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Pengfei Li, Qing Yu, Lingli Zhou, Dexin Dong, Shina Wei, Hanzheng Ya, Bo Chen, Qiwei Qin
As the major viral pathogen of grouper aquaculture, Singapore grouper iridovirus (SGIV) has caused great economic losses in China and Southeast Asia. In the previous study, we have generated highly specific ssDNA aptamers against SGIV-infected grouper spleen cells (GS) by Systematic Evolution of Ligands by Exponential Enrichment technology (SELEX), in which Q2 had the highest binding affinity of 16.43 nM. In this study, we would try to identify the specific sequences in the aptamer Q2 that exhibited the high binding affinity to SGIV-infected cells by truncating the original Q2 into some different specific segments...
January 13, 2018: Virus Research
Nicholas M Andis, Christopher W Sausen, Ashna Alladin, Matthew Bochman
PIF1 family helicases are conserved from bacteria to man. With the exception of the well-studied yeast PIF1 helicases (e.g., ScPif1 and ScRrm3), however, very little is known about how these enzymes help maintain genome stability. Indeed, we lack a basic understanding of the protein domains found N- and C-terminal to the characteristic central PIF1 helicase domain in these proteins. Here, using chimeric constructs, we show that the ScPif1 and ScRrm3 helicase domains are interchangeable and that the N-terminus of ScRrm3 is important for its function in vivo...
January 17, 2018: Biochemistry
Yvan Bettarel, Sébastien Halary, Jean-Christophe Auguet, Thanh Chi Mai, Ngoc Van Bui, Thierry Bouvier, Patrice Got, Corinne Bouvier, Sonia Monteil-Bouchard, Desnues Christelle
The grazing activity by specific marine organisms represents a growing threat to the survival of many scleractinian species. For example, the recent proliferation of the corallivorous gastropod Drupella now constitutes a critical case in all South-East Asian waters. If the damaging effects caused by this marine snail on coral polyps are relatively well known, the indirect incidence of predation on coral microbial associates is still obscure and might also potentially impair coral health. In this study, we compared the main ecological traits of coral-associated bacterial and viral communities living in the mucus layer of Acropora formosa and Acropora millepora, of healthy and predated individuals (i...
January 16, 2018: ISME Journal
Cheng-Fang Yang, Yu-Juan Zhong, Zuheng Ma, Li Li, Lin Shi, Li Chen, Chen Li, Dan Wu, Qi Chen, Yong-Wen Li
The aim of the present study was to assess the molecular mechanism of ethanol‑induced oxidative stress‑mediated apoptosis in L‑02 liver cells in order to elucidate novel pathways associated with alcoholic liver disease. L‑02 cells were treated with 400 mM ethanol with or without inhibitors. The cell viability was measured by an MTT assay. Cell apoptosis was assessed by flow cytometry and a single‑stranded DNA (ssDNA) assay. Intracellular reactive oxygen species (ROS) production of L‑02 cells was determined using the 2',7'‑dichlorofluorescein‑diacetate dye...
January 16, 2018: International Journal of Molecular Medicine
Hao Wang, Shouxin Li, Asif Mahmood, Shixing Yang, Xiaochun Wang, Quan Shen, Tongling Shan, Xutao Deng, Jingjiao Li, Xiuguo Hua, Li Cui, Eric Delwart, Wen Zhang
BACKGROUND: Free-range cattle are common in the Northeast China area, which have close contact with farmers and may carry virus threatening to cattle and farmers. METHODS: Using viral metagenomics we analyzed the virome in plasma samples collected from 80 cattle from the forested region of Northeast China. RESULTS: The virome of cattle plasma is composed of the viruses belonging to the families including Parvoviridae, Papillomaviridae, Picobirnaviridae, and divergent viral genomes showing sequence similarity to circular Rep-encoding single stranded (CRESS) DNA viruses...
January 15, 2018: Virology Journal
Yao Cen, Wen-Jing Deng, Ru-Qin Yu, Xia Chu
5'-Polynucleotide kinase (PNK) is a crucial enzyme that catalyzes the phosphorylation of nucleic acid with 5'-OH termini and this phosphorylation reaction has been involved in many important cellular activities. The evaluation of PNK activity has received an increasing attention due to the significance of PNK. Here, the polydopamine nanospheres (PDANS) could adsorb single-stranded DNA (ssDNA) through π-π stacking or hydrogen bonding between nucleobases and aromatic groups of PDANS, while the interaction between double-stranded DNA (dsDNA) with PDANS was weakened due to the changed conformation...
