Journal of Nucleic Acids最新文献_第7页

Transcriptionally Repressive Chromatin Remodelling and CpG Methylation in the Presence of Expanded CTG-Repeats at the DM1 Locus. DM1位点扩展ctg重复序列存在时转录抑制染色质重塑和CpG甲基化。

IF 2.3

Journal of Nucleic Acids Pub Date : 2013-01-01 Epub Date: 2013-12-23 DOI: 10.1155/2013/567435

Judith Rixt Brouwer, Aline Huguet, Annie Nicole, Arnold Munnich, Geneviève Gourdon

{"title":"Transcriptionally Repressive Chromatin Remodelling and CpG Methylation in the Presence of Expanded CTG-Repeats at the DM1 Locus.","authors":"Judith Rixt Brouwer, Aline Huguet, Annie Nicole, Arnold Munnich, Geneviève Gourdon","doi":"10.1155/2013/567435","DOIUrl":"https://doi.org/10.1155/2013/567435","url":null,"abstract":"An expanded CTG-repeat in the 3' UTR of the DMPK gene is responsible for myotonic dystrophy type I (DM1). Somatic and intergenerational instability cause the disease to become more severe during life and in subsequent generations. Evidence is accumulating that trinucleotide repeat instability and disease progression involve aberrant chromatin dynamics. We explored the chromatin environment in relation to expanded CTG-repeat tracts in hearts from transgenic mice carrying the DM1 locus with different repeat lengths. Using bisulfite sequencing we detected abundant CpG methylation in the regions flanking the expanded CTG-repeat. CpG methylation was postulated to affect CTCF binding but we found that CTCF binding is not affected by CTG-repeat length in our transgenic mice. We detected significantly decreased DMPK sense and SIX5 transcript expression levels in mice with expanded CTG-repeats. Expression of the DM1 antisense transcript was barely affected by CTG-repeat expansion. In line with altered gene expression, ChIP studies revealed a locally less active chromatin conformation around the expanded CTG-repeat, namely, decreased enrichment of active histone mark H3K9/14Ac and increased H3K9Me3 enrichment (repressive chromatin mark). We also observed binding of PCNA around the repeats, a candidate that could launch chromatin remodelling cascades at expanded repeats, ultimately affecting gene transcription and repeat instability. ","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/567435","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32054319","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: 45

Chemical approaches for structure and function of RNA in postgenomic era. 后基因组时代RNA结构与功能的化学研究。

IF 2.3

Journal of Nucleic Acids Pub Date : 2012-01-01 Epub Date: 2012-01-12 DOI: 10.1155/2012/369058

Tae Suk Ro-Choi, Yong Chun Choi

引用次数: 3

Directed Evolution of Proteins through In Vitro Protein Synthesis in Liposomes. 通过脂质体体外合成蛋白质的定向进化。

IF 2.3

Journal of Nucleic Acids Pub Date : 2012-01-01 Epub Date: 2012-08-16 DOI: 10.1155/2012/923214

Takehiro Nishikawa, Takeshi Sunami, Tomoaki Matsuura, Tetsuya Yomo

{"title":"Directed Evolution of Proteins through In Vitro Protein Synthesis in Liposomes.","authors":"Takehiro Nishikawa, Takeshi Sunami, Tomoaki Matsuura, Tetsuya Yomo","doi":"10.1155/2012/923214","DOIUrl":"https://doi.org/10.1155/2012/923214","url":null,"abstract":"Directed evolution of proteins is a technique used to modify protein functions through \"Darwinian selection.\" In vitro compartmentalization (IVC) is an in vitro gene screening system for directed evolution of proteins. IVC establishes the link between genetic information (genotype) and the protein translated from the information (phenotype), which is essential for all directed evolution methods, by encapsulating both in a nonliving microcompartment. Herein, we introduce a new liposome-based IVC system consisting of a liposome, the protein synthesis using recombinant elements (PURE) system and a fluorescence-activated cell sorter (FACS) used as a microcompartment, in vitro protein synthesis system, and high-throughput screen, respectively. Liposome-based IVC is characterized by in vitro protein synthesis from a single copy of a gene in a cell-sized unilamellar liposome and quantitative functional evaluation of the synthesized proteins. Examples of liposome-based IVC for screening proteins such as GFP and β-glucuronidase are described. We discuss the future directions for this method and its applications.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/923214","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30887857","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: 20

Potential of peptides as inhibitors and mimotopes: selection of carbohydrate-mimetic peptides from phage display libraries. 多肽作为抑制剂和移酶体的潜力:从噬菌体展示文库中选择模拟碳水化合物的多肽。

IF 2.3

Journal of Nucleic Acids Pub Date : 2012-01-01 Epub Date: 2012-10-10 DOI: 10.1155/2012/740982

