Journal of Nucleic Acids最新文献_第5页

Effects of stability of base pairs containing an oxazolone on DNA elongation. 含恶唑酮碱基对稳定性对DNA延伸的影响。

IF 2.3

Journal of Nucleic Acids Pub Date : 2014-01-01 Epub Date: 2014-12-07 DOI: 10.1155/2014/178350

Masayo Suzuki, Kazuya Ohtsuki, Katsuhito Kino, Teruhiko Kobayashi, Masayuki Morikawa, Takanobu Kobayashi, Hiroshi Miyazawa

{"title":"Effects of stability of base pairs containing an oxazolone on DNA elongation.","authors":"Masayo Suzuki, Kazuya Ohtsuki, Katsuhito Kino, Teruhiko Kobayashi, Masayuki Morikawa, Takanobu Kobayashi, Hiroshi Miyazawa","doi":"10.1155/2014/178350","DOIUrl":"https://doi.org/10.1155/2014/178350","url":null,"abstract":"The nucleoside 2,2,4-triamino-5(2H)-oxazolone (Oz) can result from oxidative damage to guanine residues in DNA. Despite differences among the three polymerases (Pol β, KF exo(-), and Pol η) regarding nucleotide incorporation patterns opposite Oz, all three polymerases can incorporate guanine opposite Oz. Based on ab initio calculations, we proposed a structure for a stable Oz:G base pair. Here, to assess the stability of each Oz-containing base pair (Oz:G, Oz:A, Oz:C, and Oz:T) upon DNA replication, we determined the efficiency of Pol β-, KF exo(-)-, or Pol η-catalyzed primer extension beyond each base pair. With each polymerase, extension beyond Oz:G was more efficient than that beyond Oz:A, Oz:C, or Oz:T. Moreover, thermal denaturation studies revealed that the T m value for the duplex containing Oz:G was significantly higher than those obtained for duplexes containing Oz:A, Oz:C, or Oz:T. Therefore, the results from ab initio calculations along with those from DNA replication assays and thermal denaturation experiments supported the conclusion that Oz:G is the most stable of the Oz-containing base pairs. ","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2014 ","pages":"178350"},"PeriodicalIF":2.3,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/178350","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32965296","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: 9

Erratum to "Analysis of Nucleotide Sequences of the 16S rRNA Gene of Novel Escherichia coli Strains Isolated from Feces of Human and Bali Cattle". 《从人类和巴厘牛粪便中分离的新型大肠杆菌16S rRNA基因核苷酸序列分析》的勘误。

IF 2.3

Journal of Nucleic Acids Pub Date : 2014-01-01 Epub Date: 2014-12-29 DOI: 10.1155/2014/412942

I Wayan Suardana

引用次数: 8

Discovery of Novel Leaf Rust Responsive microRNAs in Wheat and Prediction of Their Target Genes. 小麦叶锈病新反应microrna的发现及其靶基因的预测。

IF 2.3

Journal of Nucleic Acids Pub Date : 2014-01-01 Epub Date: 2014-08-12 DOI: 10.1155/2014/570176

Dhananjay Kumar, Dharmendra Singh, Pulkit Kanodia, Kumble Vinod Prabhu, Manish Kumar, Kunal Mukhopadhyay

{"title":"Discovery of Novel Leaf Rust Responsive microRNAs in Wheat and Prediction of Their Target Genes.","authors":"Dhananjay Kumar, Dharmendra Singh, Pulkit Kanodia, Kumble Vinod Prabhu, Manish Kumar, Kunal Mukhopadhyay","doi":"10.1155/2014/570176","DOIUrl":"https://doi.org/10.1155/2014/570176","url":null,"abstract":"MicroRNAs are endogenous small noncoding RNAs which play critical roles in gene regulation. Few wheat (Triticum aestivum L.) miRNA sequences are available in miRBase repertoire and knowledge of their biological functions related to biotic stress is limited. We identified 52 miRNAs, belonging to 19 families, from next-generation transcriptome sequence data based on homology search. One wheat specific novel miRNA was identified but could not be ascribed or assigned to any known miRNA family. Differentially expressed 22 miRNAs were found between susceptible and resistant wheat near-isogenic lines inoculated with leaf rust pathogen Puccinia triticina and compared with mock inoculated controls. Most miRNAs were more upregulated in susceptible NIL compared to resistant NIL. We identified 1306 potential target genes for these 52 miRNAs with vital roles in response to stimuli, signaling, and diverse metabolic and cellular processes. Gene ontology analysis showed 66, 20, and 35 target genes to be categorized into biological process, molecular function, and cellular component, respectively. A miRNA-mediated regulatory network revealed relationships among the components of the targetome. The present study provides insight into potential miRNAs with probable roles in leaf rust pathogenesis and their target genes in wheat which establish a foundation for future studies. ","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2014 ","pages":"570176"},"PeriodicalIF":2.3,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/570176","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32633957","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: 29

