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Assessment of the DNA damage using the fluorescence microscope. 利用荧光显微镜评估DNA损伤。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp024
Yuka Yamazaki, Anatoly Zinchenko, Shizuaki Murata
{"title":"Assessment of the DNA damage using the fluorescence microscope.","authors":"Yuka Yamazaki,&nbsp;Anatoly Zinchenko,&nbsp;Shizuaki Murata","doi":"10.1093/nass/nrp024","DOIUrl":"https://doi.org/10.1093/nass/nrp024","url":null,"abstract":"<p><p>DNA damage was monitored by fluorescent microscopy observations of DNA fluorescent images after hydrodynamic stretching on a microscope glass. DNA double-strand breaks lead to a decrease of the average length of observed fluorescent DNA molecules. Compared to conventional methods such as electrophoresis, the proposed method allows for the analysis of the DNA damage at very low DNA breaking frequency. In particular, this method was used to study DNA damage by weak UV irradiation in solutions of quantum dots.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"47-8"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp024","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28396107","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
Polyethylenimine derived nanoparticles for efficient gene delivery. 用于高效基因传递的聚乙烯亚胺衍生纳米颗粒。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp029
A Pathak, S Patnaik, K C Gupta
{"title":"Polyethylenimine derived nanoparticles for efficient gene delivery.","authors":"A Pathak,&nbsp;S Patnaik,&nbsp;K C Gupta","doi":"10.1093/nass/nrp029","DOIUrl":"https://doi.org/10.1093/nass/nrp029","url":null,"abstract":"<p><p>Introduction of therapeutic genes into the cells of an organism in a safe and efficient way has become a challenging task in non-viral mediated gene therapy. Here, branched polyethylenimine (bPEI, 25 kDa) was converted into nanoparticles through electrostatic interactions with anionic polysaccharides (e.g. alginic acid, Al and hyaluronic acid, HA). A small library of PEI-Al and PEI-HA nanoparticles was synthesized by varying the amounts of anionic polysaccharides and evaluated in terms of their size, surface charge, cytotoxicity, transfection efficiency, etc. Both the series of nanoparticles exhibited higher cell viability and transfection efficiency as compared to native PEI and the standard transfection reagents. In vivo targeting efficacy of PEI-HA(4.6%) nanoparticles was examined in tumor induced mice.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"57-8"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp029","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28396112","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: 12
NMR studies of HAC1 mRNA. HAC1 mRNA的核磁共振研究。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp135
Ikumi Kawahara, Kaichiro Haruta, Chojiro Kojima, Yoshiyuki Tanaka
{"title":"NMR studies of HAC1 mRNA.","authors":"Ikumi Kawahara,&nbsp;Kaichiro Haruta,&nbsp;Chojiro Kojima,&nbsp;Yoshiyuki Tanaka","doi":"10.1093/nass/nrp135","DOIUrl":"https://doi.org/10.1093/nass/nrp135","url":null,"abstract":"<p><p>HAC1 is a transcription factor related to Unfolded Protein Response (UPR) signaling in yeast. Processing of HAC1 mRNA on Endoplasmic reticulum (ER) plays a key role in UPR signaling pathway, but the recognition mechanism of HAC1 mRNA by processing enzyme Ire1p is still unclear. Here, the solution structure of HAC1 mRNA was investigated by Nuclear Magnetic Resonance (NMR) spectroscopy, focusing on the structure of the recognition site of Ire1p in HAC1 mRNA. From the NOESY spectrum, imino proton signals of 5' processing regions of HAC1 mRNA were assigned and it was found that this region forms the stem-loop structure.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"269-70"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp135","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28397470","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
Docking simulation of polyamines on a kissing-loop RNA dimer. 接吻环RNA二聚体上多胺的对接模拟。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp137
Misaki Imai, Daisuke Chikatsu, Emire Inomata, Tairo Oshima, Gota Kawai
