Antisense & nucleic acid drug development最新文献

{"title":"Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing.","authors":"Jens Harborth,&nbsp;Sayda M Elbashir,&nbsp;Kim Vandenburgh,&nbsp;Heiko Manninga,&nbsp;Stephen A Scaringe,&nbsp;Klaus Weber,&nbsp;Thomas Tuschl","doi":"10.1089/108729003321629638","DOIUrl":"https://doi.org/10.1089/108729003321629638","url":null,"abstract":"<p><p>Small interfering RNAs (siRNAs) induce sequence-specific gene silencing in mammalian cells and guide mRNA degradation in the process of RNA interference (RNAi). By targeting endogenous lamin A/C mRNA in human HeLa or mouse SW3T3 cells, we investigated the positional variation of siRNA-mediated gene silencing. We find cell-type-dependent global effects and cell-type-independent positional effects. HeLa cells were about 2-fold more responsive to siRNAs than SW3T3 cells but displayed a very similar pattern of positional variation of lamin A/C silencing. In HeLa cells, 26 of 44 tested standard 21-nucleotide (nt) siRNA duplexes reduced the protein expression by at least 90%, and only 2 duplexes reduced the lamin A/C proteins to <50%. Fluorescent chromophores did not perturb gene silencing when conjugated to the 5'-end or 3'-end of the sense siRNA strand and the 5'-end of the antisense siRNA strand, but conjugation to the 3'-end of the antisense siRNA abolished gene silencing. RNase-protecting phosphorothioate and 2'-fluoropyrimidine RNA backbone modifications of siRNAs did not significantly affect silencing efficiency, although cytotoxic effects were observed when every second phosphate of an siRNA duplex was replaced by phosphorothioate. Synthetic RNA hairpin loops were subsequently evaluated for lamin A/C silencing as a function of stem length and loop composition. As long as the 5'-end of the guide strand coincided with the 5'-end of the hairpin RNA, 19-29 base pair (bp) hairpins effectively silenced lamin A/C, but when the hairpin started with the 5'-end of the sense strand, only 21-29 bp hairpins were highly active.</p>","PeriodicalId":7996,"journal":{"name":"Antisense & nucleic acid drug development","volume":"13 2","pages":"83-105"},"PeriodicalIF":0.0,"publicationDate":"2003-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/108729003321629638","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22434832","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}

{"title":"Rapid identification of antisense mRNA-expressing clones using strand-specific RT-PCR.","authors":"Michele Cummings,&nbsp;Claire McGurk,&nbsp;John R Masters","doi":"10.1089/108729003321629656","DOIUrl":"https://doi.org/10.1089/108729003321629656","url":null,"abstract":"<p><p>Transfection of full-length antisense cDNA is used frequently to achieve stable downregulation of gene expression. However, screening for clones that express the antisense mRNA is complicated by the presence of endogenous sense mRNA. Thus, clones usually are screened for downregulation of the target protein by Western blotting, which can be time consuming. Here, we used strand-specific RT-PCR to identify antisense-expressing clones, which can then be screened for protein downregulation. This approach allows earlier identification of potentially useful clones and cuts down on the number of clones to be screened by Western blotting.</p>","PeriodicalId":7996,"journal":{"name":"Antisense & nucleic acid drug development","volume":"13 2","pages":"115-7"},"PeriodicalIF":0.0,"publicationDate":"2003-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/108729003321629656","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22434834","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}

{"title":"Analysis of a mitochondrial apoptotic pathway using Bid-targeted ribozymes in human MCF7 cells in the absence of a caspase-3-dependent pathway.","authors":"Reiko Onuki,&nbsp;Hiroaki Kawasaki,&nbsp;Tadashi Baba,&nbsp;Kazunari Taira","doi":"10.1089/108729003321629629","DOIUrl":"https://doi.org/10.1089/108729003321629629","url":null,"abstract":"<p><p>In normal cells, tumor necrosis factor-alpha (TNF-alpha) activates caspase 8 in both mitochondrion-dependent and mitochondrion-independent apoptotic pathways. It is believed that these two pathways converge, with resultant activation of effector caspases, such as caspase 6 and caspase 7. However, the precise mechanism of the activation of caspases 6 and 7 remains unknown. In this study, in order to focus on the mitochondrion-dependent pathway, we employed MCF7 human breast carcinoma cells, which do not have a functional mitochondrion-independent (caspase 3-dependent) pathway. We specifically targeted the transcript of Bid, a proapoptotic facilitator that is a substrate of caspase 8 in the mitochondrial pathway. In the TNF-alpha-treated MCF7 cells that expressed Bid-targeted ribozymes, the release of cytochrome c and the activation of caspase 9, but not of caspase 8, was delayed. Furthermore, the proteolysis of procaspase 7 was also delayed in Bid ribozyme-expressing cells. Because MCF7 cells are caspase 3 deficient, the direct cross-talk between caspase 8 and caspase 3 does not take place. Therefore, it became clear for the first time that caspase 9 by itself can activate caspase 7 in the absence of the caspase 3-dependent pathway in TNF-alpha-induced apoptosis by the use of specific ribozymes.</p>","PeriodicalId":7996,"journal":{"name":"Antisense & nucleic acid drug development","volume":"13 2","pages":"75-82"},"PeriodicalIF":0.0,"publicationDate":"2003-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/108729003321629629","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22434930","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}