Selective Evolution of Ligands by Exponential Enrichment to Identify RNA Aptamers against Shiga Toxins. 用指数富集方法鉴定抗志贺毒素RNA适体的配体选择进化。

IF 2.3

Journal of Nucleic Acids Pub Date : 2014-01-01 Epub Date: 2014-04-15 DOI: 10.1155/2014/214929

Sreerupa Challa, Saul Tzipori, Abhineet Sheoran

引用次数: 14

Simultaneous Detection of Different MicroRNA Types Using the ZIP-Code Array System. 利用邮政编码阵列系统同时检测不同MicroRNA类型。

IF 2.3

Journal of Nucleic Acids Pub Date : 2013-01-01 Epub Date: 2013-09-02 DOI: 10.1155/2013/496425

Sonja U Weishaupt, Steffen Rupp, Karin Lemuth

{"title":"Simultaneous Detection of Different MicroRNA Types Using the ZIP-Code Array System.","authors":"Sonja U Weishaupt, Steffen Rupp, Karin Lemuth","doi":"10.1155/2013/496425","DOIUrl":"https://doi.org/10.1155/2013/496425","url":null,"abstract":"MicroRNAs (miRNAs) are important negative regulators of gene expression. Their implication in tumorigenesis is based on their dysregulation in many human cancer diseases. Interestingly, in tumor cells, an altered ratio of precursor and mature miRNA levels has been described. Consequently, differences in miRNA type levels have a high potential as biomarkers and comparative high-throughput-based detection might permit a more accurate characterization of subtypes, especially in the case of very heterogeneous tumor entities. Several molecular methods exist for the detection of mature and precursor miRNAs. DNA microarrays are predestinated as a high-throughput method for comprehensive miRNA detection in tumors. However, the simultaneous array-based detection of both these miRNA types is limited because the mature miRNA sequence is identically present in both forms. Here we present a ZIP-code DNA microarray-based system in combination with a novel labeling approach, which enables the simultaneous detection of precursor and mature miRNAs in one single experiment. Using synthetic miRNA templates, we demonstrate the specificity of the method for the different miRNA types, as well as the detection range up to four orders of magnitude. Moreover, mature and precursor miRNAs were detected and validated in human tumor cells. ","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2013 ","pages":"496425"},"PeriodicalIF":2.3,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/496425","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31770129","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: 6

Oligonucleotide-Based Therapy for FTD/ALS Caused by the C9orf72 Repeat Expansion: A Perspective. 基于寡核苷酸的治疗由C9orf72重复扩增引起的FTD/ALS:一个视角。

IF 2.3

Journal of Nucleic Acids Pub Date : 2013-01-01 Epub Date: 2013-11-17 DOI: 10.1155/2013/208245

Stephanie A Fernandes, Andrew G L Douglas, Miguel A Varela, Matthew J A Wood, Yoshitsugu Aoki

{"title":"Oligonucleotide-Based Therapy for FTD/ALS Caused by the C9orf72 Repeat Expansion: A Perspective.","authors":"Stephanie A Fernandes, Andrew G L Douglas, Miguel A Varela, Matthew J A Wood, Yoshitsugu Aoki","doi":"10.1155/2013/208245","DOIUrl":"10.1155/2013/208245","url":null,"abstract":"Amyotrophic lateral sclerosis (ALS) is a progressive and lethal disease of motor neuron degeneration, leading to paralysis of voluntary muscles and death by respiratory failure within five years of onset. Frontotemporal dementia (FTD) is characterised by degeneration of frontal and temporal lobes, leading to changes in personality, behaviour, and language, culminating in death within 5-10 years. Both of these diseases form a clinical, pathological, and genetic continuum of diseases, and this link has become clearer recently with the discovery of a hexanucleotide repeat expansion in the C9orf72 gene that causes the FTD/ALS spectrum, that is, c9FTD/ALS. Two basic mechanisms have been proposed as being potentially responsible for c9FTD/ALS: loss-of-function of the protein encoded by this gene (associated with aberrant DNA methylation) and gain of function through the formation of RNA foci or protein aggregates. These diseases currently lack any cure or effective treatment. Antisense oligonucleotides (ASOs) are modified nucleic acids that are able to silence targeted mRNAs or perform splice modulation, and the fact that they have proved efficient in repeat expansion diseases including myotonic dystrophy type 1 makes them ideal candidates for c9FTD/ALS therapy. Here, we discuss potential mechanisms and challenges for developing oligonucleotide-based therapy for c9FTD/ALS. ","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2013 ","pages":"208245"},"PeriodicalIF":2.3,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/208245","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31965145","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: 9

