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Single long DNA molecule analysis using fluorescence microscopy. 单长DNA分子荧光显微镜分析。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.247
N Kaji, M Ueda, Y Baba
{"title":"Single long DNA molecule analysis using fluorescence microscopy.","authors":"N Kaji,&nbsp;M Ueda,&nbsp;Y Baba","doi":"10.1093/nass/44.1.247","DOIUrl":"https://doi.org/10.1093/nass/44.1.247","url":null,"abstract":"<p><p>Single long DNA molecule (T4 DNA) in agarose gel was visualized with a fluorescence microscope. We confirmed alternating current electric fields is effective for stretching of single DNA molecule in agarose gel. This stretching phenomenon was observed with wide range of agarose gel concentration from 0.5%(W/V) to 1.5%. From this observation, the presence of agarose gel fiber is essential for this stretching phenomenon. The stretching process of several DNA molecules in gel shows discontinuity, which is never observed in polymer systems. It would be based on topological restriction from gel fibers.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"247-8"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.247","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517656","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
Solution structure of the DNA complex with a quinacrine-netropsin hybrid molecule by NMR spectroscopy. 用核磁共振光谱分析了醌-嗜糖蛋白杂化分子的DNA复合物的溶液结构。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.235
Y Kubota, S Tani, R Uchida
{"title":"Solution structure of the DNA complex with a quinacrine-netropsin hybrid molecule by NMR spectroscopy.","authors":"Y Kubota,&nbsp;S Tani,&nbsp;R Uchida","doi":"10.1093/nass/44.1.235","DOIUrl":"https://doi.org/10.1093/nass/44.1.235","url":null,"abstract":"<p><p>The solution structures of 1:1 complexes of a quinacrine-netropsin hybrid molecule with the self-complementary DNA duplexes, d(CGCGAATTCGCG)2 and d(CGAATTCG)2, have been studied by one- and two-dimensional 1H NMR spectroscopy. The NOE data indicate that the acridine ring of the hybrid intercalates into the 5'-GpA step and its netropsin moiety spans the minor groove of the central AATT region.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"235-6"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.235","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517757","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 of 2,3-dihydroinosine derivatives by reduction using BH3-THF. BH3-THF还原合成2,3-二氢肌苷衍生物。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.113
K Hirota, R Hattori, H Sajiki, Y Monguchi, O Muraoka, G Tanabe
{"title":"Synthesis of 2,3-dihydroinosine derivatives by reduction using BH3-THF.","authors":"K Hirota,&nbsp;R Hattori,&nbsp;H Sajiki,&nbsp;Y Monguchi,&nbsp;O Muraoka,&nbsp;G Tanabe","doi":"10.1093/nass/44.1.113","DOIUrl":"https://doi.org/10.1093/nass/44.1.113","url":null,"abstract":"A novel reductive method for the chemical modification of nucleosides is described. Reaction of inosine derivatives with boran-THF resulted in the regioselective reduction of purine ring to afford the corresponding 2,3-dihydroinosine derivatives in moderate yields.","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"113-4"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.113","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518144","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
In vitro cleavage of Drosophila 2S rRNA by M1 RNA. M1 RNA对果蝇2S rRNA的体外切割。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.93
Y Hori, T Tanaka, Y Kikuchi
{"title":"In vitro cleavage of Drosophila 2S rRNA by M1 RNA.","authors":"Y Hori,&nbsp;T Tanaka,&nbsp;Y Kikuchi","doi":"10.1093/nass/44.1.93","DOIUrl":"https://doi.org/10.1093/nass/44.1.93","url":null,"abstract":"<p><p>Drosophila melanogaster initiator methionine tRNA can adopt an alternative conformation in aqueous solution. In this alternative conformation, the aminoacyl- and the anticodon stems of tRNA are unfolded and then these unfolded regions are used to form extended D- and T-stems, resulting in the formation of two tandemly joined stems and loops. This conformational alternation was recognized then cleaved by the catalytic RNA of Escherichia coli ribonuclease P (M1 RNA). The cleavage occurs within the mature sequence of tRNA. This further processing within mature sequence is called hyperprocessing. During the screening experiments of other conformational changeable D. melanogaster tRNAs by M1 RNA, we incidentally found that M1 RNA also hyperprocessed D. melanogaster 2S rRNA. Kinetic analyses of the hyperprocessing reaction of 2S rRNA by M1 RNA revealed that 2S rRNA could form a homodimer.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"93-4"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.93","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518709","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