{"title":"Delivery of antisense oligonucleotide to the cornea by iontophoresis.","authors":"M Berdugo,&nbsp;F Valamanesh,&nbsp;C Andrieu,&nbsp;C Klein,&nbsp;D Benezra,&nbsp;Y Courtois,&nbsp;F Behar-Cohen","doi":"10.1089/108729003321629647","DOIUrl":"https://doi.org/10.1089/108729003321629647","url":null,"abstract":"<p><p>We wished to evaluate the potential of iontophoresis to promote the delivery of antisense oligonucleotides (ODN) directed at the vascular endothelial growth factor (VEGF)-R2 receptor (KDR/Flk) to the cornea of the rat eye. Fluorescence (CY5)-labeled ODNs in phosphate-buffered saline (PBS) (20 microM) were locally administered to rat eyes, and their fate within the anterior segment was studied. Thirty-four male, 5-week-old Wistar rats were used for all experiments. The rats were divided in four groups. In group I (12 rats, 12 eyes), the ODNs (20 microM) were delivered by iontophoresis (300 microA for 5 minutes) using a specially designed corneal applicator. In group II (12 rats, 12 eyes), the ODNs (20 microM) were delivered using the same applicator, but no electrical current was applied. In group III (6 rats, 6 eyes), a corneal neovascular reaction was induced prior to the application of ODNs (20 microM), and iontophoresis electrical current was delivered as for group I rats. Group IV (4 rats, 4 eyes) received ODN (60 microM) iontophoresis application (300 microA for 5 minutes) and were used for ODN integrity studies. The animals were killed 5 minutes, 90 minutes, and 24 hours after a single ODN application and studied. Topically applied ODNs using the same iontophoresis applicator but without current do not penetrate the cornea and remain confined to the superficial epithelial layer. ODNs delivered with transcorneoscleral iontophoresis penetrate into all corneal layers and are also detected in the iris. In corneas with neovascularization, ODNs were particularly localized within the vascular endothelial cells of the stroma. ODNs extracted from eye tissues 24 hours after iontophoresis remained unaltered. The iontophoresis current did not cause any detectable ocular damage under these conditions. Iontophoresis promotes the delivery of ODNs to the anterior segment of the eye, including all corneal layers. Iontophoresis of ODNs directed at VEGF-R2 may be used for the design of specific antiangiogenic strategy in diseases of the cornea.</p>","PeriodicalId":7996,"journal":{"name":"Antisense & nucleic acid drug development","volume":"13 2","pages":"107-14"},"PeriodicalIF":0.0,"publicationDate":"2003-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/108729003321629647","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22434833","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}

{"title":"HIV Tat peptide enhances cellular delivery of antisense morpholino oligomers.","authors":"Hong M Moulton,&nbsp;Michelle C Hase,&nbsp;Kristen M Smith,&nbsp;Patrick L Iversen","doi":"10.1089/108729003764097322","DOIUrl":"https://doi.org/10.1089/108729003764097322","url":null,"abstract":"<p><p>Phosphorodiamidate morpholino oligomers (PMO) are uncharged antisense molecules that bind complementary sequences of RNA, inhibiting gene expression by preventing translation or by interfering with pre-mRNA splicing. The techniques used to deliver PMO into cultured cells have been mostly mechanical methods. These delivery methods, although useful, have limitations. We investigated the ability of the HIV Tat peptide (pTat) and other cationic peptides to deliver PMO into cultured cells. Fluorescence was seen in 100% of HeLa cells treated with pTat-PMO-fluorescein conjugate. pTat-PMO conjugate targeted to c-myc mRNA downregulated c-myc reporter gene expression with an IC50 of 25 microM and achieved nearly 100% inhibition. pTat-PMO conjugate targeted to a mutant splice site of beta-globin pre-mRNA dose-dependently corrected splicing and upregulated expression of the functional reporter gene. Neither unconjugated PMO nor unconjugated pTat caused antisense activities. However, compared with mechanically mediated delivery, pTat-mediated PMO delivery required higher concentrations of PMO (>10 microM) to cause antisense activity and caused some toxicity. Most pTat-PMO conjugate was associated with cell membranes, and internalized conjugate was localized in vesicles, cytosol, and nucleus. The other three cationic peptides are much less effective than pTat. pTat significantly enhances delivery of PMO in 100% of cells assayed. pTat-mediated delivery is a much simpler procedure to perform than other delivery methods.</p>","PeriodicalId":7996,"journal":{"name":"Antisense & nucleic acid drug development","volume":"13 1","pages":"31-43"},"PeriodicalIF":0.0,"publicationDate":"2003-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/108729003764097322","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22337887","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}

