Journal of Nucleic Acids最新文献_第3页

Overexpression of PCNA Attenuates Oxidative Stress-Caused Delay of Gap-Filling during Repair of UV-Induced DNA Damage 增殖细胞核抗原过表达减轻氧化应激引起的紫外线损伤修复间隙填充延迟

IF 2.3

Journal of Nucleic Acids Pub Date : 2017-01-01 DOI: 10.1155/2017/8154646

Y. Tsai, Yi-Hsiang Wang, Yin-Chang Liu

{"title":"Overexpression of PCNA Attenuates Oxidative Stress-Caused Delay of Gap-Filling during Repair of UV-Induced DNA Damage","authors":"Y. Tsai, Yi-Hsiang Wang, Yin-Chang Liu","doi":"10.1155/2017/8154646","DOIUrl":"https://doi.org/10.1155/2017/8154646","url":null,"abstract":"UVC irradiation-caused DNA lesions are repaired in mammalian cells solely by nucleotide excision repair (NER), which consists of sequential events including initial damage recognition, dual incision of damage site, gap-filling, and ligation. We have previously shown that gap-filling during the repair of UV-induced DNA lesions may be delayed by a subsequent treatment of oxidants or prooxidants such as hydrogen peroxide, flavonoids, and colcemid. We considered the delay as a result of competition for limiting protein/enzyme factor(s) during repair synthesis between NER and base excision repair (BER) induced by the oxidative chemicals. In this report, using colcemid as oxidative stress inducer, we showed that colcemid-caused delay of gap-filling during the repair of UV-induced DNA lesions was attenuated by overexpression of PCNA but not ligase-I. PCNA knockdown, as expected, delayed the gap-filling of NER but also impaired the repair of oxidative DNA damage. Fen-1 knockdown, however, did not affect the repair of oxidative DNA damage, suggesting repair of oxidative DNA damage is not of long patch BER. Furthermore, overexpression of XRCC1 delayed the gap-filling, and presumably increase of XRCC1 pulls PCNA away from gap-filling of NER for BER, consistent with our hypothesis that delay of gap-filling of NER attributes the competition between NER and BER.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2017/8154646","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48117168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10

On the Helical Structure of Guanosine 5'-Monophosphate Formed at pH 5: Is It Left- or Right-Handed? ph5下形成的5′-单磷酸鸟苷的螺旋结构:是左旋的还是右旋的?

IF 2.3

Journal of Nucleic Acids Pub Date : 2017-01-01 Epub Date: 2017-11-02 DOI: 10.1155/2017/6798759

Gang Wu, Irene C M Kwan, Zhimin Yan, Yining Huang, Eric Ye

引用次数: 2

Aptamers as the Agent in Decontamination Assays (Apta-Decontamination Assays): From the Environment to the Potential Application In Vivo. 适配体作为去污测定试剂(适配体去污测定):从环境到体内的潜在应用。

IF 2.3

Journal of Nucleic Acids Pub Date : 2017-01-01 Epub Date: 2017-10-26 DOI: 10.1155/2017/3712070

Mawethu Pascoe Bilibana, Marimuthu Citartan, Tzi Shien Yeoh, Timofey S Rozhdestvensky, Thean-Hock Tang

{"title":"Aptamers as the Agent in Decontamination Assays (Apta-Decontamination Assays): From the Environment to the Potential Application In Vivo.","authors":"Mawethu Pascoe Bilibana, Marimuthu Citartan, Tzi Shien Yeoh, Timofey S Rozhdestvensky, Thean-Hock Tang","doi":"10.1155/2017/3712070","DOIUrl":"https://doi.org/10.1155/2017/3712070","url":null,"abstract":"The binding specificity and affinity of aptamers have long been harnessed as the key elements in the development of aptamer-based assays, particularly aptasensing application. One promising avenue that is currently explored based on the specificity and affinity of aptamers is the application of aptamers in the decontamination assays. Aptamers have been successfully harnessed as the decontamination agents to remove contaminants from the environment and to decontaminate infectious elements. The reversible denaturation property inherent in aptamers enables the repeated usage of aptamers, which can immensely save the cost of decontamination. Analogous to the point-of-care diagnostics, there is no doubt that aptamers can also be deployed in the point-of-care aptamer-based decontamination assay, whereby decontamination can be performed anywhere and anytime for instantaneous decision-making. It is also prophesied that aptamers can also serve more than as a decontaminant, probably as a tool to capture and kill hazardous elements, particularly pathogenic agents.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2017 ","pages":"3712070"},"PeriodicalIF":2.3,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2017/3712070","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35634640","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: 14

