161
Keiichiro Kanatani, Yuji Ochi, Akimitsu Okamoto, Isao Saito
{"title":"DNA nanomotor using duplex-quadruplex conformational transition.","authors":"Keiichiro Kanatani,&nbsp;Yuji Ochi,&nbsp;Akimitsu Okamoto,&nbsp;Isao Saito","doi":"10.1093/nass/3.1.161","DOIUrl":"https://doi.org/10.1093/nass/3.1.161","url":null,"abstract":"<p><p>For DNA nanomotor, we synthesized 8-Py-dG and incorporated it into d(T3G2)4 which can form quadruplex. We measured CD spectra for this ODN. The result suggested that this ODN was changed from quadruplex to duplex by the hybridization with the complementary strand. Further, this ODN had a very interesting property of fluorescence. The fluorescent intensity could be controlled whether the complementary strand was existed, or not.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"161-2"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.161","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40824664","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
A novel strategy for reversible control of conformation and DNA/RNA recognition of peptide ribonucleic acid (PRNA) by external factors. 外部因素可逆控制肽核糖核酸(PRNA)构象和DNA/RNA识别的新策略。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.213
Takehiko Wada, Hirofumi Sato, Yoshihisa Inoue
{"title":"A novel strategy for reversible control of conformation and DNA/RNA recognition of peptide ribonucleic acid (PRNA) by external factors.","authors":"Takehiko Wada,&nbsp;Hirofumi Sato,&nbsp;Yoshihisa Inoue","doi":"10.1093/nass/3.1.213","DOIUrl":"https://doi.org/10.1093/nass/3.1.213","url":null,"abstract":"<p><p>A novel nucleic acid model using peptide ribonucleic acid (PRNA), which contains 5'-amino-5'-deoxyribonucleoside as a recognition site for nucleic acids, has been designed, synthesized and applied to the external reversible control of recognition behavior of the complementary oligomeric DNA through the orientational switching of the nucleobase induced by borates. In case of PRNA 12-mers, efficient orientational change of nucleobases was observed. Furthermore, these oligomeric PRNAs form a stable complex with complementary DNA's and the recognition behavior of oligomeric PRNAs with DNA's is controlled by the borate added as an external factor.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"213-4"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.213","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40824936","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 NMR studies of substituent effects on the N-H...N hydrogen bond in duplex DNA using 2'-deoxynebularine and 15N labeled 5-substituted-2'-deoxyuridine base pairs. 取代基对N-H…用2'-脱氧尿嘧啶和15N标记的5-取代-2'-脱氧尿嘧啶碱基对在双链DNA中形成N个氢键。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.57
Rei Ishikawa, Akira Ono, Masatsune Kainosho
{"title":"The NMR studies of substituent effects on the N-H...N hydrogen bond in duplex DNA using 2'-deoxynebularine and 15N labeled 5-substituted-2'-deoxyuridine base pairs.","authors":"Rei Ishikawa,&nbsp;Akira Ono,&nbsp;Masatsune Kainosho","doi":"10.1093/nass/3.1.57","DOIUrl":"https://doi.org/10.1093/nass/3.1.57","url":null,"abstract":"<p><p>The effects of substitutions on various NMR parameters, which may influence the hydrogen bond strengths of Watson-Crick base pairs, were investigated for DNA dodecamers containing 5-substituted-2'-deoxyuridine derivatives and 2'-deoxynebularine in the oligomers, 5'-d(CGCGNA TX CGCG)-3'; where N and X are 2'-deoxy nebularine and [N3-(15)N]-2'-deoxyuridine derivatives. The substitution effects on NMR parameters were linearly correlated with the pKa values of the 2'-dexoyuridine derivatives.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"57-8"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.57","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825185","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
Recognition of tRNA bottom half by bacterial ribonuclease P. 细菌核糖核酸酶对tRNA下半部分的识别。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.281
Yasuhiro Nagai, Tomoaki Ando, Terumichi Tanaka, Yo Kikuchi