Incorporation of nonnatural amino acids into proteins by using five-base codon-anticodon pairs. 利用五碱基密码子-反密码子对将非天然氨基酸整合到蛋白质中。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.99
T Hohsaka, M Sisido
{"title":"Incorporation of nonnatural amino acids into proteins by using five-base codon-anticodon pairs.","authors":"T Hohsaka,&nbsp;M Sisido","doi":"10.1093/nass/44.1.99","DOIUrl":"https://doi.org/10.1093/nass/44.1.99","url":null,"abstract":"<p><p>A novel strategy for the incorporation of nonnatural amino acids into proteins was developed by using five-base codon-anticodon pairs. The streptavidin mRNA containing five-base codon CGGUA and the chemically aminoacylated tRNA with five-base anticodon UACCG were prepared, and added into E. coli in vitro translation system. As a result, the nonnatural amino acid was successfully incorporated into desired position of the protein. Other five-base codons CGGN1N2, where N1 and N2 indicate one of four nucleotides, were also available for the incorporation of the nonnatural amino acid.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"99-100"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.99","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518712","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
Screening in vivo for RNA-binding peptides from combinatorial libraries. 从组合文库中筛选rna结合肽。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.269
K Harada, S Horiya, H Zehavi, A D Frankel
{"title":"Screening in vivo for RNA-binding peptides from combinatorial libraries.","authors":"K Harada,&nbsp;S Horiya,&nbsp;H Zehavi,&nbsp;A D Frankel","doi":"10.1093/nass/44.1.269","DOIUrl":"https://doi.org/10.1093/nass/44.1.269","url":null,"abstract":"<p><p>We have modified a previously developed genetic assay system for RNA-polypeptide interactions in a attempt to more readily identify RNA-binding peptides. The first modification involved the design of a \"complex\" library that would contain a variety of RNA-binding polypeptides. The second modification involved the use of neomycin phosphotransferase (NPT II) as the reporter gene, therefore allowing \"selection\" of RNA-binding peptides by kanamycin resistance. The improved screening system should allow the identification of peptides that bind to a variety of RNA structures.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"269-70"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.269","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22518720","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
Characterization of immediate early genes expressed in chlorovirus infection. 氯病毒感染中直接早期基因表达的特征。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.161
T Kawasaki, K Nishida, M Fujie, S Usami, T Yamada
{"title":"Characterization of immediate early genes expressed in chlorovirus infection.","authors":"T Kawasaki,&nbsp;K Nishida,&nbsp;M Fujie,&nbsp;S Usami,&nbsp;T Yamada","doi":"10.1093/nass/44.1.161","DOIUrl":"https://doi.org/10.1093/nass/44.1.161","url":null,"abstract":"<p><p>By Southern blot analysis of restriction fragments of a chlorovirus CVK2 genomic contig with probes of RNA expressed immediate early in infection, sixteen genes were specifically found to be expressed in the host cells. These genes include those for aminoacyl-tRNA synthetase, nucleolin, ribosomal protein S5, hyaluronan synthase, TFIID etc. All of these transcripts were polyadenylated and most likely expressed in the host nucleus. The structural characteristics of these genes are discussed in connection with their expression mechanism. The biological importance of the gene products in viral infection are also considered.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"161-2"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.161","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517391","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