Physiological Roles of DNA Double-Strand Breaks. DNA 双链断裂的生理作用

IF 2.3

Journal of Nucleic Acids Pub Date : 2017-01-01 Epub Date: 2017-10-18 DOI: 10.1155/2017/6439169

Farhaan A Khan, Syed O Ali

{"title":"Physiological Roles of DNA Double-Strand Breaks.","authors":"Farhaan A Khan, Syed O Ali","doi":"10.1155/2017/6439169","DOIUrl":"10.1155/2017/6439169","url":null,"abstract":"Genomic integrity is constantly threatened by sources of DNA damage, internal and external alike. Among the most cytotoxic lesions is the DNA double-strand break (DSB) which arises from the cleavage of both strands of the double helix. Cells boast a considerable set of defences to both prevent and repair these breaks and drugs which derail these processes represent an important category of anticancer therapeutics. And yet, bizarrely, cells deploy this very machinery for the intentional and calculated disruption of genomic integrity, harnessing potentially destructive DSBs in delicate genetic transactions. Under tight spatiotemporal regulation, DSBs serve as a tool for genetic modification, widely used across cellular biology to generate diverse functionalities, ranging from the fundamental upkeep of DNA replication, transcription, and the chromatin landscape to the diversification of immunity and the germline. Growing evidence points to a role of aberrant DSB physiology in human disease and an understanding of these processes may both inform the design of new therapeutic strategies and reduce off-target effects of existing drugs. Here, we review the wide-ranging roles of physiological DSBs and the emerging network of their multilateral regulation to consider how the cell is able to harness DNA breaks as a critical biochemical tool.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2017 ","pages":"6439169"},"PeriodicalIF":2.3,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5664317/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35643797","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

Systemic Identification of Hevea brasiliensis EST-SSR Markers and Primer Screening. 巴西橡胶树EST-SSR标记的系统鉴定及引物筛选

IF 2.3

Journal of Nucleic Acids Pub Date : 2017-01-01 Epub Date: 2017-01-23 DOI: 10.1155/2017/6590902

Benjun Hou, Suping Feng, Yaoting Wu

{"title":"Systemic Identification of Hevea brasiliensis EST-SSR Markers and Primer Screening.","authors":"Benjun Hou, Suping Feng, Yaoting Wu","doi":"10.1155/2017/6590902","DOIUrl":"https://doi.org/10.1155/2017/6590902","url":null,"abstract":"This research aimed to systematically identify and preliminarily validate the Hevea brasiliensis expressed sequence tag (EST) information using Simple Sequence Repeat (SSR) and provide evidence for further development of SSR molecular marker. The definition of general SSR features of Hevea EST splicing sequences and development of SSR primers founded the basis of diversity analysis and variety identification for Hevea tree resource. 1134 SSR loci were identified in the EST splicing sequence and distributed in 840 Unigene. The occurrence rate of SSR loci was 23.9%, and the average distribution distance of EST-SSR was 2.59 kb. The major repeat type was mononucleotide repeat motif, which accounted for 38.89%, while the corresponding value was 36.95% for dinucleotide repeat motif and 18.17% for trinucleotide repeat motif; the proportion of other motifs was only 5.99%. The superior repeat motifs for mononucleotide, dinucleotide, and trinucleotide were A/T, AG/CT, and AAG/CTT, respectively. 739 pair of primers were designed for 1134 SSR loci. PCR amplification was performed on Hevea Reyan5-11, Reyan87-6-47, and PR107, and 180 pairs of primers were selected which were able to amplify polymorphism bands.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2017 ","pages":"6590902"},"PeriodicalIF":2.3,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2017/6590902","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34760158","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: 13