{"title":"Recognition of tRNA bottom half by bacterial ribonuclease P.","authors":"Yasuhiro Nagai,&nbsp;Tomoaki Ando,&nbsp;Terumichi Tanaka,&nbsp;Yo Kikuchi","doi":"10.1093/nass/3.1.281","DOIUrl":"https://doi.org/10.1093/nass/3.1.281","url":null,"abstract":"<p><p>Bacterial ribonuclease P (RNase P) contains a catalytic RNA that cleaves precursor tRNA to form the 5'-end of mature tRNA. Bacterial RNase P mainly recognizes the acceptor stem and T arm modules of tRNA molecules. The region consisting of T arm, acceptor stem and 3' CCA motif in the tRNA is generally termed \"top half\", and the region consisting of the others, anticodon arm, extra loop and D arm, is called \"bottom half\". The stems in the top half contribute to recognition, but effects of the bottom half have not been elucidated. To study the effects of the bottom half on the RNase P recognition, we have synthesized several mutant substrates that have the bottom half on different positions along the top half stem. Most of these mutants were cleaved by Escherichia coli RNase P precisely at the expected position, but the cleavage efficiencies were very different especially at low Mg2+ concentration. We also found that RNase P holoenzyme prefered somewhat mutated tRNA precursor to the wild-type tRNA precursor.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"281-2"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.281","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825195","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
Inhibition of restriction enzyme's DNA sequence recognition by PUVA treatment. PUVA对限制性内切酶DNA序列识别的抑制作用。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.297
Fujinori Hanawa, Mamoru Okamoto, G H Neil Towers
{"title":"Inhibition of restriction enzyme's DNA sequence recognition by PUVA treatment.","authors":"Fujinori Hanawa,&nbsp;Mamoru Okamoto,&nbsp;G H Neil Towers","doi":"10.1093/nass/3.1.297","DOIUrl":"https://doi.org/10.1093/nass/3.1.297","url":null,"abstract":"<p><p>Applying various restriction enzymes on a specially designed 1.5 kb DNA fragment revealed that the inhibitory effects of PUVA treatment on restriction endonuclease activities are caused by recognition inhibition. In this study, Restriction enzymes which have a 5'-TpA sequence at the cleaving site (Kpn I, Xba I, Pme I, and Dra I), and non-cleaving site (Pac I) in recognition sites, or have two 5'-TpA sequences at the recognition site and a non-specific sequence between recognition and cleaving site (BciV I) were inhibited by PUVA treatment. Most of the other restriction enzymes used in this study which do not have a 5'-TpA sequence at their restriction site were not inhibited by PUVA treatment, although a 5'-TpA sequence is located adjacent (Sma I) or very close (BamH I, Sac I and Pst I) to the recognition and cleaving site for them.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"297-8"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.297","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825203","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
Crystal structure of a decamer RNA r(ggcggucgcu)2 with terminal and tandem G x U wobble base-pairs. 具有末端和串联G x U摆动碱基对的十聚体RNA r(ggcggucgcu)2的晶体结构。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.225
R Utsunomiya, P K R Kumar, Z Fujimoto, H Mizuno
{"title":"Crystal structure of a decamer RNA r(ggcggucgcu)2 with terminal and tandem G x U wobble base-pairs.","authors":"R Utsunomiya,&nbsp;P K R Kumar,&nbsp;Z Fujimoto,&nbsp;H Mizuno","doi":"10.1093/nass/3.1.225","DOIUrl":"https://doi.org/10.1093/nass/3.1.225","url":null,"abstract":"<p><p>The data set of the crystal structure of a self-complementary RNA duplex r(ggcggucgcu)2 with terminal and tandem G x U wobble base-pairs has been collected to 2.3 A resolution. Crystals belong to the tetragonal space group P4(1)2(1)2 or P4(3)2(1)2; a = b = 50.0 A, c = 102.7 A, and alpha = beta = gamma = 90 degrees, with two duplexes in the asymmetric unit. The structural analysis using the MAD method is currently in progress.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"225-6"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.225","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40824274","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
Control of intracellular delivery and inhibition of genetic expression by DNA-peptide conjugates. dna -肽偶联物控制细胞内递送和抑制基因表达。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.237
Takanori Kubo, Yosuke Anno, Mayuka Yano, Kengo Takamori, Rumiana Bakalova, Hideki Ohba, Masayuki Fujii
{"title":"Control of intracellular delivery and inhibition of genetic expression by DNA-peptide conjugates.","authors":"Takanori Kubo,&nbsp;Yosuke Anno,&nbsp;Mayuka Yano,&nbsp;Kengo Takamori,&nbsp;Rumiana Bakalova,&nbsp;Hideki Ohba,&nbsp;Masayuki Fujii","doi":"10.1093/nass/3.1.237","DOIUrl":"https://doi.org/10.1093/nass/3.1.237","url":null,"abstract":"<p><p>Various types of DNA-peptide conjugates were synthesized by solid phase fragment condensation (SPFC). DNA-LNS (nuclear localizing signal) peptide conjugate was proved to be delivered and localized into cellular nucleus and exhibited higher antisense inhibitory effect against telomerase than antisense phosphorothioate DNA. In contrast, DNAzymes conjugated with NES (nuclear export signal) peptide was shown to be taken up and localized in cytoplasm. Inhibitory effect of the conjugate DNAzyme against BCR-ABL tyrosine kinase was evaluated to be more significant than the native DNAzyme.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"237-8"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.237","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40824280","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
