Oligonucleotides最新文献_第10页

Label-free electrochemical detection of short sequences related to the hepatitis B virus using 4,4'-diaminoazobenzene based on multiwalled carbon nanotube-modified GCE. 基于多壁碳纳米管修饰GCE的4,4'-二氨基偶氮苯无标记电化学检测乙型肝炎病毒相关短序列

Oligonucleotides Pub Date : 2008-12-01 DOI: 10.1089/oli.2008.0143

Xue-Mei Li, Zhi-Ming Zhan, Heng-Qiang Ju, Shu-Sheng Zhang

引用次数: 19

Efficient suppression of tissue factor synthesis using antisense oligonucleotides selected by an enhanced strategy for evaluation of structural characteristics. 有效抑制组织因子合成使用反义寡核苷酸选择的增强策略，以评估结构特征。

Oligonucleotides Pub Date : 2008-12-01 DOI: 10.1089/oli.2008.0144

Yvonne Förster, Bernd Schwenzer

{"title":"Efficient suppression of tissue factor synthesis using antisense oligonucleotides selected by an enhanced strategy for evaluation of structural characteristics.","authors":"Yvonne Förster, Bernd Schwenzer","doi":"10.1089/oli.2008.0144","DOIUrl":"https://doi.org/10.1089/oli.2008.0144","url":null,"abstract":"Selection of optimal antisense constructs is still a problem. Among a huge number of antisense oligonucleotides (AS-ONs) only a small piece show inhibitory efficacy. We want to develop an enhanced strategy for specific selection of effective AS-ONs based on prediction of secondary structure of the target messenger RNA (mRNA) and analysis of thermodynamic properties of the mRNA/AS-ON hybrid. Numerous AS-ONs targeted on human tissue factor (TF) mRNA were investigated to evaluate the relevance of different thermodynamic and structural properties on inhibitory efficacy. Cell viability, TF protein and TF mRNA were determined after transfection of bladder cancer cell line J82. Inhibitory efficacy was related to GC content, target region within the TF mRNA and stability of the mRNA/AS-ON hybrid or affinity of the AS-ON to the target mRNA. We found effective AS-ONs targeted on translated region or 3'-untranslated region of TF RNA. We also detected a great correlation between inhibitory efficacy and GC content as well as stability of the mRNA/AS-ON hybrid.","PeriodicalId":19523,"journal":{"name":"Oligonucleotides","volume":"18 4","pages":"355-64"},"PeriodicalIF":0.0,"publicationDate":"2008-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/oli.2008.0144","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27798547","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

Stability study of unmodified siRNA and relevance to clinical use. 未修饰siRNA的稳定性研究及其与临床应用的相关性。

Oligonucleotides Pub Date : 2008-12-01 DOI: 10.1089/oli.2008.0149

Robyn P Hickerson, Alexander V Vlassov, Qian Wang, Devin Leake, Heini Ilves, Emilio Gonzalez-Gonzalez, Christopher H Contag, Brian H Johnston, Roger L Kaspar