Teruhiko Matsubara

{"title":"Potential of peptides as inhibitors and mimotopes: selection of carbohydrate-mimetic peptides from phage display libraries.","authors":"Teruhiko Matsubara","doi":"10.1155/2012/740982","DOIUrl":"https://doi.org/10.1155/2012/740982","url":null,"abstract":"Glycoconjugates play various roles in biological processes. In particular, oligosaccharides on the surface of animal cells are involved in virus infection and cell-cell communication. Inhibitors of carbohydrate-protein interactions are potential antiviral drugs. Several anti-influenza drugs such as oseltamivir and zanamivir are derivatives of sialic acid, which inhibits neuraminidase. However, it is very difficult to prepare a diverse range of sugar derivatives by chemical synthesis or by the isolation of natural products. In addition, the pathogenic capsular polysaccharides of bacteria are carbohydrate antigens, for which a safe and efficacious method of vaccination is required. Phage-display technology has been improved to enable the identification of peptides that bind to carbohydrate-binding proteins, such as lectins and antibodies, from a large repertoire of peptide sequences. These peptides are known as \"carbohydrate-mimetic peptides (CMPs)\" because they mimic carbohydrate structures. Compared to carbohydrate derivatives, it is easy to prepare mono- and multivalent peptides and then to modify them to create various derivatives. Such mimetic peptides are available as peptide inhibitors of carbohydrate-protein interactions and peptide mimotopes that are conjugated with adjuvant for vaccination.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/740982","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31000344","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: 24

Challenges and opportunities for small molecule aptamer development. 小分子适体开发的挑战与机遇。

IF 2.3

Journal of Nucleic Acids Pub Date : 2012-01-01 Epub Date: 2012-10-24 DOI: 10.1155/2012/748913

Maureen McKeague, Maria C Derosa

引用次数: 369

Small RNA expression profiling by high-throughput sequencing: implications of enzymatic manipulation. 高通量测序的小RNA表达谱分析:酶操作的含义。

IF 2.3

Journal of Nucleic Acids Pub Date : 2012-01-01 Epub Date: 2012-06-20 DOI: 10.1155/2012/360358

Fanglei Zhuang, Ryan T Fuchs, G Brett Robb

引用次数: 41

PCR amplification and transcription for site-specific labeling of large RNA molecules by a two-unnatural-base-pair system. PCR扩增和转录的位点特异性标记的大RNA分子的两个非自然碱基对系统。

IF 2.3

Journal of Nucleic Acids Pub Date : 2012-01-01 Epub Date: 2012-06-26 DOI: 10.1155/2012/230943

Michiko Kimoto, Rie Yamashige, Shigeyuki Yokoyama, Ichiro Hirao

{"title":"PCR amplification and transcription for site-specific labeling of large RNA molecules by a two-unnatural-base-pair system.","authors":"Michiko Kimoto, Rie Yamashige, Shigeyuki Yokoyama, Ichiro Hirao","doi":"10.1155/2012/230943","DOIUrl":"https://doi.org/10.1155/2012/230943","url":null,"abstract":"For the site-specific labeling and modification of RNA by genetic alphabet expansion, we developed a PCR and transcription system using two hydrophobic unnatural base pairs: 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) and 2-nitro-4-propynylpyrrole (Px) as a third pair for PCR amplification and Ds and pyrrole-2-carbaldehyde (Pa) for the incorporation of functional components as modified Pa bases into RNA by T7 transcription. To prepare Ds-containing DNA templates with long chains, the Ds-Px pair was utilized in a fusion PCR method, by which we demonstrated the synthesis of 282-bp DNA templates containing Ds at specific positions. Using these Ds-containing DNA templates and a biotin-linked Pa substrate (Biotin-PaTP) as a modified Pa base, 260-mer RNA transcripts containing Biotin-Pa at a specific position were generated by T7 RNA polymerase. This two-unnatural-base-pair system, combining the Ds-Px and Ds-Pa pairs with modified Pa substrates, provides a powerful tool for the site-specific labeling and modification of desired positions in large RNA molecules.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/230943","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30760822","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: 19

Metal Ion Chelates as Surrogates of Nucleobases for the Recognition of Nucleic Acid Sequences: The Pd(2+) Complex of 2,6-Bis(3,5-dimethylpyrazol-1-yl)purine Riboside. 替代核碱基识别核酸序列的金属离子螯合物:2,6-二(3,5-二甲基吡唑-1-基)嘌呤核苷的Pd(2+)配合物。

IF 2.3

Journal of Nucleic Acids Pub Date : 2012-01-01 Epub Date: 2012-05-13 DOI: 10.1155/2012/196845