Multipyrene tandem probes for point mutations detection in DNA. 用于 DNA 点突变检测的多芘串联探针。

IF 2.3

Journal of Nucleic Acids Pub Date : 2013-01-01 Epub Date: 2013-12-24 DOI: 10.1155/2013/860457

Svetlana A Kholodar, Darya S Novopashina, Mariya I Meschaninova, Alya G Venyaminova

引用次数: 0

Mesenchymal stem cell therapy in diabetes mellitus: progress and challenges. 间充质干细胞治疗糖尿病:进展和挑战。

IF 2.3

Journal of Nucleic Acids Pub Date : 2013-01-01 Epub Date: 2013-05-15 DOI: 10.1155/2013/194858

Nagwa El-Badri, Mohamed A Ghoneim

{"title":"Mesenchymal stem cell therapy in diabetes mellitus: progress and challenges.","authors":"Nagwa El-Badri, Mohamed A Ghoneim","doi":"10.1155/2013/194858","DOIUrl":"https://doi.org/10.1155/2013/194858","url":null,"abstract":"Advanced type 2 diabetes mellitus is associated with significant morbidity and mortality due to cardiovascular, nervous, and renal complications. Attempts to cure diabetes mellitus using islet transplantation have been successful in providing a source for insulin secreting cells. However, limited donors, graft rejection, the need for continued immune suppression, and exhaustion of the donor cell pool prompted the search for a more sustained source of insulin secreting cells. Stem cell therapy is a promising alternative for islet transplantation in type 2 diabetic patients who fail to control hyperglycemia even with insulin injection. Autologous stem cell transplantation may provide the best outcome for those patients, since autologous cells are readily available and do not entail prolonged hospital stays or sustained immunotoxic therapy. Among autologous adult stem cells, mesenchymal stem cells (MSCs) therapy has been applied with varying degrees of success in both animal models and in clinical trials. This review will focus on the advantages of MSCs over other types of stem cells and the possible mechanisms by which MSCs transplant restores normoglycemia in type 2 diabetic patients. Sources of MSCs including autologous cells from diabetic patients and the use of various differentiation protocols in relation to best transplant outcome will be discussed.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2013 ","pages":"194858"},"PeriodicalIF":2.3,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/194858","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31502709","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: 43

Immobilization of DNA aptamers on polyester cloth for antigen detection by dot blot immunoenzymatic assay (aptablot). 涤纶布上DNA适体的固定化，用于点印迹免疫酶法(aptablot)抗原检测。

IF 2.3

Journal of Nucleic Acids Pub Date : 2013-01-01 Epub Date: 2013-10-30 DOI: 10.1155/2013/936542

Sally Smiley, Maria Derosa, Burton Blais

引用次数: 7

Comparative (computational) analysis of the DNA methylation status of trinucleotide repeat expansion diseases. 三核苷酸重复扩增病DNA甲基化状态的比较(计算)分析。

IF 2.3

Journal of Nucleic Acids Pub Date : 2013-01-01 Epub Date: 2013-12-23 DOI: 10.1155/2013/689798

Mohammadmersad Ghorbani, Simon J E Taylor, Mark A Pook, Annette Payne

{"title":"Comparative (computational) analysis of the DNA methylation status of trinucleotide repeat expansion diseases.","authors":"Mohammadmersad Ghorbani, Simon J E Taylor, Mark A Pook, Annette Payne","doi":"10.1155/2013/689798","DOIUrl":"https://doi.org/10.1155/2013/689798","url":null,"abstract":"Previous studies have examined DNA methylation in different trinucleotide repeat diseases. We have combined this data and used a pattern searching algorithm to identify motifs in the DNA surrounding aberrantly methylated CpGs found in the DNA of patients with one of the three trinucleotide repeat (TNR) expansion diseases: fragile X syndrome (FRAXA), myotonic dystrophy type I (DM1), or Friedreich's ataxia (FRDA). We examined sequences surrounding both the variably methylated (VM) CpGs, which are hypermethylated in patients compared with unaffected controls, and the nonvariably methylated CpGs which remain either always methylated (AM) or never methylated (NM) in both patients and controls. Using the J48 algorithm of WEKA analysis, we identified that two patterns are all that is necessary to classify our three regions CCGG∗ which is found in VM and not in AM regions and AATT∗ which distinguished between NM and VM + AM using proportional frequency. Furthermore, comparing our software with MEME software, we have demonstrated that our software identifies more patterns than MEME in these short DNA sequences. Thus, we present evidence that the DNA sequence surrounding CpG can influence its susceptibility to be de novo methylated in a disease state associated with a trinucleotide repeat. ","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2013 ","pages":"689798"},"PeriodicalIF":2.3,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/689798","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32054320","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