{"title":"Docking simulation of polyamines on a kissing-loop RNA dimer.","authors":"Misaki Imai,&nbsp;Daisuke Chikatsu,&nbsp;Emire Inomata,&nbsp;Tairo Oshima,&nbsp;Gota Kawai","doi":"10.1093/nass/nrp137","DOIUrl":"https://doi.org/10.1093/nass/nrp137","url":null,"abstract":"<p><p>Polyamines, especially branched polyamines such as tetrakis(3-aminopropyl)ammonium (Taa), stabilize the tertiary structure of RNA molecules. In this study, we examined the polyamine binding site of the HIV-1 dimerization initiation site (DIS) in the kissing-loop dimer by the docking simulation. It was found that Taa binds predominantly to the kissing loop interaction site of DIS.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"273-4"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp137","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28397472","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
Cationic comb-type copolymer as a nucleic acid chaperone for DNA quadruplex. 阳离子梳型共聚物作为DNA四重体的核酸伴侣。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp031
Rui Moriyama, Naohiko Shimada, Arihiro Kano, Atsushi Maruyama
{"title":"Cationic comb-type copolymer as a nucleic acid chaperone for DNA quadruplex.","authors":"Rui Moriyama,&nbsp;Naohiko Shimada,&nbsp;Arihiro Kano,&nbsp;Atsushi Maruyama","doi":"10.1093/nass/nrp031","DOIUrl":"https://doi.org/10.1093/nass/nrp031","url":null,"abstract":"<p><p>The intermolecular DNA quadruplex is attractive materials for design of nanomolecular constructs and machines. This folding kinetics is, however, slow, hampering its application to these materials. We have reported that the cationic comb-type copolymer accelerated duplex and triplex formation. In this study, the effect of the copolymer on the intermolecular quadruplex folding was investigated. The copolymer was found to accelerate the association of intermolecular quadruplex by three-orders. Furthermore, the copolymer induced the strand exchange reaction between intermolecular quadruplex and its single-stranded counterparts. We suggested that the copolymer acts as a nucleic acid chaperone for the intermolecular quadruplex.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"61-2"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp031","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28398374","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
Photoinduced electron transfer reaction in diaminostilbene-tethered DNA duplexes. 二氨基二苯乙烯链DNA双链的光诱导电子转移反应。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp101
Takeo Ito, Aiko Hayashi, Tsukasa Uchida, Kazuhito Tanabe, Hisatsugu Yamada, Sei-Ichi Nishimoto
{"title":"Photoinduced electron transfer reaction in diaminostilbene-tethered DNA duplexes.","authors":"Takeo Ito,&nbsp;Aiko Hayashi,&nbsp;Tsukasa Uchida,&nbsp;Kazuhito Tanabe,&nbsp;Hisatsugu Yamada,&nbsp;Sei-Ichi Nishimoto","doi":"10.1093/nass/nrp101","DOIUrl":"https://doi.org/10.1093/nass/nrp101","url":null,"abstract":"<p><p>DNA duplexes containing diaminostilbene (DAS) as a photoinduced electron donor were synthesized to investigate mechanisms of electron injection into DNA and the succeeding electron transfer in the duplexes. DAS-Capped hairpin DNA showed a high structural stability thereby attains large interaction between DAS and the terminal base pair. DAS-Tethered DNA by a single linker at the end of the duplex was also synthesized and the yields of photoinduced electron transfer through mismatched base pairs were quantified. Both duplexes showed similar electron transfer efficiencies depending on the base pairs, which suggests DAS stacks well on the \"pi-way\" of the duplex DNA.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"201-2"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp101","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28398394","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
Photoelectrochemical identification of 5-methylcytosine modification in DNA: combination of photosensitization and enzymatic cleavage. DNA中5-甲基胞嘧啶修饰的光电化学鉴定:光敏和酶切的结合。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp103
Kazuhito Tanabe, Hisatsugu Yamada, Takeo Ito, Sei-ichi Nishimoto
{"title":"Photoelectrochemical identification of 5-methylcytosine modification in DNA: combination of photosensitization and enzymatic cleavage.","authors":"Kazuhito Tanabe,&nbsp;Hisatsugu Yamada,&nbsp;Takeo Ito,&nbsp;Sei-ichi Nishimoto","doi":"10.1093/nass/nrp103","DOIUrl":"https://doi.org/10.1093/nass/nrp103","url":null,"abstract":"<p><p>We present a novel photoelectrochemical approach for discriminating between cytosine and 5-methylcytosine in DNA when used in combination with enzymatic digestion. A photosensitizer-linked DNA duplex bearing 5-methylcytosine or cytosine at a given restriction site of the strand was immobilized on a gold electrode and digested with enzyme, and the photocurrent response was measured. We observed high photocurrent density that was selective for the methylated duplex.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"205-6"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp103","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28398396","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