{"title":"A high-efficacy antisense RIalpha poly-DNP 21-nt RNA.","authors":"Long Shen,&nbsp;Xiaolan Chen,&nbsp;Jui H Wang","doi":"10.1089/108729003764097359","DOIUrl":"https://doi.org/10.1089/108729003764097359","url":null,"abstract":"<p><p>The antisense inhibitor poly-2'-O-(2,4-dinitrophenyl)-5'-GGCUGCGUGCCUCCUCACUGG (antisense poly-DNP RNA-21) has been synthesized by in vitro transcription followed by chemical derivatization. Its base sequence is complementary to that of nucleotides 110-130 in the mRNA of the regulatory RIalpha subunit of PKA (RIalpha/PKA), which is overexpressed in MCF-7 breast cancer cells and A549 lung cancer cells. The bioavailable and RNase-resistant antisense poly-DNP RNA-21 was found to inhibit cell growth with 50% inhibitory concentration (IC50) values of 0.05 nM in MCF-7 cells and 4 nM in A549 cells. The control 21-nt RNAs with the same poly-DNP oligonucleotide (ODN) platform but with scrambled, sense, or mismatched base sequence are inactive. Treatment of MCF-7 cells with antisense poly-DNP RNA-21 abolishes both the steady-state concentration of RIalpha mRNA and the synthesis of RIalpha protein. At sufficiently high concentration, antisense poly-DNP RNA-21 selectively kills the targeted cancer cells by inducing apoptosis. The observed sequence specificity and extremely low IC50 values of antisense poly-DNP RNA-21 suggest that it is a promising candidate for in vivo testing as an effective anticancer agent.</p>","PeriodicalId":7996,"journal":{"name":"Antisense & nucleic acid drug development","volume":"13 1","pages":"67-74"},"PeriodicalIF":0.0,"publicationDate":"2003-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/108729003764097359","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22337890","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}

{"title":"Comparison of the suppressive effects of antisense oligonucleotides and siRNAs directed against the same targets in mammalian cells.","authors":"Makoto Miyagishi,&nbsp;Mariko Hayashi,&nbsp;Kazunari Taira","doi":"10.1089/108729003764097296","DOIUrl":"https://doi.org/10.1089/108729003764097296","url":null,"abstract":"<p><p>RNA interference appears to be a potentially powerful tool for studies of genes of unknown function. However, differences in efficacy at different target sites remain problematic when small interfering RNA (siRNA) is used as an effector. Similar problems are associated with attempts at gene inactivation using antisense oligonucleotides (ODNs) and ribozymes. We performed a comparative analysis of the suppressive effects of three knockdown methods, namely, methods based on RNA interference (RNAi), antisense ODNs, and ribozymes, using a luciferase reporter system. Dose-response experiments revealed that the IC50 value for the siRNA was about 100-fold lower than that of the antisense ODN. Our results provide useful information about the positional effects in RNAi, which might help to improve the design of effective siRNAs.</p>","PeriodicalId":7996,"journal":{"name":"Antisense & nucleic acid drug development","volume":"13 1","pages":"1-7"},"PeriodicalIF":0.0,"publicationDate":"2003-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/108729003764097296","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22337980","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}

{"title":"Prediction of clinical responses in a simulated phase III trial of Crohn's patients administered the antisense phosphorothioate oligonucleotide ISIS 2302: comparison of proposed dosing regimens.","authors":"Rosie Z Yu,&nbsp;John Q Su,&nbsp;John S Grundy,&nbsp;Richard S Geary,&nbsp;K Lea Sewell,&nbsp;Andrew Dorr,&nbsp;Arthur A Levin","doi":"10.1089/108729003764097340","DOIUrl":"https://doi.org/10.1089/108729003764097340","url":null,"abstract":"<p><p>ISIS 2302, an antisense phosphorothioate oligonucleotide (ODN) targeting human intercellular adhesion molecule-1 (ICAM-1) mRNA, is currently being evaluated for treatment of patients with Crohn's disease. From data collected in phase II clinical studies with ISIS 2302, validated population pharmacokinetic and exposure-response models were developed and used to simulate the plasma exposure and clinical response results for a proposed phase III trial design involving 100 patients treated with active drug and 50 patients treated with placebo. Simulated results of 1000 replications of the trial were calculated for various proposed dosing regimens. Overall, the simulated results indicated that a fixed dose regimen (250-400 mg, depending on patient sex and total body weight) given three times weekly provides both desirable ISIS 2302 plasma exposure and a high rate of clinical response in this patient population. However, the simulated results also suggest that inclusion of a larger number of patients than projected may be necessary to provide a desirable probability of study success (i.e., >80%), regarding demonstration of statistically significant differences between the active treatment and placebo groups for the primary clinical response measure (CCR rate).</p>","PeriodicalId":7996,"journal":{"name":"Antisense & nucleic acid drug development","volume":"13 1","pages":"57-66"},"PeriodicalIF":0.0,"publicationDate":"2003-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/108729003764097340","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22337889","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}

