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Nucleic acids symposium series (2004)最新文献

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Synthesis and properties of new RNA molecules incorporating 2'-O-aryluridine derivatives. 含2′- o -芳基尿苷衍生物的新型RNA分子的合成及其性质。
Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp059
Yusuke Oeda, Yoshihiro Iijima, Hirosuke Tsunoda, Akihiro Okubo, Kohji Seio, Mitsuo Sekine

A variety of 2'-O-arylnucleosides with functional groups were synthesized by the microwave-assisted reaction of 2,2'-anhydrouridine with phenol derivatives. The 2'-O-arylnucleosides thus obtained were incorporated into 2'-O-Me RNA or DNA oligomers and their hybridization properties were studied by T(m) measurements.

以2,2′-无氢吡啶与苯酚衍生物为原料,采用微波辅助反应合成了多种含官能团的2′- o -芳基核苷。将得到的2′- o -芳基核苷掺入到2′-O-Me RNA或DNA低聚物中,并通过T(m)测量研究其杂交特性。
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引用次数: 1
Structure and real-time monitoring of the enzymatic reaction of APOBEC3G which is involved in anti-HIV activity. 参与抗hiv活性的APOBEC3G酶促反应的结构和实时监测。
Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp044
Ayako Furukawa, Takashi Nagata, Akimasa Matsugami, Yuichirou Habu, Ryuichi Sugiyama, Fumiaki Hayashi, Naohiro Kobayashi, Shigeyuki Yokoyama, Hiroshi Takaku, Masato Katahira

Human apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G) is known to play a role in intrinsic cellular immunity against human immunodeficiency virus type 1 (HIV-1). The antiretroviral activity of APOBEC3G is associated with hypermutation of viral DNA through cytidine deamination. APOBEC3G contains two cytidine deaminase domains that are characterized by a highly conserved zinc-coordinating motif. It is known that only the C-terminal domain of APOBEC3G (c-APOBEC3G) is involved in the catalytic activity. Here, we present the solution structure and the interaction with single-stranded DNA of c-APOBEC3G. Furthermore, we have succeeded for the first time in monitoring the deamination reaction of c-APOBEC3G in real-time using NMR signals. The monitoring has demonstrated that the deamination reaction occurs in a strict 3'-->5'

已知人载脂蛋白B mrna编辑酶催化多肽样3G (APOBEC3G)在对抗人类免疫缺陷病毒1型(HIV-1)的内在细胞免疫中发挥作用。APOBEC3G的抗逆转录病毒活性与病毒DNA通过胞苷脱胺的高突变有关。APOBEC3G包含两个胞苷脱氨酶结构域,其特征是高度保守的锌配位基序。已知只有APOBEC3G的c端结构域(c-APOBEC3G)参与催化活性。在这里,我们展示了c-APOBEC3G的溶液结构和与单链DNA的相互作用。此外,我们首次成功地利用核磁共振信号实时监测了c-APOBEC3G的脱胺反应。监测结果表明,脱氨反应发生在严格的3′~ >5′范围内。
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引用次数: 12
A selective and sensitive detection of SNP between rice cultivars by using DNA photoligation. 利用DNA光定位技术选择性、灵敏地检测水稻品种间SNP。
Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp100
Yoshinaga Yoshimura, Hajime Okada, Tomoko Ohtake, Tadashi Tsukaguchi, Kenzo Fujimoto

We describe a selective and sensitive single-nucleotide polymorphism (SNP) typing of genes from rice cultivars by using DNA photoligation. This SNP typing method facilitates qualitative determination of genes from indica and japonica rice, and showed a high degree of single nucleotide specificity.

我们利用DNA光定位技术对水稻品种的基因进行了选择性和敏感的单核苷酸多态性(SNP)分型。该方法有利于籼稻和粳稻基因的定性鉴定,具有高度的单核苷酸特异性。
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引用次数: 2
Radiolytic one-electron reductive cyclization of oligodeoxynucleotides possessing a disulfide bond. 具有二硫键的寡脱氧核苷酸的放射性单电子还原环化。
Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp089
Eiji Matsumoto, Kazuhito Tanabe, Sei-ichi Nishimoto

Radiolytic one-electron reduction of oligodeoxynucleotides (ODNs) possessing a disulfide bond induced strand exchange reaction in a hypoxia selective manner. In this study, we attempted to apply this radiolytic reaction to stem-and-loop structured ODNs. Hypoxic X-irradiation to an aqueous solution of stem-and-loop structured ODNs produced a cyclized DNA in good yield via an intrastrand ligation reaction.

