Journal of Nucleic Acids最新文献_第10页

A two-piece derivative of a group I intron RNA as a platform for designing self-assembling RNA templates to promote Peptide ligation. 一组内含子RNA的两段衍生物，作为设计自组装RNA模板以促进肽连接的平台。

IF 2.3

Journal of Nucleic Acids Pub Date : 2012-01-01 Epub Date: 2012-08-22 DOI: 10.1155/2012/305867

Takahiro Tanaka, Hiroyuki Furuta, Yoshiya Ikawa

引用次数: 2

Recent advances in chemical modification of Peptide nucleic acids. 肽核酸化学修饰研究进展。

IF 2.3

Journal of Nucleic Acids Pub Date : 2012-01-01 Epub Date: 2012-09-06 DOI: 10.1155/2012/518162

Eriks Rozners

引用次数: 44

Alternative splicing in oncogenic kinases: from physiological functions to cancer. 致癌激酶的选择性剪接:从生理功能到癌症。

IF 2.3

Journal of Nucleic Acids Pub Date : 2012-01-01 Epub Date: 2011-10-05 DOI: 10.1155/2012/639062

Sabine Druillennec, Coralie Dorard, Alain Eychène

引用次数: 25

Splicing programs and cancer. 剪接程序和癌症。

IF 2.3

Journal of Nucleic Acids Pub Date : 2012-01-01 Epub Date: 2011-10-24 DOI: 10.1155/2012/269570

Sophie Germann, Lise Gratadou, Martin Dutertre, Didier Auboeuf

引用次数: 46

In vitro selection of fab fragments by mRNA display and gene-linking emulsion PCR. 用mRNA展示和基因连锁乳剂聚合酶链反应筛选fab片段。

IF 2.3

Journal of Nucleic Acids Pub Date : 2012-01-01 Epub Date: 2012-09-23 DOI: 10.1155/2012/371379

Takeshi Sumida, Hiroshi Yanagawa, Nobuhide Doi

{"title":"In vitro selection of fab fragments by mRNA display and gene-linking emulsion PCR.","authors":"Takeshi Sumida, Hiroshi Yanagawa, Nobuhide Doi","doi":"10.1155/2012/371379","DOIUrl":"https://doi.org/10.1155/2012/371379","url":null,"abstract":"In vitro selection by display methods has been an effective tool for engineering recombinant antibodies. mRNA display based on a cell-free translation system has the advantages of larger library sizes and quicker selection procedures compared with cell-based display methods such as phage display. However, mRNA display has been limited to select single-chain polypeptides such as scFvs due to its characteristic of linking a nascent polypeptide with its encoding mRNA on the ribosome. Here we demonstrated a new way of selecting heterodimeric Fab fragments by using mRNA display combined with emulsion PCR. We designed a pair of complementary 5' UTR sequences that can link the Fab heavy and light chain genes together by overlap-extension PCR in water-in-oil emulsions. We confirmed that two mRNA-displayed polypeptides for heavy and light chain of a model Fab fragment were associated into the active form and that a specific Fab fragment gene was enriched over 100-fold per round of a model affinity selection followed by the gene-linking emulsion PCR. We further performed directed evolution of Fab fragments with higher binding activity from a randomized Fab fragment library.","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/10.1155/2012/371379","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30965408","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

Specific Roles of MicroRNAs in Their Interactions with Environmental Factors. microrna在与环境因子相互作用中的特殊作用。

IF 2.3

Journal of Nucleic Acids Pub Date : 2012-01-01 Epub Date: 2012-10-31 DOI: 10.1155/2012/978384

Juan Wang, Qinghua Cui

引用次数: 34

Inhibition of HIV Replication by Cyclic and Hairpin PNAs Targeting the HIV-1 TAR RNA Loop. 靶向HIV-1 TAR RNA环的环状和发夹PNAs抑制HIV复制

IF 2.3

Journal of Nucleic Acids Pub Date : 2012-01-01 Epub Date: 2012-09-17 DOI: 10.1155/2012/591025

Gregory Upert, Audrey Di Giorgio, Alok Upadhyay, Dinesh Manvar, Nootan Pandey, Virendra N Pandey, Nadia Patino

{"title":"Inhibition of HIV Replication by Cyclic and Hairpin PNAs Targeting the HIV-1 TAR RNA Loop.","authors":"Gregory Upert, Audrey Di Giorgio, Alok Upadhyay, Dinesh Manvar, Nootan Pandey, Virendra N Pandey, Nadia Patino","doi":"10.1155/2012/591025","DOIUrl":"https://doi.org/10.1155/2012/591025","url":null,"abstract":"Human immunodeficiency virus-1 (HIV-1) replication and gene expression entails specific interaction of the viral protein Tat with its transactivation responsive element (TAR), to form a highly stable stem-bulge-loop structure. Previously, we described triphenylphosphonium (TPP) cation-based vectors that efficiently deliver nucleotide analogs (PNAs) into the cytoplasm of cells. In particular, we showed that the TPP conjugate of a linear 16-mer PNA targeting the apical stem-loop region of TAR impedes Tat-mediated transactivation of the HIV-1 LTR in vitro and also in cell culture systems. In this communication, we conjugated TPP to cyclic and hairpin PNAs targeting the loop region of HIV-1 TAR and evaluated their antiviral efficacy in a cell culture system. We found that TPP-cyclic PNAs containing only 8 residues, showed higher antiviral potency compared to hairpin PNAs of 12 or 16 residues. We further noted that the TPP-conjugates of the 8-mer cyclic PNA as well as the 16-mer linear PNA displayed similar antiviral efficacy. However, cyclic PNAs were shown to be highly specific to their target sequences. This communication emphasizes on the importance of small constrained cyclic PNAs over both linear and hairpin structures for targeting biologically relevant RNA hairpins.","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/10.1155/2012/591025","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30949327","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

