Journal of Nucleic Acids最新文献

{"title":"Structural and Functional Characterization of RecG Helicase under Dilute and Molecular Crowding Conditions.","authors":"Sarika Saxena,&nbsp;Satoru Nagatoishi,&nbsp;Daisuke Miyoshi,&nbsp;Naoki Sugimoto","doi":"10.1155/2012/392039","DOIUrl":"https://doi.org/10.1155/2012/392039","url":null,"abstract":"<p><p>In an ATP-dependent reaction, the Escherichia coli RecG helicase unwinds DNA junctions in vitro. We present evidence of a unique protein conformational change in the RecG helicase from an α-helix to a β-strand upon an ATP binding under dilute conditions using circular dichroism (CD) spectroscopy. In contrast, under molecular crowding conditions, the α-helical conformation was stable even upon an ATP binding. These distinct conformational behaviors were observed to be independent of Na(+) and Mg(2+). Interestingly, CD measurements demonstrated that the spectra of a frayed duplex decreased with increasing of the RecG concentration both under dilute and molecular crowding conditions in the presence of ATP, suggesting that RecG unwound the frayed duplex. Our findings raise the possibility that the α-helix and β-strand forms of RecG are a preactive and an active structure with the helicase activity, respectively.</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2012 ","pages":"392039"},"PeriodicalIF":2.3,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/392039","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30856616","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":"UvrD Participation in Nucleotide Excision Repair Is Required for the Recovery of DNA Synthesis following UV-Induced Damage in Escherichia coli.","authors":"Kelley N Newton,&nbsp;Charmain T Courcelle,&nbsp;Justin Courcelle","doi":"10.1155/2012/271453","DOIUrl":"https://doi.org/10.1155/2012/271453","url":null,"abstract":"<p><p>UvrD is a DNA helicase that participates in nucleotide excision repair and several replication-associated processes, including methyl-directed mismatch repair and recombination. UvrD is capable of displacing oligonucleotides from synthetic forked DNA structures in vitro and is essential for viability in the absence of Rep, a helicase associated with processing replication forks. These observations have led others to propose that UvrD may promote fork regression and facilitate resetting of the replication fork following arrest. However, the molecular activity of UvrD at replication forks in vivo has not been directly examined. In this study, we characterized the role UvrD has in processing and restoring replication forks following arrest by UV-induced DNA damage. We show that UvrD is required for DNA synthesis to recover. However, in the absence of UvrD, the displacement and partial degradation of the nascent DNA at the arrested fork occur normally. In addition, damage-induced replication intermediates persist and accumulate in uvrD mutants in a manner that is similar to that observed in other nucleotide excision repair mutants. These data indicate that, following arrest by DNA damage, UvrD is not required to catalyze fork regression in vivo and suggest that the failure of uvrD mutants to restore DNA synthesis following UV-induced arrest relates to its role in nucleotide excision repair.</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2012 ","pages":"271453"},"PeriodicalIF":2.3,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/271453","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30969648","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":"Artificial specific binders directly recovered from chemically modified nucleic acid libraries.","authors":"Yuuya Kasahara, Masayasu Kuwahara","doi":"10.1155/2012/156482","DOIUrl":"10.1155/2012/156482","url":null,"abstract":"<p><p>Specific binders comprised of nucleic acids, that is, RNA/DNA aptamers, are attractive functional biopolymers owing to their potential broad application in medicine, food hygiene, environmental analysis, and biological research. Despite the large number of reports on selection of natural DNA/RNA aptamers, there are not many examples of direct screening of chemically modified nucleic acid aptamers. This is because of (i) the inferior efficiency and accuracy of polymerase reactions involving transcription/reverse-transcription of modified nucleotides compared with those of natural nucleotides, (ii) technical difficulties and additional time and effort required when using modified nucleic acid libraries, and (iii) ambiguous efficacies of chemical modifications in binding properties until recently; in contrast, the effects of chemical modifications on biostability are well studied using various nucleotide analogs. Although reports on the direct screening of a modified nucleic acid library remain in the minority, chemical modifications would be essential when further functional expansion of nucleic acid aptamers, in particular for medical and biological uses, is considered. This paper focuses on enzymatic production of chemically modified nucleic acids and their application to random screenings. In addition, recent advances and possible future research are also described.</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2012 ","pages":"156482"},"PeriodicalIF":2.3,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472525/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30998752","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":"Functional Annotation of Small Noncoding RNAs Target Genes Provides Evidence for a Deregulated Ubiquitin-Proteasome Pathway in Spinocerebellar Ataxia Type 1.","authors":"Stephan Persengiev,&nbsp;Ivanela Kondova,&nbsp;Ronald E Bontrop","doi":"10.1155/2012/672536","DOIUrl":"https://doi.org/10.1155/2012/672536","url":null,"abstract":"<p><p>Spinocerebellar ataxia type 1 (SCA1) is a neurodegenerative disorder caused by the expansion of CAG repeats in the ataxin 1 (ATXN1) gene. In affected cerebellar neurons of patients, mutant ATXN1 accumulates in ubiquitin-positive nuclear inclusions, indicating that protein misfolding is involved in SCA1 pathogenesis. In this study, we functionally annotated the target genes of the small noncoding RNAs (ncRNAs) that were selectively activated in the affected brain compartments. The primary targets of these RNAs, which exhibited a significant enrichment in the cerebellum and cortex of SCA1 patients, were members of the ubiquitin-proteasome system. Thus, we identified and functionally annotated a plausible regulatory pathway that may serve as a potential target to modulate the outcome of neurodegenerative diseases.