{"title":"Stability study of unmodified siRNA and relevance to clinical use.","authors":"Robyn P Hickerson, Alexander V Vlassov, Qian Wang, Devin Leake, Heini Ilves, Emilio Gonzalez-Gonzalez, Christopher H Contag, Brian H Johnston, Roger L Kaspar","doi":"10.1089/oli.2008.0149","DOIUrl":"10.1089/oli.2008.0149","url":null,"abstract":"RNA interference offers enormous potential to develop therapeutic agents for a variety of diseases. To assess the stability of siRNAs under conditions relevant to clinical use with particular emphasis on topical delivery considerations, a study of three different unmodified siRNAs was performed. The results indicate that neither repeated freeze/thaw cycles, extended incubations (over 1 year at 21 degrees C), nor shorter incubations at high temperatures (up to 95 degrees C) have any effect on siRNA integrity as measured by nondenaturing polyacrylamide gel electrophoresis and functional activity assays. Degradation was also not observed following exposure to hair or skin at 37 degrees C. However, incubation in fetal bovine or human sera at 37 degrees C led to degradation and loss of activity. Therefore, siRNA in the bloodstream is likely inactivated, thereby limiting systemic exposure. Interestingly, partial degradation (observed by gel electrophoresis) did not always correlate with loss of activity, suggesting that partially degraded siRNAs retain full functional activity. To demonstrate the functional activity of unmodified siRNA, EGFP-specific inhibitors were injected into footpads and shown to inhibit preexisting EGFP expression in a transgenic reporter mouse model. Taken together, these data indicate that unmodified siRNAs are viable therapeutic candidates.","PeriodicalId":19523,"journal":{"name":"Oligonucleotides","volume":"18 4","pages":"345-54"},"PeriodicalIF":0.0,"publicationDate":"2008-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829675/pdf/oli.2008.0149.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27719919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dz13, a DNAzyme targeting c-jun, induces off-target cytotoxicity in endothelial cells with features of nonapoptotic programmed cell death. Dz13是一种靶向c-jun的DNAzyme，在内皮细胞中诱导脱靶细胞毒性，具有非凋亡程序性细胞死亡的特征。

Oligonucleotides Pub Date : 2008-09-01 DOI: 10.1089/oli.2008.0139

Mary Margaret Gozar, Amber Goodchild, Toby Passioura, Andrew King, Angela Lai, Craig Witherington, Laurent Rivory

{"title":"Dz13, a DNAzyme targeting c-jun, induces off-target cytotoxicity in endothelial cells with features of nonapoptotic programmed cell death.","authors":"Mary Margaret Gozar, Amber Goodchild, Toby Passioura, Andrew King, Angela Lai, Craig Witherington, Laurent Rivory","doi":"10.1089/oli.2008.0139","DOIUrl":"https://doi.org/10.1089/oli.2008.0139","url":null,"abstract":"We have previously shown that Dz13, a catalytic DNA molecule (DNAzyme) designed against c-jun, is cytotoxic to nonquiescent cells by a mechanism independent of c-jun mRNA cleavage. In this report, we evaluated programmed cell death (PCD) pathways in order to gain further insight into the mechanism of action of Dz13. Using human dermal microvascular endothelial cells (HMEC-1), we found that Dz13-mediated cell death is characterized by mitochondrial depolarization, caspase-8 activation, lysosomal increase, and autophagosome formation. Classical DNA laddering and translocation of mitochondrial proteins were not observed. An array of inhibitors, including those targeting caspases, failed to abrogate cytotoxicity and mitochondrial depolarization. Cytotoxicity did not proceed from endoplasmic reticulum (ER) stress. The possible involvement of PARP-1 in Dz13-mediated cytotoxicity was indicated by its differential release as gauged by protein extraction data and its apparent binding to Dz13, as evidenced by protein pull-down experiments. This study on Dz13-mediated cytotoxicity presents a detailed investigation into the interplay of cell death effectors involved in apoptosis, autophagy, and necrosis, and demonstrates a novel form of oligonucleotide-mediated cytotoxicity with features of PCD.","PeriodicalId":19523,"journal":{"name":"Oligonucleotides","volume":"18 3","pages":"257-68"},"PeriodicalIF":0.0,"publicationDate":"2008-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/oli.2008.0139","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27593484","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

Near-infrared fluorescent oligodeoxyribonucleotide reporters for sensing NF-kappaB DNA interactions in vitro. 用于NF-kappaB DNA相互作用检测的近红外荧光寡脱氧核糖核苷酸报告。