Development of next generation 4'-selenonucleosides. 新一代4′-硒核苷的发展。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp004
Lak Shin Jeong, Dilip K Tosh, Won Jun Choi
{"title":"Development of next generation 4'-selenonucleosides.","authors":"Lak Shin Jeong,&nbsp;Dilip K Tosh,&nbsp;Won Jun Choi","doi":"10.1093/nass/nrp004","DOIUrl":"https://doi.org/10.1093/nass/nrp004","url":null,"abstract":"<p><p>Next generation 4'-selenonucleosides as potential antiviral and antitumor agents were synthesized using a Pummerer type condensation as a key step.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"7-8"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28470940","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
Optimization of the sequence of twisted intercalating nucleic acids (TINA) forming triple helix with the polypurine tract of the proviral HIV DNA. 与HIV前病毒DNA多嘌呤道形成三螺旋的扭曲嵌入核酸(TINA)序列的优化。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp070
Alexandre S Boutorine, Osman Doluca, Vyacheslav V Filichev
{"title":"Optimization of the sequence of twisted intercalating nucleic acids (TINA) forming triple helix with the polypurine tract of the proviral HIV DNA.","authors":"Alexandre S Boutorine,&nbsp;Osman Doluca,&nbsp;Vyacheslav V Filichev","doi":"10.1093/nass/nrp070","DOIUrl":"https://doi.org/10.1093/nass/nrp070","url":null,"abstract":"<p><p>Twisted intercalating nucleic acids form stable triplexes with polypurine tracts of double-stranded DNA. Their affinity depends on their length, primary structure and base contents, parallel or antiparallel orientation of oligonucleotides respectively to DNA, number of TINA residues and their relative positions. Basing on parallel CT, GT and antiparallel GT triplex-forming 16-mer oligonucleotides targeted to polypurine tract of HIV proviral DNA, we synthesized eleven different oligonucleotides with 2-4 TINA insertions in different positions. Studies of their interaction with target duplex by gel shift, fluorescence spectroscopy, circular dichroism and thermal denaturation demonstrated that antiparallel GT oligonucleotides form more stable triplexes than parallel TC or TG ones. Two best candidates were selected for the further studies. The first one (5'-AGGGxGGGTTTxTGTTTT-3', Kd = 219 nM) contains only two TINA insertions and does not aggregate in non-denaturing conditions, in contrast to majority of other oligonucleotides.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"139-40"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp070","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28470958","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
Design of extremely facile 3'- and 5'- ends free molecular beacons using C8 alkylamino substituted 2'-deoxyguanosine. 用C8烷基胺取代2′-脱氧鸟苷，设计极易操作的3′和5′端自由分子信标。
Nucleic acids symposium series (2004) Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp071
Katsuhiko Matsumoto, Yuta Shinohara, Kyoko Numajiri, Shinya Ishioroshi, Takashi Morii, Yoshio Saito, Isao Saito
{"title":"Design of extremely facile 3'- and 5'- ends free molecular beacons using C8 alkylamino substituted 2'-deoxyguanosine.","authors":"Katsuhiko Matsumoto,&nbsp;Yuta Shinohara,&nbsp;Kyoko Numajiri,&nbsp;Shinya Ishioroshi,&nbsp;Takashi Morii,&nbsp;Yoshio Saito,&nbsp;Isao Saito","doi":"10.1093/nass/nrp071","DOIUrl":"https://doi.org/10.1093/nass/nrp071","url":null,"abstract":"<p><p>A novel fluorescent oligonucleotide probe containing pyrene-labeled C8 alkylamino-substituted 2'-deoxyguanosine and a practically useful 3'- and 5'- ends-free self-quenched molecular beacons (MB) were designed. A unique MB detectable by pyrene excimer fluorescence was also demonstrated.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"141-2"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp071","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28475056","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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