{"title":"Interactions of hairpin oligo-2'-O-methylribonucleotides containing methylphosphonate linkages with HIV TAR RNA.","authors":"Tomoko Hamma,&nbsp;Paul S Miller","doi":"10.1089/108729003764097313","DOIUrl":"https://doi.org/10.1089/108729003764097313","url":null,"abstract":"<p><p>Methylphosphonate-modified oligo-2'-O-methylribonucleotides 15-20 nucleotides (nt) in length were prepared whose sequences are complementary to the 5' and 3' sides of the upper hairpin of HIV trans-acting response element (TAR) RNA. These anti-TAR oligonucleotides (ODNs) form stable hairpins whose melting temperatures (Tm) range from 55 degrees C to 80 degrees C. Despite their rather high thermal stabilities, the hairpin oligo-2'-O-methylribonucleotides formed very stable complexes with TAR RNA, with dissociation constants in the nanomolar concentration range at 37 degrees C. The affinities of the hairpin oligomers for TAR RNA were influenced by the positions of the methylphosphonate linkages. The binding affinity was reduced approximately 17-fold by the presence of two methylphosphonate linkages in the TAR loop complementary region (TLCR) of the oligomer, whereas methylphosphonate linkages outside this region increased binding affinity approximately 3-fold. The configurations of the methylphosphonate linkages in the TLCR also affected binding affinity, with the RpRp isomer showing significantly higher binding than the SpSp isomer. In addition to serving as probes of the interactions between the oligomer and TAR RNA, the presence of the methylphosphonate linkages in combination with the hairpin structure increases the resistance of these oligomers to degradation by exonucleases found in mammalian serum. The combination of high binding affinity and nuclease resistance of the hairpin ODNs containing methylphosphonate linkages suggests their potential utility as antisense compounds.</p>","PeriodicalId":7996,"journal":{"name":"Antisense & nucleic acid drug development","volume":"13 1","pages":"19-30"},"PeriodicalIF":0.0,"publicationDate":"2003-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/108729003764097313","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22337982","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}

{"title":"Elucidation and characterization of oligonucleotide-accessible sites on HIV-2 leader region RNA.","authors":"Emily L Deer,&nbsp;Boramee Douk,&nbsp;Jean-Marc Lanchy,&nbsp;J Stephen Lodmell","doi":"10.1089/108729003764097331","DOIUrl":"https://doi.org/10.1089/108729003764097331","url":null,"abstract":"<p><p>The retroviruses, including the human pathogens HIV-1 and HIV-2, are diploid inasmuch as they encapsidate two copies of their RNA genome. Prior to or during encapsidation, two copies of full-length genomic RNA recognize and stably bind each other in a process called dimerization. RNA structures within the viral genome promote dimerization in both HIV-1 and HIV-2 and are located in the 5'-untranslated leader region. Inhibition of dimerization by mutation of these RNA signals has been demonstrated to drastically reduce viral infectivity and replication kinetics and, thus, represents a potential target for antiretroviral therapy. In this study, we identified sites in HIV-2 leader region RNA that are functionally accessible to hybridization with oligonucleotides (ODNs) by reverse transcription with random ODN libraries (RT-ROL). We then tested specific ODNs directed against these regions for their efficacy in inhibiting RNA dimerization in vitro. We determined that of several hybridization-competent ODNs, only two were very effective in inhibiting RNA dimerization. Both of these ODNs were complementary to viral RNA at the primer binding site (PBS). These results identify regions with high accessibility to ODN binding on HIV-2 RNA and help to map the region(s) essential for dimerization within the viral RNA.</p>","PeriodicalId":7996,"journal":{"name":"Antisense & nucleic acid drug development","volume":"13 1","pages":"45-55"},"PeriodicalIF":0.0,"publicationDate":"2003-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/108729003764097331","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22337888","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}