On Characterizing the Interactions between Proteins and Guanine Quadruplex Structures of Nucleic Acids. 蛋白质与核酸鸟嘌呤四重结构相互作用的表征。

IF 2.3

Journal of Nucleic Acids Pub Date : 2017-01-01 Epub Date: 2017-11-09 DOI: 10.1155/2017/9675348

Ewan K S McRae, Evan P Booy, Gay Pauline Padilla-Meier, Sean A McKenna

{"title":"On Characterizing the Interactions between Proteins and Guanine Quadruplex Structures of Nucleic Acids.","authors":"Ewan K S McRae, Evan P Booy, Gay Pauline Padilla-Meier, Sean A McKenna","doi":"10.1155/2017/9675348","DOIUrl":"10.1155/2017/9675348","url":null,"abstract":"Guanine quadruplexes (G4s) are four-stranded secondary structures of nucleic acids which are stabilized by noncanonical hydrogen bonding systems between the nitrogenous bases as well as extensive base stacking, or pi-pi, interactions. Formation of these structures in either genomic DNA or cellular RNA has the potential to affect cell biology in many facets including telomere maintenance, transcription, alternate splicing, and translation. Consequently, G4s have become therapeutic targets and several small molecule compounds have been developed which can bind such structures, yet little is known about how G4s interact with their native protein binding partners. This review focuses on the recognition of G4s by proteins and small peptides, comparing the modes of recognition that have thus far been observed. Emphasis will be placed on the information that has been gained through high-resolution crystallographic and NMR structures of G4/peptide complexes as well as biochemical investigations of binding specificity. By understanding the molecular features that lead to specificity of G4 binding by native proteins, we will be better equipped to target protein/G4 interactions for therapeutic purposes.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2017 ","pages":"9675348"},"PeriodicalIF":2.3,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2017/9675348","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35664421","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: 39

Expression of Genes and Their Polymorphism Influences the Risk of Knee Osteoarthritis. 基因表达及其多态性影响膝关节骨关节炎的风险。

IF 2.3

Journal of Nucleic Acids Pub Date : 2017-01-01 Epub Date: 2017-10-09 DOI: 10.1155/2017/3138254

Abhishek Mishra, Rajeshwar Nath Srivastava, Sachin Awasthi, Devendra Parmar, Priya Mishra

{"title":"Expression of Genes and Their Polymorphism Influences the Risk of Knee Osteoarthritis.","authors":"Abhishek Mishra, Rajeshwar Nath Srivastava, Sachin Awasthi, Devendra Parmar, Priya Mishra","doi":"10.1155/2017/3138254","DOIUrl":"https://doi.org/10.1155/2017/3138254","url":null,"abstract":"Introduction: Genetic factors including the level of expression of the fingerprint of genes involved in the development of bones and cartilage such as GDF-5 or ESR-α or CALM-1 are known to be strong determinants of the osteoarthritis (OA) in Caucasian and Oriental populations. Because of high prevalence of OA in Indian population and availability of limited genetic data, we determined whether similar genetic factors are involved in Indians as well.Methods: A case control study was carried out involving 500 patients of knee OA and equal number of healthy controls. Genotyping analyses in whole blood, mRNA, and protein expressions in peripheral blood lymphocytes (PBLs) were performed using established protocols.Results: Our results showed a significantly decreased level of mRNA and protein expressions for GDF-5, ESR-α, and CALM-1 genes in PBLs of OA cases when compared to healthy controls. The frequency of variant genotypes of these genes was also increased significantly in cases of OA compared to controls.Conclusion: Our results demonstrated that the decrease in expression of GDF-5, ESR-α, and CALM-1 in PBLs and association of polymorphism in these genes may be important in predicting the severity and thereby the progression of OA in Indian population.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2017 ","pages":"3138254"},"PeriodicalIF":2.3,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2017/3138254","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35247370","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: 12

In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids? 合成核苷酸和天然碱基损伤如何改变g -四重核酸的结构稳定性?