Cleavage of stretched DNA on glass by histones observed with fluorescence microscopy. 荧光显微镜观察组蛋白对玻璃上拉伸DNA的切割作用。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.187
Yoshihiro Takeda, Fumitaka Mafuné, Tamotsu Kondow
{"title":"Cleavage of stretched DNA on glass by histones observed with fluorescence microscopy.","authors":"Yoshihiro Takeda,&nbsp;Fumitaka Mafuné,&nbsp;Tamotsu Kondow","doi":"10.1093/nass/3.1.187","DOIUrl":"https://doi.org/10.1093/nass/3.1.187","url":null,"abstract":"<p><p>A stretched single lambda DNA molecule labeled with TOTO-1 dye molecules was immobilized on a cover slip by casting a solution of DNA-lipid polyion complex containing TOTO-1 dye, and were loaded with an aqueous solution of histone. Fluorescence microscopy applied to the single DNA showed that (1) the TOTO-1 dye molecules intercalated in the stretched DNA molecule were vertically aligned almost completely with respect to the DNA axis, and (2) the stretched DNA was cleaved by interaction with histone molecules.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"187-8"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.187","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40824485","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
Clear distinction of pyrimidine bases on the complementary strand by fluorescence change of novel fluorescent nucleosides. 利用新型荧光核苷的荧光变化清晰区分互补链上的嘧啶碱基。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.171
Kazuo Tanaka, Akimitsu Okamoto, Isao Saito
{"title":"Clear distinction of pyrimidine bases on the complementary strand by fluorescence change of novel fluorescent nucleosides.","authors":"Kazuo Tanaka,&nbsp;Akimitsu Okamoto,&nbsp;Isao Saito","doi":"10.1093/nass/3.1.171","DOIUrl":"https://doi.org/10.1093/nass/3.1.171","url":null,"abstract":"<p><p>New fluorescent nucleosides, methoxybenzodeazaadenine ((MD)A) and methoxybenzodeazainosine ((MD)I) which can sharply distinguish between C and T bases, respectably. The hybridization of an ODN probe containing (MD)A and (MD)I with a target DNA facilitates the judgment with the fluorescence spectra of the type of pyrimidine bases located at a specific site on the target DNA. The (MD)A- and (MD)I containing ODN are very effective probes for pyrimidine SNP typing.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"171-2"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.171","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825085","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
Antisense effects of DNA-peptide conjugates. dna -肽偶联物的反义作用。
Nucleic acids research. Supplement (2001) Pub Date : 2003-01-01 DOI: 10.1093/nass/3.1.179
Takanori Kubo, Rumiana Bakalova, Hideki Ohba, Masayuki Fujii
{"title":"Antisense effects of DNA-peptide conjugates.","authors":"Takanori Kubo,&nbsp;Rumiana Bakalova,&nbsp;Hideki Ohba,&nbsp;Masayuki Fujii","doi":"10.1093/nass/3.1.179","DOIUrl":"https://doi.org/10.1093/nass/3.1.179","url":null,"abstract":"<p><p>Antisense conjugate DNA covalently bound to functional amines, sugars or peptides such as nuclear localization signals (NLS), nuclear export signals (NES) and artificial amphiphilic alpha-helical and beta-sheet peptides were synthesized by solid phase fragment condensation (SPFC). Inhibitory effects on human telomerase of synthesized antisense conjugate DNAs were evaluated by TRAP assay. Antisense conjugate DNAs showed several times higher inhibitory effects on telomerase activity compared to native antisense DNA in cell lysis solutions. Antisense conjugate DNAs showed comparable or higher as same as inhibitory activity compared with antisense phosphorothioate DNA (S-DNA). Interestingly, antisense conjugate DNA showed much higher inhibition against telomerase activity with native antisense DNA or antisense phosphorothioate DNA in cellular system. We observed enhanced cellular uptake and positively controlled intracellular localization of conjugate DNAs by use of confocal fluorescent microscope.</p>","PeriodicalId":86149,"journal":{"name":"Nucleic acids research. Supplement (2001)","volume":" 3","pages":"179-80"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/3.1.179","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40825089","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: 8
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