Oligonucleotides Pub Date : 2008-09-01 DOI: 10.1089/oli.2008.0135

Surong Zhang, Valeri Metelev, David Tabatadze, Paul Zamecnik, Alexei Bogdanov

{"title":"Near-infrared fluorescent oligodeoxyribonucleotide reporters for sensing NF-kappaB DNA interactions in vitro.","authors":"Surong Zhang, Valeri Metelev, David Tabatadze, Paul Zamecnik, Alexei Bogdanov","doi":"10.1089/oli.2008.0135","DOIUrl":"10.1089/oli.2008.0135","url":null,"abstract":"Two types of reporters for optical sensing of NF-kappaB p50 protein-oligodeoxyribonucleotide (ODN) duplex interactions were designed and compared in vitro. The reporters were based on the effect of fluorescence resonance energy transfer (FRET) between the pair donor Cy5.5 near-infrared (NIR) fluorochrome and either 800CW emitting fluorescence dye acceptor (800CW-Cy), or a nonemitting QSY 21 dye quencher (QSY-Cy). The donor and the acceptor dyes were covalently linked to the complementary oligonucleotides, respectively: Cy dye was conjugated to 3'-thiol, whereas 800CW or QSY21 were conjugated to a hydrophilic internucleoside phosphate amino linker. The reporters were tested initially using recombinant NF-kappaB p50 protein binding assays. Both reporters were binding p50 protein, which protected oligonucleotide duplex from degradation in the presence of exonuclease.The incubation of 800CW-Cy reporter in the presence of control or IL-1beta treated human endothelial cells showed the uptake of the reporter in the cytoplasm and the nucleus. The measurement of NIR fluorescence ratio (i.e. Cy5.5/800CW) showed a partial loss of FRET and the increased Cy5.5 fluorescence in nontreated, control cells. Thus, the specific p50 binding to ODN duplex reporters affected the donor-acceptor fluorochrome pair. NF-kappaB p50 exhibited the protective effect on FRET between NIR fluorochromes linked to the complementary strands of the reporter duplex.","PeriodicalId":19523,"journal":{"name":"Oligonucleotides","volume":"18 3","pages":"235-43"},"PeriodicalIF":0.0,"publicationDate":"2008-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2948448/pdf/oli.2008.0135.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27593483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Molecular imaging study on in vivo distribution and pharmacokinetics of modified small interfering RNAs (siRNAs). 修饰小干扰rna (sirna)体内分布及药代动力学的分子影像学研究。

Oligonucleotides Pub Date : 2008-09-01 DOI: 10.1089/oli.2008.0133

Thomas Viel, Raphael Boisgard, Bertrand Kuhnast, Benoit Jego, Karine Siquier-Pernet, Françoise Hinnen, Frédéric Dollé, Bertrand Tavitian

{"title":"Molecular imaging study on in vivo distribution and pharmacokinetics of modified small interfering RNAs (siRNAs).","authors":"Thomas Viel, Raphael Boisgard, Bertrand Kuhnast, Benoit Jego, Karine Siquier-Pernet, Françoise Hinnen, Frédéric Dollé, Bertrand Tavitian","doi":"10.1089/oli.2008.0133","DOIUrl":"https://doi.org/10.1089/oli.2008.0133","url":null,"abstract":"Molecular imaging was used to study the biodistribution, pharmacokinetics, and activity of naked small interfering RNAs (siRNAs). siRNAs with riboses chemically modified in the 2' position were compared with unmodified siRNA. In vitro, replacement of the 2'-hydroxyl (2'OH) group of certain nucleotides in an siRNA sequence by a fluorine atom (2'F) on both antisense (AS) and sense (S) strands [2'F(AS/S)], or by a methoxy group (2'OMe) on the S strand [2'OH(AS)/2'OMe(S)], was compatible with RNA interference. Different siRNAs [2'F(AS/S), 2'OH(AS)/2'OMe(S), and 2'OH(AS/S)] were labeled with fluorine-18 (conjugation with [(18)F]FPyBrA), and comparative dynamic and quantitative imaging was performed with positron emission tomography. After intravenous injections of [(18)F]siRNAs in rodents, total radioactivity was rapidly eliminated by the kidneys and the liver. Tissue distribution of the different siRNAs were similar, and their bioavailability (as judged from blood persistence and stability) increased in the order 2'OH(AS/S) = 2'OH(AS)/2'OMe(S) < 2'F(AS/S). However, in our in vivo model, the 2'F(AS/S) siRNA, despite its higher bioavailability, was not able to induce a higher interference effect with respect to the 2'OH(AS/S) siRNA. Molecular imaging approaches, applied in the present work to both natural and chemically modified siRNAs, can contribute to the development of these macromolecules as therapeutic agents.","PeriodicalId":19523,"journal":{"name":"Oligonucleotides","volume":"18 3","pages":"201-12"},"PeriodicalIF":0.0,"publicationDate":"2008-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/oli.2008.0133","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27623961","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: 40

