Journal of Nucleic Acids最新文献

{"title":"R-Loop Formation In Trans at an AGGAG Repeat.","authors":"Kazuya Toriumi,&nbsp;Takuma Tsukahara,&nbsp;Ryo Hanai","doi":"10.1155/2013/629218","DOIUrl":"https://doi.org/10.1155/2013/629218","url":null,"abstract":"<p><p>Formation of RNA-DNA hybrid, or R-loop, was studied in vitro by transcribing an AGGAG repeat with T7 RNA polymerase. When ribonuclease T1 was present, R-loop formation in cis was diminished, indicating that the transcript was separated from the template and reassociated with it. The transcript was found to form an R-loop in trans with DNA comprising the AGGAG repeat, when the DNA was supercoiled. Results of chemical modification indicated that the duplex opened at the AGGAG repeat under negative supercoiling. </p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2013 ","pages":"629218"},"PeriodicalIF":2.3,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/629218","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31759023","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}

{"title":"Using aptamers for cancer biomarker discovery.","authors":"Yun Min Chang, Michael J Donovan, Weihong Tan","doi":"10.1155/2013/817350","DOIUrl":"10.1155/2013/817350","url":null,"abstract":"<p><p>Aptamers are single-stranded synthetic DNA- or RNA-based oligonucleotides that fold into various shapes to bind to a specific target, which includes proteins, metals, and molecules. Aptamers have high affinity and high specificity that are comparable to that of antibodies. They are obtained using iterative method, called (Systematic Evolution of Ligands by Exponential Enrichment) SELEX and cell-based SELEX (cell-SELEX). Aptamers can be paired with recent advances in nanotechnology, microarray, microfluidics, and other technologies for applications in clinical medicine. One particular area that aptamers can shed a light on is biomarker discovery. Biomarkers are important in diagnosis and treatment of cancer. In this paper, we will describe ways in which aptamers can be used to discover biomarkers for cancer diagnosis and therapeutics.</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2013 ","pages":"817350"},"PeriodicalIF":2.3,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562578/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31232500","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}

{"title":"Artificially created nucleic acids and peptides/proteins in chemical biology.","authors":"Masayasu Kuwahara,&nbsp;Yingfu Li,&nbsp;Eriks Rozners,&nbsp;Hiroshi Murakami","doi":"10.1155/2013/219263","DOIUrl":"https://doi.org/10.1155/2013/219263","url":null,"abstract":"Nucleic acids—DNA and RNA—have been chosen by Mother Nature as the key players for orchestrating the preservation, transfer, and expression of genetic information in all the biological systems on Earth. RNA has also been enlisted to carry out other important cellular functions, such as catalysis and molecular recognition. Within the hands of scientists, the function of nucleic acids has been significantly expanded beyond what is known in nature, and as a result, we are now in the possession of a large array of synthetic, nucleic acid-based catalysts (ribozymes and DNAzymes) and receptors (DNA and RNA aptamers). DNA as a genetic material itself has also been subjected to various chemical modifications in efforts to derive significantly altered or even completely new genetic systems. These systems can be used to create novel peptides and proteins that offer enhanced activities or even completely new properties over their natural protein counterparts. Furthermore, many artificially engineered nucleic acids and proteins have found useful applications as biosensors, diagnostic agents, and therapeutic drugs. This special issue is assembled to reflect recent progress in the important research arena of artificially engineered nucleic acids and proteins. \u0000 \u0000This issue comprises 10 reviews and 7 research articles that can be grouped into three sections. The first section deals mainly with research on xeno-nucleic acids (XNAs)—nonnatural nucleic acid analogs with significantly altered sugar and/or phosphate backbones. D.-A. Catana et al. provide a review on the use of dinucleotides of dioxaphosphorinane-constrained nucleic acids (CNAs) to tune nucleic acid structures. This is followed by a review by E. Rozners on recent advances in chemical modifications of peptide nucleic acids (PNAs). G. Upert et al. then present a research article on designing cyclic and hairpin PNAs as inhibitors for HIV replication. Z. Wang et al. also present a research article where PNA probes were utilized for live cell imaging of mRNA expression. In their research article, T. Yamamoto et al. examine the gene-silencing effect of bridged/locked nucleic acids (BNA/LNAs). This section is closed out with a research article by S. Saxena et al. in which the molecular crowding effect on the structure and function of RecG (a helicase) was examined. \u0000 \u0000The second section includes four reviews and three research articles discussing the creation of novel peptides, proteins, transfer RNAs, and peptide mimicries using various selection or screening methods. K. Fukunaga and M. Taki provide a review on the phage display technique with a particular focus on tips for conducting successful phage display experiments. Within the same topic, T. Matsubara reviews the use of phage display for the creation of carbohydrate-mimetic peptides. These are followed by a research article by T. Sumida et al. exploiting the mRNA display technique for the selection of anti-p53 Fab fragments. There are two papers conc","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2013 ","pages":"219263"},"PeriodicalIF":2.3,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/219263","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31232499","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}