</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2012 ","pages":"672536"},"PeriodicalIF":2.3,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/672536","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31000342","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":"Expansion of the genetic alphabet: unnatural nucleobases and their applications.","authors":"Subhendu Sekhar Bag,&nbsp;Jennifer M Heemstra,&nbsp;Yoshio Saito,&nbsp;David M Chenoweth","doi":"10.1155/2012/718582","DOIUrl":"https://doi.org/10.1155/2012/718582","url":null,"abstract":"Nucleic acids are essential biomolecules that encode all of the information necessary for life. Specific pairing of A with T (or U) and C with G during replication, transcription, and translation is the key to effective transmission of genetic information between generations, as well as accurate conversion of genetic information into protein sequence. Given the magnitude of the tasks orchestrated by the Watson-Crick base pairing, it is striking to consider that biological systems accomplish these tasks using only four nucleobases. Realizing the powerful nature of base-pair recognition, researchers have been inspired to ask the question of whether the genetic code can be artificially expanded to generate biological systems having novel functions. It was this question that led Alex Rich in 1962 to propose the concept of orthogonal base pairing between iso-G and iso-C and inspired Professor Steven A. Benner in the late 1980s to expand the genetic alphabet from four to six letters. Benner's early research focused on the development of new base pairs having hydrogen bonding patterns orthogonal to those in the canonical Watson-Crick base pairs. In 1994, Professor Eric T. Kool opened a new functional dimension with the creation of nonhydrogen bonding unnatural nucleobase surrogates. \u0000 \u0000Expansion of the genetic alphabet has dramatically increased the functional potential of DNA, for example, by enabling site-directed oligonucleotide labeling and in vitro selections with oligonucleotides having increased chemical diversity. Translation of an expanded DNA alphabet into RNA is a challenging task, but one which has potential to give rise to semisynthetic organisms with increased biodiversity. This special issue highlights recent accomplishments at the interface of organic chemistry and molecular biology which hold promise to further expand the potential of nucleic acids having unnatural nucleobases. Specifically, the reports in this special issue focus on the synthesis of unnatural nucleobases and nucleic acid backbones, the exploration of their structure and duplex stabilizing ability, and the polymerase mediated replication and transcription of DNA containing unnatural nucleobases. \u0000 \u0000T. Lonnberg and a coworker report the synthesis and study of a bis(pyrazolyl)purine ribonucleoside having increased hydrophobic surface area and the ability to form complex with metal ions. The hydrogen bonding pattern of this nucleoside makes it complementary to thymine and uridine. The authors demonstrate that the bis(pyrazolyl) nucleobase is capable of forming a Pd2+-mediated base pair with uridine in the monomeric state. When incorporated into an oligonucleotide, the bis(pyrazolyl) nucleobase stabilizes DNA duplexes when paired with thymine, but this stabilization appears to result from increased π-stacking interactions rather than metal complexation. These studies open the door to applications using unnatural nucleobases to increase the binding affinity of probes and the","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2012 ","pages":"718582"},"PeriodicalIF":2.3,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/718582","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31155664","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":"Features of \"All LNA\" Duplexes Showing a New Type of Nucleic Acid Geometry.","authors":"Charlotte Förster,&nbsp;André Eichert,&nbsp;Dominik Oberthür,&nbsp;Christian Betzel,&nbsp;Reinhard Geßner,&nbsp;Andreas Nitsche,&nbsp;Jens P Fürste","doi":"10.1155/2012/156035","DOIUrl":"https://doi.org/10.1155/2012/156035","url":null,"abstract":"<p><p>\"Locked nucleic acids\" (LNAs) belong to the backbone-modified nucleic acid family. The 2'-O,4'-C-methylene-β-D-ribofuranose nucleotides are used for single or multiple substitutions in RNA molecules and thereby introduce enhanced bio- and thermostability. This renders LNAs powerful tools for diagnostic and therapeutic applications. RNA molecules maintain the overall canonical A-type conformation upon substitution of single or multiple residues/nucleotides by LNA monomers. The structures of \"all\" LNA homoduplexes, however, exhibit significant differences in their overall geometry, in particular a decreased twist, roll and propeller twist. This results in a widening of the major groove, a decrease in helical winding, and an enlarged helical pitch. Therefore, the LNA duplex structure can no longer be described as a canonical A-type RNA geometry but can rather be brought into proximity to other backbone-modified nucleic acids, like glycol nucleic acids or peptide nucleic acids. LNA-modified nucleic acids provide thus structural and functional features that may be successfully exploited for future application in biotechnology and drug discovery.