Potent knockdown of the X RNA of hepatitis B by a novel chimeric siRNA-ribozyme construct and modulation of intracellular target RNA by selectively disabled mutants. 新型嵌合sirna -核酶结构对乙型肝炎X RNA的有效敲除和选择性失能突变体对细胞内靶RNA的调节

Oligonucleotides Pub Date : 2008-09-01 DOI: 10.1089/oli.2008.0134

Nidhi Gupta, Aalia S Bano, Yogeshwar Sharma, Akhil C Banerjea

{"title":"Potent knockdown of the X RNA of hepatitis B by a novel chimeric siRNA-ribozyme construct and modulation of intracellular target RNA by selectively disabled mutants.","authors":"Nidhi Gupta, Aalia S Bano, Yogeshwar Sharma, Akhil C Banerjea","doi":"10.1089/oli.2008.0134","DOIUrl":"https://doi.org/10.1089/oli.2008.0134","url":null,"abstract":"A multitarget approach is needed for effective gene silencing that combines more than one antiviral strategy. With this in mind, we designed a wild-type (wt) and selectively disabled chimeric mutant (mt) constructs that consisted of small hairpin siRNA joined by a short intracellular cleavable linker to a known hammerhead ribozyme, both targeted against the full-length X RNA of hepatitis B. These chimeric RNAs possessed the ability to cleave the target RNA under in vitro conditions and were efficiently processed at the cleavable site. When this wt chimeric RNA construct was introduced into a liver-specific mammalian cell line, HepG2, along with the HBx substrate encoding DNA, very significant (approximately 70%) intracellular downregulation in the levels of target RNA was observed. When the siRNA portion of this chimeric construct was mutated, keeping the ribozyme (Rz) region unchanged, it caused only approximately 25% intracellular reduction. On the contrary, when only the Rz was made catalytically inactive, about 55% reduction in the target RNA was observed. Construct possessing mt Rz and mt siRNA caused only 10% reduction. This wt chimeric construct also resulted in almost complete knockdown of intracellular HBx protein production, and the mt versions were less effective. The intracellular reduction of target RNA with either wt or mt constructs also interfered with the known functions of HBx protein with varying efficiencies. Thus, in this proof of concept study we show that the levels of the target RNA were reduced potently by the wt chimeric siRNA-Rz construct, which could be modulated with mt versions of the same.","PeriodicalId":19523,"journal":{"name":"Oligonucleotides","volume":"18 3","pages":"225-33"},"PeriodicalIF":0.0,"publicationDate":"2008-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/oli.2008.0134","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27600386","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

Hybridization signal enhancement via long-stranded probe for detection of DNA using aquadichloro (benzimidazole)-copper(II) as hybridization indicator. 以水氯(苯并咪唑)-铜(II)为杂交指示剂，利用长链探针增强杂交信号检测DNA。