Sharmin Taherpour, Tuomas Lönnberg

{"title":"Metal Ion Chelates as Surrogates of Nucleobases for the Recognition of Nucleic Acid Sequences: The Pd(2+) Complex of 2,6-Bis(3,5-dimethylpyrazol-1-yl)purine Riboside.","authors":"Sharmin Taherpour, Tuomas Lönnberg","doi":"10.1155/2012/196845","DOIUrl":"https://doi.org/10.1155/2012/196845","url":null,"abstract":"A 2,6-bis(3,5-dimethylpyrazol-1-yl)purine ribonucleoside has been prepared and incorporated as a conventionally protected phosphoramidite into a 9-mer 2'-O-methyl oligoribonucleotide. According to 1H NMR spectroscopic studies, this nucleoside forms with Pd(2+) and uridine a ternary complex that is stable at a micromolar concentration range. CD spectroscopic studies on oligonucleotide hybridization, in turn, suggest that the Pd(2+) chelate of this artificial nucleoside, when incorporated in a 2'-O-methyl-RNA oligomer, is able to recognize thymine within an otherwise complementary DNA strand. The duplex containing thymidine opposite to the artificial nucleoside turned out to be somewhat more resistant to heating than its counterpart containing 2'-deoxycytidine in place of thymidine, but only in the presence of Pd(2+). According to UV-melting measurements, replacement of 2'-O-methyladenosine with the artificial nucleoside markedly enhances hybridization with a DNA target, irrespective of the identity of the opposite base and the presence of Pd(2+). With the thymidine containing DNA target, the T(m) value is 2-4°C higher than with targets containing any other nucleoside opposite to the artificial nucleoside, but the dependence on Pd(2+) is much less clear than in the case of the CD studies.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/196845","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30659900","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: 10

Imaging mRNA Expression in Live Cells via PNA·DNA Strand Displacement-Activated Probes. 通过 PNA-DNA 链置换激活探针成像活细胞中的 mRNA 表达。

IF 2.3

Journal of Nucleic Acids Pub Date : 2012-01-01 Epub Date: 2012-09-26 DOI: 10.1155/2012/962652

Zhenghui Wang, Ke Zhang, Karen L Wooley, John-Stephen Taylor

{"title":"Imaging mRNA Expression in Live Cells via PNA·DNA Strand Displacement-Activated Probes.","authors":"Zhenghui Wang, Ke Zhang, Karen L Wooley, John-Stephen Taylor","doi":"10.1155/2012/962652","DOIUrl":"10.1155/2012/962652","url":null,"abstract":"Probes for monitoring mRNA expression in vivo are of great interest for the study of biological and biomedical problems, but progress has been hampered by poor signal to noise and effective means for delivering the probes into live cells. Herein we report a PNA·DNA strand displacement-activated fluorescent probe that can image the expression of iNOS (inducible nitric oxide synthase) mRNA, a marker of inflammation. The probe consists of a fluorescein labeled antisense PNA annealed to a shorter DABCYL(plus)-labeled DNA which quenches the fluorescence, but when the quencher strand is displaced by the target mRNA the fluorescence is restored. DNA was used for the quencher strand to facilitate electrostatic binding of the otherwise netural PNA strand to a cationic shell crosslinked knedel-like (cSCK) nanoparticle which can deliver the PNA·DNA duplex probe into cells with less toxicity and greater efficiency than other transfection agents. RAW 264.7 mouse macrophage cells transfected with the iNOS PNA·DNA probe via the cSCK showed a 16 to 54-fold increase in average fluorescence per cell upon iNOS stimulation. The increase was 4 to 7-fold higher than that for a non-complementary probe, thereby validating the ability of a PNA·DNA strand displacement-activated probe to image mRNA expression in vivo.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463960/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30969650","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

Nucleic-Acid-binding chromophores as efficient indicators of aptamer-target interactions. 核酸结合发色团作为适体-靶标相互作用的有效指标。

IF 2.3

Journal of Nucleic Acids Pub Date : 2012-01-01 Epub Date: 2012-10-10 DOI: 10.1155/2012/247280

Kwabena Sarpong, Bhaskar Datta

{"title":"Nucleic-Acid-binding chromophores as efficient indicators of aptamer-target interactions.","authors":"Kwabena Sarpong, Bhaskar Datta","doi":"10.1155/2012/247280","DOIUrl":"https://doi.org/10.1155/2012/247280","url":null,"abstract":"The binding affinity and specificity of nucleic acid aptamers have made them valuable candidates for use as sensors in diagnostic applications. In particular, chromophore-functionalized aptamers offer a relatively simple format for detection and quantification of target molecules. We describe the use of nucleic-acid-staining reagents as an effective tool for detecting and signaling aptamer-target interactions. Aptamers varying in size and structure and targeting a range of molecules have been used in conjunction with commercially available chromophores to indicate and quantify the presence of cognate targets with high sensitivity and selectivity. Our assay precludes the covalent modification of nucleic acids and relies on the differential fluorescence signal of chromophores when complexed with aptamers with or without their cognate target. We also evaluate factors that are critical for the stability of the complex between the aptamer and chromophore in presence or absence of target molecules. Our results indicate the possibility of controlling those factors to enhance the sensitivity of target detection by the aptamers used in such assays.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/247280","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31000341","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: 15