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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。
Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp074
Shinobu Sato, Keiichi Ohtsuka, Shigeori Takenaka

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.

新合成的萘二亚胺1取代端有两个二硫代烷基团,通过1的二硫代烷基团固定双链DNA。结合后,双链DNA可以固定在石英晶体微天平(QCM)芯片的金表面。一旦固定,配合物将作为杂交标记基于其频率降低。QCM实验表明,带有24分链单链区域的DNA双链也可以固定在QCM芯片的金表面上,并且与24分链的互补DNA杂交后频率下降,但与非互补DNA杂交后频率下降,表明有特异性杂交。这一结果表明,1提供了一种新的将完整DNA固定在金上的方法,并且固定的DNA可以与靶DNA杂交。
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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。
Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp085
Shuhei Kusano, Keiichi Hattori, Shuhei Imoto, Fumi Nagatsugi

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.

在此之前,我们利用含有2-氨基-6-乙烯嘌呤衍生物的寡脱氧核苷酸(ODN)与DNA靶位点的胞嘧啶碱基进行了高效和选择性的交联反应(1)。基于这些结果,我们设计了新型交联剂,该交联剂是具有两个氢键位点的嘧啶衍生物,乙烯基作为反应基团。本文报道了具有新型交联剂潜力的嘧啶衍生物的合成研究结果。
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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。
Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp115
Shu-ichi Nakano, Hidenobu Hirayama, Naoki Sugimoto

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.

核苷酸折叠伴随着阳离子结合,屏蔽了磷酸基团的电负性电位,缩合层中的金属离子主要与碱基配对的核苷酸扩散结合。虽然在特定位点结合的金属离子已经得到了很好的研究,但扩散结合的阳离子的信息还没有得到充分的研究,这些阳离子的结合亲和力通常比在特定位点结合的阳离子弱。我们探索了一种方便的实验系统,使用自互补的核苷酸序列来分析扩散结合到DNA或RNA碱基对的阳离子配体。为了研究非同源水条件下金属离子与核苷酸的相互作用,研究了含有大量聚乙二醇的溶液。我们发现聚乙二醇(例如,20% wt%)显著影响了金属离子与核苷酸的结合,这表明分子环境对核苷酸-阳离子相互作用的重要性。
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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。
Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp116
Masayuki Tera, Keisuke Iida, Kazuo Shin-ya, Kazuo Nagasawa

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.

富含鸟嘌呤的DNA序列形成独特的三维构象,称为g -四重构象(G-q)。在端粒和某些癌基因启动子中发现了G-q结构。近年来,人们认为G-q具有缩短端粒和转录调控等生物学活性。本文合成了选择性G-q结合物,并对其生物活性进行了评价。
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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。
Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp117
Keisuke Iida, Masayuki Tera, Kazuo Shin-Ya, Kazuo Nagasawa

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.

端粒抑素(TMS: 1)是一种有效的选择性端粒g -四联体结合剂。对接研究表明,两个TMS分子被插入到一个端粒g -四联体中。本文设计并合成了六恶唑TMS衍生物(6OTD)二聚体,并对其g -四联体的稳定性能进行了评价。
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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。
Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp118
Hidetaka Torigoe, Eugene Horio, Takashi Takehara, Kaoru Kaneda, Tetsuo Kozasa

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.

我们检测了出芽酵母端粒DNA序列SCTELGG4: 5'-(TGGGTGTG)(4)-3'和SCTELGG4: 5'-(TGGGTGTGG)(4)-3'在Na(+)或K(+)存在下的结构特性。SCTELG4与Na(+)的构象是平行四联体DNA和非结构化单链DNA的混合物。另一方面,SCTELGG4与Na(+)的构象是平行和反平行的四联体DNA的混合物。K(+)的存在增加了SCTELG4的平行四联体与非结构化单链的比例。在K(+)的作用下,几乎所有的SCTELGG4的构象都改变为平行四复体。这些结果表明,SCTELG4和SCTELGG4的结构变化可能是由阳离子类型引起的。我们得出结论,出芽酵母端粒DNA序列的构象取决于碱基序列和阳离子类型。
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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。
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

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.

在刚性双环[3.1.0]己烷模板上合成了含有南北脱氧鸟苷的凝血酶结合适体(TBAs)。适配体dG14和dG15位置上的2'-脱氧鸟苷被这些限制了北/反和南/顺构象的类似物所取代。在第14位用锁定的South/syn-dG核苷取代产生的适体与先天的、未修饰的适体具有相同的稳定性和全局结构。用相同的South/syndG核苷替换位置15诱导了适体的强烈不稳定性,而对端North/anti-dG核苷的不稳定性较小。值得注意的是,在假糖构象和糖基扭转角与天然结构相反的位置14插入一个North/anti-dG核苷,导致g -四聚体结构被核磁共振检测到完全破坏,并被广泛的分子动力学模拟证实。
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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。
Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp058
Ken Yamada, Hirosuke Tsunoda, Akihiro Ohkubo, Kohji Seio, Mitsuo Sekine

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.

合成了一种新的4-N-酰基化脱氧胞苷衍生物,4-N-(1h -吡咯-2-羰基)脱氧胞苷,并在较碱性条件下具有稳定性。利用聚戊酰氧甲基(POM)保护吡咯残基,在不同位置成功合成了含有该修饰脱氧核苷的寡脱氧核苷酸(odn)。用1.5 M NaOMe/MeOH处理POM组。含有修饰脱氧胞苷的odn表现出优于未修饰odn的杂交特性。我们发现胞嘧啶碱基与芳香酰基型取代基的酰化导致DNA双链的热稳定性显著提高。这是这种修正中第一个值得注意的观察结果。本文还报道了4-N-(1h -吡咯-2-羰基)脱氧胞苷衍生物的合成及其杂化性质。
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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。
Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp134
Tsukasa Mashima, Akimasa Matsugami, Shun Nakano, Masafumi Inoue, Masatora Fukuda, Takashi Morii, Masato Katahira

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.

通过体外筛选获得了一个抗ATP的核糖核肽适配体。该核糖核肽适配体包括一个随机选择的RNA,与Rev-responsive element (RRE)结合,并与HIV Rev蛋白衍生的肽相结合。核糖核肽适配体在rev衍生肽存在的情况下选择性地结合ATP。本文采用核磁共振技术对该核糖核苷酸适配体进行了结构分析。在rev衍生肽存在的情况下,适体RNA部分的二级结构(与RRE连接的选定RNA区域)以ado结合形式确定。G:A和G:G碱基对与正则碱基对一起构成RRE的双工结构。选择的RNA区域在靶标结合中起着至关重要的作用。已经发现,位于选定RNA区域的两个U残基通过形成U:A:U碱基三重体来捕获Ado。HNN-COSY实验通过检测U:A:U碱基三元组中Watson-Crick和Hoogsteen A:U碱基对氢键上的自旋-自旋耦合直接证实了这一点。
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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。
Pub Date : 2009-01-01 DOI: 10.1093/nass/nrp139
Hisaaki Tateoka, Ikumi Kawahara, Satomi Hasegawa, Kaichiro Haruta, Yoshinori Kondo, Chojiro Kojima, Yoshiyuki Tanaka

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.

最近,在锤头核酶中,新发现的环环相互作用对它们的激活很重要。因此,我们用这个额外的环序列和它的突变核酶,以及它们的底物RNA链化学合成了一个锤头核酶,以澄清它们的可切割序列。用阴离子交换柱层析纯化后,我们可以得到44mer和20mer的RNA。
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引用次数: 0
期刊
Nucleic acids symposium series (2004)
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