{"title":"Simultaneous Use of MutS and RecA for Suppression of Nonspecific Amplification during PCR.","authors":"Kenji Fukui,&nbsp;Seiki Kuramitsu","doi":"10.1155/2013/823730","DOIUrl":"https://doi.org/10.1155/2013/823730","url":null,"abstract":"<p><p>Thermus thermophilus MutS, a thermostable mismatch-recognizing protein, is utilized in PCR to suppress nonspecific amplification by preventing synthesis from mismatched primers. T. thermophilus RecA also decreases nonspecific amplification by promoting proper hybridization between the primer and template. We observed that MutS and RecA function under the same reaction conditions and that MutS and RecA do not preclude each other. Furthermore, there were some DNA sequences for which only one of the 2 proteins effectively suppressed nonspecific amplification. The simultaneous use of MutS and RecA is a more attractive error-suppressing technique than the use of either of the 2 proteins alone. </p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2013 ","pages":"823730"},"PeriodicalIF":2.3,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/823730","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31678799","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}

{"title":"Transcriptionally Repressive Chromatin Remodelling and CpG Methylation in the Presence of Expanded CTG-Repeats at the DM1 Locus.","authors":"Judith Rixt Brouwer,&nbsp;Aline Huguet,&nbsp;Annie Nicole,&nbsp;Arnold Munnich,&nbsp;Geneviève Gourdon","doi":"10.1155/2013/567435","DOIUrl":"https://doi.org/10.1155/2013/567435","url":null,"abstract":"<p><p>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. </p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2013 ","pages":"567435"},"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}

{"title":"Chemical approaches for structure and function of RNA in postgenomic era.","authors":"Tae Suk Ro-Choi,&nbsp;Yong Chun Choi","doi":"10.1155/2012/369058","DOIUrl":"https://doi.org/10.1155/2012/369058","url":null,"abstract":"<p><p>In the study of cellular RNA chemistry, a major thrust of research focused upon sequence determinations for decades. Structures of snRNAs (4.5S RNA I (Alu), U1, U2, U3, U4, U5, and U6) were determined at Baylor College of Medicine, Houston, Tex, in an earlier time of pregenomic era. They show novel modifications including base methylation, sugar methylation, 5'-cap structures (types 0-III) and sequence heterogeneity. This work offered an exciting problem of posttranscriptional modification and underwent numerous significant advances through technological revolutions during pregenomic, genomic, and postgenomic eras. Presently, snRNA research is making progresses involved in enzymology of snRNA modifications, molecular evolution, mechanism of spliceosome assembly, chemical mechanism of intron removal, high-order structure of snRNA in spliceosome, and pathology of splicing. These works are destined to reach final pathway of work \"Function and Structure of Spliceosome\" in addition to exciting new exploitation of other noncoding RNAs in all aspects of regulatory functions.</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2012 ","pages":"369058"},"PeriodicalIF":2.3,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/369058","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30471046","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}

{"title":"Challenges and opportunities for small molecule aptamer development.","authors":"Maureen McKeague,&nbsp;Maria C Derosa","doi":"10.1155/2012/748913","DOIUrl":"https://doi.org/10.1155/2012/748913","url":null,"abstract":"<p><p>Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2012 ","pages":"748913"},"PeriodicalIF":2.3,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/748913","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31047774","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}

{"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,&nbsp;Tuomas Lönnberg","doi":"10.1155/2012/196845","DOIUrl":"https://doi.org/10.1155/2012/196845","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2012 ","pages":"196845"},"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}

{"title":"Directed Evolution of Proteins through In Vitro Protein Synthesis in Liposomes.","authors":"Takehiro Nishikawa,&nbsp;Takeshi Sunami,&nbsp;Tomoaki Matsuura,&nbsp;Tetsuya Yomo","doi":"10.1155/2012/923214","DOIUrl":"https://doi.org/10.1155/2012/923214","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2012 ","pages":"923214"},"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}

{"title":"Small RNA expression profiling by high-throughput sequencing: implications of enzymatic manipulation.","authors":"Fanglei Zhuang,&nbsp;Ryan T Fuchs,&nbsp;G Brett Robb","doi":"10.1155/2012/360358","DOIUrl":"https://doi.org/10.1155/2012/360358","url":null,"abstract":"<p><p>Eukaryotic regulatory small RNAs (sRNAs) play significant roles in many fundamental cellular processes. As such, they have emerged as useful biomarkers for diseases and cell differentiation states. sRNA-based biomarkers outperform traditional messenger RNA-based biomarkers by testing fewer targets with greater accuracy and providing earlier detection for disease states. Therefore, expression profiling of sRNAs is fundamentally important to further advance the understanding of biological processes, as well as diagnosis and treatment of diseases. High-throughput sequencing (HTS) is a powerful approach for both sRNA discovery and expression profiling. Here, we discuss the general considerations for sRNA-based HTS profiling methods from RNA preparation to sequencing library construction, with a focus on the causes of systematic error. By examining the enzymatic manipulation steps of sRNA expression profiling, this paper aims to demystify current HTS-based sRNA profiling approaches and to aid researchers in the informed design and interpretation of profiling experiments.</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2012 ","pages":"360358"},"PeriodicalIF":2.3,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/360358","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30750045","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}