IF 1.3

Journal of Nucleic Acids Pub Date : 2017-01-01 Epub Date: 2017-10-18 DOI: 10.1155/2017/1641845

Janos Sagi

{"title":"In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids?","authors":"Janos Sagi","doi":"10.1155/2017/1641845","DOIUrl":"10.1155/2017/1641845","url":null,"abstract":"Synthetic analogs of natural nucleotides have long been utilized for structural studies of canonical and noncanonical nucleic acids, including the extensively investigated polymorphic G-quadruplexes (GQs). Dependence on the sequence and nucleotide modifications of the folding landscape of GQs has been reviewed by several recent studies. Here, an overview is compiled on the thermodynamic stability of the modified GQ folds and on how the stereochemical preferences of more than 70 synthetic and natural derivatives of nucleotides substituting for natural ones determine the stability as well as the conformation. Groups of nucleotide analogs only stabilize or only destabilize the GQ, while the majority of analogs alter the GQ stability in both ways. This depends on the preferred syn or anti N-glycosidic linkage of the modified building blocks, the position of substitution, and the folding architecture of the native GQ. Natural base lesions and epigenetic modifications of GQs explored so far also stabilize or destabilize the GQ assemblies. Learning the effect of synthetic nucleotide analogs on the stability of GQs can assist in engineering a required stable GQ topology, and exploring the in vitro action of the single and clustered natural base damage on GQ architectures may provide indications for the cellular events.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2017 ","pages":"1641845"},"PeriodicalIF":1.3,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5664352/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35643795","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

Selection of DNA Aptamers for Ovarian Cancer Biomarker CA125 Using One-Pot SELEX and High-Throughput Sequencing. 使用单锅SELEX和高通量测序选择卵巢癌生物标志物CA125的DNA适体

IF 2.3

Journal of Nucleic Acids Pub Date : 2017-01-01 Epub Date: 2017-02-09 DOI: 10.1155/2017/9879135

Delia J Scoville, Tae Kyu Brian Uhm, Jamie A Shallcross, Rebecca J Whelan

{"title":"Selection of DNA Aptamers for Ovarian Cancer Biomarker CA125 Using One-Pot SELEX and High-Throughput Sequencing.","authors":"Delia J Scoville, Tae Kyu Brian Uhm, Jamie A Shallcross, Rebecca J Whelan","doi":"10.1155/2017/9879135","DOIUrl":"https://doi.org/10.1155/2017/9879135","url":null,"abstract":"CA125 is a mucin glycoprotein whose concentration in serum correlates with a woman's risk of developing ovarian cancer and also indicates response to therapy in diagnosed patients. Accurate detection of this large, complex protein in patient samples is of great clinical relevance. We suggest that powerful new diagnostic tools may be enabled by the development of nucleic acid aptamers with affinity for CA125. Here, we report on our use of One-Pot SELEX to isolate single-stranded DNA aptamers with affinity for CA125, followed by high-throughput sequencing of the selected oligonucleotides. This data-rich approach, combined with bioinformatics tools, enabled the entire selection process to be characterized. Using fluorescence anisotropy and affinity probe capillary electrophoresis, the binding affinities of four aptamer candidates were evaluated. Two aptamers, CA125_1 and CA125_12, both without primers, were found to bind to clinically relevant concentrations of the protein target. Binding was differently influenced by the presence of Mg2+ ions, being required for binding of CA125_1 and abrogating binding of CA125_12. In conclusion, One-Pot SELEX was found to be a promising selection method that yielded DNA aptamers to a clinically important protein target.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2017 ","pages":"9879135"},"PeriodicalIF":2.3,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2017/9879135","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34800867","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

Corrigendum to "Plant MicroRNA Prediction by Supervised Machine Learning Using C5.0 Decision Trees". “使用C5.0决策树的监督机器学习预测植物MicroRNA”的勘误表。

IF 2.3

Journal of Nucleic Acids Pub Date : 2017-01-01 Epub Date: 2017-10-24 DOI: 10.1155/2017/7876832

Philip H Williams, Rodney P Eyles, Georg Weiller

引用次数: 1