具有二硫键的寡脱氧核苷酸(ODNs)的单电子辐射还原以缺氧选择性方式诱导链交换反应。在这项研究中,我们试图将这种辐射分解反应应用于茎环结构的odn。低氧x射线照射到茎环结构odn的水溶液中,通过链内连接反应产生高产量的环化DNA。
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引用次数: 0
Analysis of an RNA adduct formed from aminophenylnorharman. 氨基苯基诺哈曼形成的RNA加合物的分析。
Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp106
Koichi Nishimura, Yukari Totsuka, Takashi Higuchi, Nobuo Kawahara, Takashi Sugimura, Keiji Wakabayashi

The endogenous mutagenic/carcinogenic 9- (4'-aminophenyl) -9H- pyrido [3,4-b] indole (aminophenylnorharman, APNH) is formed from norharman and aniline in the presence of cytochrome P-450s. The major APNH-DNA adduct has been reported to be 2'-deoxyguanosin-8-yl-aminophenylnorhaman (dG-C8-APNH). In addition, demonstrated formation of APNH-RNA adduct and conducted a structural analysis using various spectrometric approaches. The compound produced from guanosine (Guo) and N-acetoxy-APNH, an ultimate mutagenic form of APNH, was concluded to be guanosin-8-yl-APNH (Guo-C8-APNH) on the basis of various spectroscopic analysis. The same adduct was found in the livers of rats administered APNH. The total adduct levels of APNH-RNA were six times higher than total APNH-DNA adducts in the same rat liver samples.

内源性致突变/致癌物质9-(4′-氨基苯基)- 9h -吡啶[3,4-b]吲哚(aminophenylnorharman, APNH)是由norharman和苯胺在细胞色素p -450存在下形成的。据报道,APNH-DNA的主要加合物是2'-脱氧鸟苷-8-基氨基苯基诺哈曼(dG-C8-APNH)。此外,证明了APNH-RNA加合物的形成,并使用各种光谱方法进行了结构分析。鸟苷(Guo)与n-乙酰氧基-APNH (APNH的最终致突变性形式)合成的化合物经多种光谱分析确定为鸟苷-8-yl-APNH (Guo- c8 -APNH)。在给予APNH的大鼠肝脏中也发现了相同的加合物。在相同的大鼠肝脏样本中,APNH-RNA的总加合物水平比APNH-DNA的总加合物高6倍。
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引用次数: 2
The oxidation of 2'-deoxy-8-oxoguanosine by iodine. 碘对2'-脱氧-8-氧鸟苷的氧化作用
Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp110
Masayuki Morikawa, Teruhiko Kobayashi, Takanobu Kobayashi, Rie Komori, Yoshihisa Sei, Hiroshi Miyazawa, Katsuhito Kino

8-Oxoguanine is the typical oxidative product, but 8-oxoguanine is further oxidized by several oxidizing agents. Here, we investigated the oxidation of 2'-deoxy-8-oxoguanosine with aqueous iodine.

8-氧鸟嘌呤是典型的氧化产物,但8-氧鸟嘌呤还会被几种氧化剂进一步氧化。在这里,我们研究了2'-脱氧-8-氧鸟苷与水碘的氧化。
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引用次数: 2
Synthesis and properties of a novel artificial nucleoside that acts as a redox switch. 一种新型人工核苷氧化还原开关的合成及其性质。
Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp054
Takeshi Baba, Tetsuya Kodama, Takeshi Imanishi, Satoshi Obika

Oligonucleotide that can reversibly alter the duplex-forming ability in response to an external factor has potential to be applied to various genome technologies, e.g. antisense and gene diagnosis technology. A novel bridged nucleoside which is capable of sensing an oxidant and reductant was designed and synthesized. The nucleoside formed a disulfide bridge between C2' and C4' positions, which would enhance its duplex-forming ability under oxidative conditions. Contrastingly, the disulfide bridge was cleaved under reductive conditions; it could cause decrease of duplex-forming ability.

能够可逆地改变双工形成能力以响应外部因素的寡核苷酸具有应用于各种基因组技术的潜力,例如反义和基因诊断技术。设计并合成了一种新型的能感应氧化剂和还原剂的桥接核苷。核苷在C2′和C4′之间形成了一个二硫桥,这将增强其在氧化条件下的双相形成能力。相比之下,二硫桥在还原条件下是劈裂的;它会导致双相成形能力的下降。
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引用次数: 3
Identification of DNA binding specificity for TLS. TLS DNA结合特异性的鉴定。
Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp124
Kentaro Takahama, Shigeki Arai, Riki Kurokawa, Takanori Oyoshi

TLS (Translocated in liposarcoma) has been characterized as a rearranged gene in chromosomal translocations specific of human myxoid liposarcoma. The various cellular functions of TLS participating either in transcription or splicing processes are thought the involvement of an interaction of TLS with DNA and/or RNA. To investigate insight into DNA-TLS interaction, we performed Electrophoretic mobility shift assay of TLS with G-quadruplex DNA. It revealed that TLS especially bound to single stranded human telomeric DNA in the presence of potassium ion while it was not able to bind double stranded human telomeric DNA and single stranded human telomeric DNA in the presence of sodium ion.