</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2012 ","pages":"156035"},"PeriodicalIF":2.3,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/156035","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30665542","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":"Unwinding and rewinding: double faces of helicase?","authors":"Yuliang Wu","doi":"10.1155/2012/140601","DOIUrl":"https://doi.org/10.1155/2012/140601","url":null,"abstract":"<p><p>Helicases are enzymes that use ATP-driven motor force to unwind double-stranded DNA or RNA. Recently, increasing evidence demonstrates that some helicases also possess rewinding activity-in other words, they can anneal two complementary single-stranded nucleic acids. All five members of the human RecQ helicase family, helicase PIF1, mitochondrial helicase TWINKLE, and helicase/nuclease Dna2 have been shown to possess strand-annealing activity. Moreover, two recently identified helicases-HARP and AH2 have only ATP-dependent rewinding activity. These findings not only enhance our understanding of helicase enzymes but also establish the presence of a new type of protein: annealing helicases. This paper discusses what is known about these helicases, focusing on their biochemical activity to zip and unzip double-stranded DNA and/or RNA, their possible regulation mechanisms, and biological functions.</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2012 ","pages":"140601"},"PeriodicalIF":2.3,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/140601","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30830619","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 chemical approaches to understand RNA structure and function in biology.","authors":"Dmitry A Stetsenko,&nbsp;Arthur van Aerschot","doi":"10.1155/2012/972575","DOIUrl":"https://doi.org/10.1155/2012/972575","url":null,"abstract":"Interest of the research community in the aspects of chemical biology of RNA has increased vastly over the last twenty years, primarily due to the discovery of RNAi, our deepened understanding of the role of miRNA in the subtle regulation of vital cellular processes, and the realization of the fact that the RNA world—the realm where RNA plays the key parties as a self-replicating molecule and a universal catalyst—is still pretty much with us today as the ribosomal RNA performs its catalytic solo in the formation of the peptide bond in the ribosome. To answer the needs of Biology, Chemistry had, in turn, multiplied and perfected its approaches to study the molecular mechanisms underlying RNA functions in living systems. So, the idea behind this special issue is to show our readership a screenshot of what could be, and has been, achieved recently by applying chemical methods to solve the problems of RNA biology. Ten articles have been carefully selected out of the bunch of those submitted to provide, we believe, a balanced view of different facets of RNA structure and function and, also, of the array of chemical tools to enable us to peek into them.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2012 ","pages":"972575"},"PeriodicalIF":2.3,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/972575","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30551706","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":"A Concept for Selection of Codon-Suppressor tRNAs Based on Read-Through Ribosome Display in an In Vitro Compartmentalized Cell-Free Translation System.","authors":"Atsushi Ogawa,&nbsp;Masayoshi Hayami,&nbsp;Shinsuke Sando,&nbsp;Yasuhiro Aoyama","doi":"10.1155/2012/538129","DOIUrl":"https://doi.org/10.1155/2012/538129","url":null,"abstract":"<p><p>Here is presented a concept for in vitro selection of suppressor tRNAs. It uses a pool of dsDNA templates in compartmentalized water-in-oil micelles. The template contains a transcription/translation trigger, an amber stop codon, and another transcription trigger for the anticodon- or anticodon loop-randomized gene for tRNA(Ser). Upon transcription are generated two types of RNAs, a tRNA and a translatable mRNA (mRNA-tRNA). When the tRNA suppresses the stop codon (UAG) of the mRNA, the full-length protein obtained upon translation remains attached to the mRNA (read-through ribosome display) that contains the sequence of the tRNA. In this way, the active suppressor tRNAs can be selected (amplified) and their sequences read out. The enriched anticodon (CUA) was complementary to the UAG stop codon and the enriched anticodon-loop was the same as that in the natural tRNA(Ser).</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2012 ","pages":"538129"},"PeriodicalIF":2.3,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/538129","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30863394","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":"A two-piece derivative of a group I intron RNA as a platform for designing self-assembling RNA templates to promote Peptide ligation.","authors":"Takahiro Tanaka,&nbsp;Hiroyuki Furuta,&nbsp;Yoshiya Ikawa","doi":"10.1155/2012/305867","DOIUrl":"https://doi.org/10.1155/2012/305867","url":null,"abstract":"<p><p>Multicomponent RNA-peptide complexes are attractive from the viewpoint of artificial design of functional biomacromolecular systems. We have developed self-folding and self-assembling RNAs that serve as templates to assist chemical ligation between two reactive peptides with RNA-binding capabilities. The design principle of previous templates, however, can be applied only to limited classes of RNA-binding peptides. In this study, we employed a two-piece derivative of a group I intron RNA from the Tetrahymena large subunit ribosomal RNA (LSU rRNA) as a platform for new template RNAs. In this group I intron-based self-assembling platform, modules for the recognition of substrate peptides can be installed independently from modules holding the platform structure. The new self-assembling platform allows us to expand the repertoire of substrate peptides in template RNA design.</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2012 ","pages":"305867"},"PeriodicalIF":2.3,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/305867","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30895269","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}