Genetically encoded libraries of nonstandard peptides. 非标准肽基因编码文库。

IF 2.3

Journal of Nucleic Acids Pub Date : 2012-01-01 Epub Date: 2012-10-14 DOI: 10.1155/2012/713510

Takashi Kawakami, Hiroshi Murakami

{"title":"Genetically encoded libraries of nonstandard peptides.","authors":"Takashi Kawakami, Hiroshi Murakami","doi":"10.1155/2012/713510","DOIUrl":"https://doi.org/10.1155/2012/713510","url":null,"abstract":"The presence of a nonproteinogenic moiety in a nonstandard peptide often improves the biological properties of the peptide. Non-standard peptide libraries are therefore used to obtain valuable molecules for biological, therapeutic, and diagnostic applications. Highly diverse non-standard peptide libraries can be generated by chemically or enzymatically modifying standard peptide libraries synthesized by the ribosomal machinery, using posttranslational modifications. Alternatively, strategies for encoding non-proteinogenic amino acids into the genetic code have been developed for the direct ribosomal synthesis of non-standard peptide libraries. In the strategies for genetic code expansion, non-proteinogenic amino acids are assigned to the nonsense codons or 4-base codons in order to add these amino acids to the universal genetic code. In contrast, in the strategies for genetic code reprogramming, some proteinogenic amino acids are erased from the genetic code and non-proteinogenic amino acids are reassigned to the blank codons. Here, we discuss the generation of genetically encoded non-standard peptide libraries using these strategies and also review recent applications of these libraries to the selection of functional non-standard peptides.","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/10.1155/2012/713510","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31002149","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: 26

Expression Profiling of a Heterogeneous Population of ncRNAs Employing a Mixed DNA/LNA Microarray. 使用混合DNA/ rna微阵列的异质ncrna群体表达谱分析。

IF 2.3

Journal of Nucleic Acids Pub Date : 2012-01-01 Epub Date: 2012-06-10 DOI: 10.1155/2012/283560

Konstantinia Skreka, Marek Zywicki, Michael Karbiener, Alexander Hüttenhofer, Marcel Scheideler, Mathieu Rederstorff

{"title":"Expression Profiling of a Heterogeneous Population of ncRNAs Employing a Mixed DNA/LNA Microarray.","authors":"Konstantinia Skreka, Marek Zywicki, Michael Karbiener, Alexander Hüttenhofer, Marcel Scheideler, Mathieu Rederstorff","doi":"10.1155/2012/283560","DOIUrl":"https://doi.org/10.1155/2012/283560","url":null,"abstract":"Mammalian transcriptomes mainly consist of non protein coding RNAs. These ncRNAs play various roles in all cells and are involved in multiple regulation pathways. More recently, ncRNAs have also been described as valuable diagnostic tools. While RNA-seq approaches progressively replace microarray-based technologies for high-throughput expression profiling, they are still not routinely used in diagnostic. Microarrays, on the other hand, are more widely used for diagnostic profiling, especially for very small ncRNA (e.g., miRNAs), employing locked nucleic acid (LNA) arrays. However, LNA microarrays are quite expensive for high-throughput studies targeting longer ncRNAs, while DNA arrays do not provide satisfying results for the analysis of small RNAs. Here, we describe a mixed DNA/LNA microarray platform, where directly labeled small and longer ncRNAs are hybridized on LNA probes or custom DNA probes, respectively, enabling sensitive and specific analysis of a complex RNA population on a unique array in one single experiment. The DNA/LNA system, requiring relatively low amounts of total RNA, which complies with diagnostic references, was successfully applied to the analysis of differential ncRNA expression in mouse embryonic stem cells and adult brain cells.","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/10.1155/2012/283560","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30750043","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: 3

Combinatorial Synthesis, Screening, and Binding Studies of Highly Functionalized Polyamino-amido Oligomers for Binding to Folded RNA. 结合折叠RNA的高功能化多氨基寡聚物的组合合成、筛选和结合研究。

IF 2.3

Journal of Nucleic Acids Pub Date : 2012-01-01 Epub Date: 2012-08-21 DOI: 10.1155/2012/971581

Jonathan K Pokorski, Daniel H Appella

{"title":"Combinatorial Synthesis, Screening, and Binding Studies of Highly Functionalized Polyamino-amido Oligomers for Binding to Folded RNA.","authors":"Jonathan K Pokorski, Daniel H Appella","doi":"10.1155/2012/971581","DOIUrl":"https://doi.org/10.1155/2012/971581","url":null,"abstract":"Folded RNA molecules have recently emerged as critical regulatory elements in biological pathways, serving not just as carriers of genetic information but also as key components in enzymatic assemblies. In particular, the transactivation response element (TAR) of the HIV genome regulates transcriptional elongation by interacting specifically with the Tat protein, initiating the recruitment of the elongation complex. Preventing this interaction from occurring in vivo halts HIV replication, thus making RNA-binding molecules an intriguing pharmaceutical target. Using α-amino acids as starting materials, we have designed and synthesized a new class of polyamino-amido oligomers, called PAAs, specifically for binding to folded RNA structures. The PAA monomers were readily incorporated into a 125-member combinatorial library of PAA trimers. In order to rapidly assess RNA binding, a quantum dot-based fluorescent screen was developed to visualize RNA binding on-resin. The binding affinities of hits were quantified using a terbium footprinting assay, allowing us to identify a ligand (SFF) with low micromolar affinity (k(d) = 14 μM) for TAR RNA. The work presented herein represents the development of a flexible scaffold that can be easily synthesized, screened, and subsequently modified to provide ligands specific for binding to folded RNAs.","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/10.1155/2012/971581","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30887858","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: 1