Analysis of interaction between RNA aptamer and protein using nucleotide analogs. 利用核苷酸类似物分析RNA适体与蛋白质的相互作用。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.163
S Sekiya, K Fukuda, J Hwang, N Kakiuchi, K Taira, I Kusakabe, S Nishikawa
{"title":"Analysis of interaction between RNA aptamer and protein using nucleotide analogs.","authors":"S Sekiya,&nbsp;K Fukuda,&nbsp;J Hwang,&nbsp;N Kakiuchi,&nbsp;K Taira,&nbsp;I Kusakabe,&nbsp;S Nishikawa","doi":"10.1093/nass/44.1.163","DOIUrl":"https://doi.org/10.1093/nass/44.1.163","url":null,"abstract":"<p><p>Non-structural protein 3 (NS3) derived from Hepatitis C virus (HCV) is essential for viral proliferation and has two functional domains; trypsin-like serine protease and helicase. Recently we obtained three types of RNA aptamers (G9-I, -II and -III) bound to NS3 protease domain (delta NS3) by in vitro selection and confirmed their strong inhibition for protease activity. These aptamers have a common sequence, 5'-GA(A/U)UGGGAC-3', forming a loop structure by Mulfold secondary structure modeling. G9-I shows a three-way junction and G9-II and -III have four-way junction structures. To characterize the active structure of these aptamers, we applied modification interference analysis using nucleotide analogs and identified common important nucleotides in these three aptamers.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"163-4"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.163","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517392","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 novel acyclic nucleotides. 新型无环核苷酸的合成及其性质。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.47
M Sakata, M Fujii
{"title":"Synthesis and properties of novel acyclic nucleotides.","authors":"M Sakata,&nbsp;M Fujii","doi":"10.1093/nass/44.1.47","DOIUrl":"https://doi.org/10.1093/nass/44.1.47","url":null,"abstract":"<p><p>Acyclic adenosine and thymidine analogs derived from L- and D-threonie were synthesised and incorporated into oligonucleotides by automated protocols using a standard phosphoramidite method. UV melting experiments with thus obtained oligonucleotides showed that incorporation of those acyclic nucleosides did not destabilize the hybrid duplexes and that the stabilities of them are influenced by the stereochemical structures of acyclic analogs. Modification of 3'-end of oligonucleotide with acyclic analogs protected the oligonucleotide against 3'-exonuclease.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"47-8"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.47","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517739","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 bases for substrate recognition and repair system of base-excision DNA repair proteins. 碱基切除DNA修复蛋白的底物识别和修复系统的结构基础。
Nucleic acids symposium series Pub Date : 2000-01-01 DOI: 10.1093/nass/44.1.57
S Fujii, Y Yamagata
{"title":"Structural bases for substrate recognition and repair system of base-excision DNA repair proteins.","authors":"S Fujii,&nbsp;Y Yamagata","doi":"10.1093/nass/44.1.57","DOIUrl":"https://doi.org/10.1093/nass/44.1.57","url":null,"abstract":"<p><p>The model structure of Escherichia coli AlkA (3-methyladenine-DNA glycosylase II) protein complexed with the double helical DNA is elucidated from X-ray structures of related DNA glycosylase enzymes and mutagenic studies. The free enzyme structure has no difficulty in building the platform to afford the bended and wedge DNA with the flipped out nucleotide. The helix-hairpin-helix motif and the insertion residue L125 in free structure can be located without severe contacts. The alkylated base is surrounded with a variety of aromatic rings, such as W218, W272, Y273 and F18. The aromatic indole ring of tryptophan is a good candidate for forming the stacking with the positively charged base moiety pi-cation interaction). Some hydrophobic residues, such as V128 and L240, also attend to substrate recognition.</p>","PeriodicalId":19394,"journal":{"name":"Nucleic acids symposium series","volume":" 44","pages":"57-8"},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/44.1.57","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22517744","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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