Oligonucleotides Pub Date : 2008-09-01 DOI: 10.1089/oli.2008.0132

Xue-Mei Li, Shan-Shan Gu, Shu-Sheng Zhang

{"title":"Hybridization signal enhancement via long-stranded probe for detection of DNA using aquadichloro (benzimidazole)-copper(II) as hybridization indicator.","authors":"Xue-Mei Li, Shan-Shan Gu, Shu-Sheng Zhang","doi":"10.1089/oli.2008.0132","DOIUrl":"https://doi.org/10.1089/oli.2008.0132","url":null,"abstract":"A simple and sensitive method for electrochemical detection of DNA was designed. This DNA sensor was based on a \"sandwich\" detection strategy, which involved a long capture probe DNA immobilized on glassy carbon electrodes that flanked both the reference DNA and target DNA. Electrochemical signals were measured by cyclic voltammetry (CV) and differential pulse voltammetry (DPV) using aquadichloro(benzimidazole)-copper(II), Cu(bzim)(H(2)O)Cl(2), as an electroactive indicator. An improving amount of Cu(bzim)(H(2)O)Cl(2) was interacted with the hybrid DNA via the incorporation of a long-probe DNA and a reference DNA in this sensor. As a result of this effect, this sensor design significantly enhanced the sensitivity. With 48-mer probe DNA and 27-mer reference DNA, the proposed method could be used for detection of 21-mer ssDNA ranging from 1.32 x 10(-7) to 2.52 x 10(-6) M with a detection limit of 2.94 x 10(-8) M. Electrochemical DNA biosensors were also developed using the same long-probe sequence as the target sequence with the novel hybridization indicator, Cu(bzim) (H(2)O)Cl(2). The detection limits for the complementary 21-mer target and 27-mer target were 9.52 x 10(-8) M and 5.81 x 10(-8) M, respectively. The results showed that the sensor with long-probe DNA and reference DNA is far more sensitive than that with nonswitch assay.","PeriodicalId":19523,"journal":{"name":"Oligonucleotides","volume":"18 3","pages":"287-94"},"PeriodicalIF":0.0,"publicationDate":"2008-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/oli.2008.0132","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27641714","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 use of 10-23 DNAzyme to selectively destroy the allele of mRNA with a unique purine-pyrimidine dinucleotide. 利用10-23 DNAzyme选择性地破坏具有独特嘌呤嘧啶二核苷酸的mRNA等位基因。

Oligonucleotides Pub Date : 2008-09-01 DOI: 10.1089/oli.2008.0138

Tong-Hong Wang, Wan-Ting Li, Szu-Hsien Yu, Lo-Chun Au

引用次数: 14

A triplex ribozyme expression system based on a single hairpin ribozyme. 基于单个发夹核酶的三重核酶表达系统。

Oligonucleotides Pub Date : 2008-09-01 DOI: 10.1089/oli.2008.0130

Guillermo Aquino-Jarquin, María Luisa Benítez-Hess, Joseph A DiPaolo, Luis M Alvarez-Salas

{"title":"A triplex ribozyme expression system based on a single hairpin ribozyme.","authors":"Guillermo Aquino-Jarquin, María Luisa Benítez-Hess, Joseph A DiPaolo, Luis M Alvarez-Salas","doi":"10.1089/oli.2008.0130","DOIUrl":"https://doi.org/10.1089/oli.2008.0130","url":null,"abstract":"Triplex ribozyme (RZ) configurations allow for the individual activity of trans-acting RZs in multiple expression cassettes (multiplex), thereby increasing target cleavage relative to conventionally expressed RZs. Although hairpin RZs have been advantageously compared to hammerhead RZs, their longer size and structural features complicated triplex design. We present a triplex expression system based on a single hairpin RZ with transcleavage capability and simple engineering. The system was tested in vitro using cis- and trans-cleavage kinetic assays against a known target RNA from HPV-16 E6/E7 mRNA. Single and multiplex triplex RZ constructs were more efficient in cleaving the target than tandem-cloned hairpin RZs, suggesting that the release of individual RZs enhanced trans-cleavage kinetics. Multiplex systems constructed with two different hairpin RZs resulted in better trans-cleavage compared to standard double-RZ constructs. In addition, the triplex RZ performed cis- and trans-cleavage in cervical cancer cells. The use of triplex configurations with multiplex RZs permit differential targeting of the same or different RNA, thus improving potential use against unstable targets. This prototype will provide the basis for the development of future RZ-based therapies and technologies.","PeriodicalId":19523,"journal":{"name":"Oligonucleotides","volume":"18 3","pages":"213-24"},"PeriodicalIF":0.0,"publicationDate":"2008-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/oli.2008.0130","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27600117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5