Journal of Nucleic Acids最新文献_第3页

G-Quadruplexes (GQU). G-四元组（GQU）。

IF 2.3

Journal of Nucleic Acids Pub Date : 2018-04-30 eCollection Date: 2018-01-01 DOI: 10.1155/2018/1079191

Shozeb Haider, Gary N Parkinson, Thomas C Marsh

引用次数: 3

A Sequence-Dependent DNA Condensation Induced by Prion Protein. 朊病毒蛋白诱导的序列依赖性DNA凝聚。

IF 2.3

Journal of Nucleic Acids Pub Date : 2018-02-20 eCollection Date: 2018-01-01 DOI: 10.1155/2018/9581021

Alakesh Bera, Sajal Biring

{"title":"A Sequence-Dependent DNA Condensation Induced by Prion Protein.","authors":"Alakesh Bera, Sajal Biring","doi":"10.1155/2018/9581021","DOIUrl":"https://doi.org/10.1155/2018/9581021","url":null,"abstract":"Different studies indicated that the prion protein induces hybridization of complementary DNA strands. Cell culture studies showed that the scrapie isoform of prion protein remained bound with the chromosome. In present work, we used an oxazole dye, YOYO, as a reporter to quantitative characterization of the DNA condensation by prion protein. We observe that the prion protein induces greater fluorescence quenching of YOYO intercalated in DNA containing only GC bases compared to the DNA containing four bases whereas the effect of dye bound to DNA containing only AT bases is marginal. DNA-condensing biological polyamines are less effective than prion protein in quenching of DNA-bound YOYO fluorescence. The prion protein induces marginal quenching of fluorescence of the dye bound to oligonucleotides, which are resistant to condensation. The ultrastructural studies with electron microscope also validate the biophysical data. The GC bases of the target DNA are probably responsible for increased condensation in the presence of prion protein. To our knowledge, this is the first report of a human cellular protein inducing a sequence-dependent DNA condensation. The increased condensation of GC-rich DNA by prion protein may suggest a biological function of the prion protein and a role in its pathogenesis.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2018 ","pages":"9581021"},"PeriodicalIF":2.3,"publicationDate":"2018-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2018/9581021","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36012618","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

Electrochemical and AFM Characterization of G-Quadruplex Electrochemical Biosensors and Applications. g -四联电化学生物传感器的电化学和AFM表征及其应用。

IF 2.3

Journal of Nucleic Acids Pub Date : 2018-01-31 eCollection Date: 2018-01-01 DOI: 10.1155/2018/5307106

Ana-Maria Chiorcea-Paquim, Ramon Eritja, Ana Maria Oliveira-Brett

{"title":"Electrochemical and AFM Characterization of G-Quadruplex Electrochemical Biosensors and Applications.","authors":"Ana-Maria Chiorcea-Paquim, Ramon Eritja, Ana Maria Oliveira-Brett","doi":"10.1155/2018/5307106","DOIUrl":"https://doi.org/10.1155/2018/5307106","url":null,"abstract":"Guanine-rich DNA sequences are able to form G-quadruplexes, being involved in important biological processes and representing smart self-assembling nanomaterials that are increasingly used in DNA nanotechnology and biosensor technology. G-quadruplex electrochemical biosensors have received particular attention, since the electrochemical response is particularly sensitive to the DNA structural changes from single-stranded, double-stranded, or hairpin into a G-quadruplex configuration. Furthermore, the development of an increased number of G-quadruplex aptamers that combine the G-quadruplex stiffness and self-assembling versatility with the aptamer high specificity of binding to a variety of molecular targets allowed the construction of biosensors with increased selectivity and sensitivity. This review discusses the recent advances on the electrochemical characterization, design, and applications of G-quadruplex electrochemical biosensors in the evaluation of metal ions, G-quadruplex ligands, and other small organic molecules, proteins, and cells. The electrochemical and atomic force microscopy characterization of G-quadruplexes is presented. The incubation time and cations concentration dependence in controlling the G-quadruplex folding, stability, and nanostructures formation at carbon electrodes are discussed. Different G-quadruplex electrochemical biosensors design strategies, based on the DNA folding into a G-quadruplex, the use of G-quadruplex aptamers, or the use of hemin/G-quadruplex DNAzymes, are revisited.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2018 ","pages":"5307106"},"PeriodicalIF":2.3,"publicationDate":"2018-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2018/5307106","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36019525","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

Cell-SELEX Identifies a “Sticky” RNA Aptamer Sequence Cell SELEX鉴定“粘性”RNA适体序列

IF 2.3

Journal of Nucleic Acids Pub Date : 2017-01-17 DOI: 10.1155/2017/4943072

P. Ray, R. White

引用次数: 13

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