TLS(易位于脂肪肉瘤)被认为是人黏液样脂肪肉瘤特异性染色体易位中的重排基因。TLS参与转录或剪接过程的各种细胞功能被认为涉及与DNA和/或RNA的相互作用。为了深入了解DNA-TLS的相互作用,我们对TLS与g -四重体DNA进行了电泳迁移转移试验。结果表明,在钾离子存在下,TLS能与单链人端粒DNA结合,而在钠离子存在下,TLS不能与双链人端粒DNA和单链人端粒DNA结合。
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引用次数: 10
Influence of 3'-azido-2',3'-dideoxyguanosine treatment on telomere length in human telomerase-immortalized human fibroblast cells. 3′-叠氮-2′,3′-二脱氧鸟苷处理对端粒酶永生化人成纤维细胞端粒长度的影响。
Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp125
Yuichi Kurashina, Xiaohong Liu, Chiemi Kato, Naoki Inoue, Mineo Saneyoshi, Toyofumi Yamaguchi

In order to study telomerase activation in normal cells, a telomerase-immortalized fibroblast cell line, hTERT-BJ1, treated with a telomerase inhibitor, 3'-azido-2',3'-dideoxyguanosine (AZddG), is considered to be a good model. Long-term treatment with AZddG resulted in telomere shortening from 10-20 kbp to 5-6 kbp in cultured hTERT BJ1 cells. However, the telomere length then stabilized. As expected, removal of AZddG from the culture medium induced telomere lengthening in the cells, suggesting that telomerase activity was recovered upon AZddG removal. The effect of recovery of telomerase activity in hTERT-BJ1 cells will be investigated in future studies.

为了研究正常细胞中端粒酶的活化,端粒酶永活的成纤维细胞系hTERT-BJ1被认为是一个很好的模型,该模型使用端粒酶抑制剂3'-叠氮-2',3'-双脱氧鸟苷(AZddG)处理。AZddG长期治疗可使培养的hTERT BJ1细胞端粒从10-20 kbp缩短至5-6 kbp。然而,端粒长度随后趋于稳定。不出所料,从培养基中去除AZddG诱导细胞端粒延长,表明去除AZddG后端粒酶活性恢复。端粒酶活性恢复对hTERT-BJ1细胞的影响将在未来的研究中进一步探讨。
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引用次数: 0
Site-specific modification of RNA by functionality-transfer ODN probes. 功能转移ODN探针对RNA的位点特异性修饰。
Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp034
Kazumitsu Onizuka, Yosuke Taniguchi, Takamasa Nishioka, Shigeki Sasaki

Efficient methods for the modification of RNA molecules have been expected as innovative biological tools and therapeutic methods. In this study, the development of a general method for site-specific RNA modification by the functionality-transfer ODN probes has been investigated. Site-specific and cytosine-selective RNA modifications were achieved by the functionality-transfer reaction. It was shown that the base and site-selectivity were due to the close proximity of the reactants in the DNA-RNA duplexes.

RNA分子修饰的有效方法已被期望作为创新的生物工具和治疗方法。在这项研究中,开发了一种通过功能转移ODN探针进行位点特异性RNA修饰的通用方法。通过功能转移反应实现了位点特异性和胞嘧啶选择性RNA修饰。结果表明,碱基选择性和位点选择性是由于DNA-RNA双链中反应物的接近性所致。
{"title":"Site-specific modification of RNA by functionality-transfer ODN probes.","authors":"Kazumitsu Onizuka,&nbsp;Yosuke Taniguchi,&nbsp;Takamasa Nishioka,&nbsp;Shigeki Sasaki","doi":"10.1093/nass/nrp034","DOIUrl":"https://doi.org/10.1093/nass/nrp034","url":null,"abstract":"<p><p>Efficient methods for the modification of RNA molecules have been expected as innovative biological tools and therapeutic methods. In this study, the development of a general method for site-specific RNA modification by the functionality-transfer ODN probes has been investigated. Site-specific and cytosine-selective RNA modifications were achieved by the functionality-transfer reaction. It was shown that the base and site-selectivity were due to the close proximity of the reactants in the DNA-RNA duplexes.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"67-8"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp034","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28398377","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
期刊
Nucleic acids symposium series (2004)
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