April 1, 2018: Talanta
H H Katkar, M Muthukumar
One of the major theoretical methods in understanding polymer translocation through a nanopore is the Fokker-Planck formalism based on the assumption of quasi-equilibrium of polymer conformations. The criterion for applicability of the quasi-equilibrium approximation for polymer translocation is that the average translocation time per Kuhn segment, ⟨τ⟩/NK, is longer than the relaxation time τ0 of the polymer. Toward an understanding of conditions that would satisfy this criterion, we have performed coarse-grained three dimensional Langevin dynamics and multi-particle collision dynamics simulations...
January 14, 2018: Journal of Chemical Physics
Liu Wang, Zhicheng Huang, Rui Wang, Yibo Liu, Cheng Qian, Jian Wu, Juewen Liu
Monitoring the progress of polymerase chain reactions (PCR) is of critical importance in bioanalytical chemistry and molecular biology. While real-time PCR thermocyclers are ideal for this purpose, its high cost has limited applications in resource-poor areas. Direct visual detection would be a more attractive alternative. To monitor PCR amplification, DNA staining dyes such as SYBR Green I (SG) are often used. Although these dyes give higher fluorescence when binding to double-stranded (ds) DNA products, they also yield strong background fluorescence in the presence of a high concentration of single-stranded (ss) DNA primers...
January 12, 2018: ACS Applied Materials & Interfaces
Richa Nigam, Roy Anindya
Repair of alkylation damage in DNA is essential for maintaining genome integrity. Escherichia coli (E.coli) protein AlkB removes various alkyl DNA adducts including N1-methyladenine (N1meA) and N3-methylcytosine (N3meC) by oxidative demethylation. Previous studies showed that AlkB preferentially removes N1meA and N3meC from single-stranded DNA (ssDNA). It can also remove N1meA and N3meC from double-stranded DNA by base-flipping. Notably, ssDNA produced during DNA replication and recombination, remains bound to E...
January 8, 2018: Biochemical and Biophysical Research Communications
Jing-Rong Fan, Hong-Xing Zhang, Yu-Guang Mu, Qing-Chuan Zheng
The transcription regulator teicoplanin-associate locus regulator (TcaR) plays a vital role in interfering with ssDNA replication and resisting ssDNA phage invasion. Although recent studies demonstrated that TcaR had strong interaction with ssDNA, the dynamics and interaction mechanism of dimeric TcaR bound to ssDNA have not been rationalized at the atomic level. In our study, MD simulations combined with MM-GB/SA calculations were employed to study recognition mechanism between TcaR and ssDNA. The results illuminate that electrostatic interaction is the main driving force for the binding process...
December 5, 2017: Journal of Molecular Graphics & Modelling
Kentaro Ito, Yasuto Murayama, Masayuki Takahashi, Hiroshi Iwasaki
During homologous recombination, Rad51 forms a nucleoprotein filament with single-stranded DNA (ssDNA) that undergoes strand exchange with homologous double-stranded DNA (dsDNA). Here, we use real-time analysis to show that strand exchange by fission yeast Rad51 proceeds via two distinct three-strand intermediates, C1 and C2. Both intermediates contain Rad51, but whereas the donor duplex remains intact in C1, the ssDNA strand is intertwined with the complementary strand of the donor duplex in C2. Swi5-Sfr1, an evolutionarily conserved recombination activator, facilitates the C1-C2 transition and subsequent ssDNA release from C2 to complete strand exchange in an ATP-hydrolysis-dependent manner...
January 2018: Nature Structural & Molecular Biology
Yuliya S Krasikova, Nadejda I Rechkunova, Ekaterina A Maltseva, Olga I Lavrik
Replication protein A (RPA) and the xeroderma pigmentosum group A (XPA) protein are indispensable for both pathways of nucleotide excision repair (NER). Here we analyze the interaction of RPA and XPA with DNA containing a flap and different size gaps that imitate intermediates of the late NER stages. Using gel mobility shift assays, we found that RPA affinity for DNA decreased when DNA contained both extended gap and similar sized flap in comparison with gapped-DNA structure. Moreover, crosslinking experiments with the flap-gap DNA revealed that RPA interacts mainly with the ssDNA platform within the long gap and contacts flap in DNA with a short gap...
2018: PloS One
Laura Baltierra-Jasso, Michael Morten, Steven William Magennis
Non-enzymatic DNA strand displacement is an important mechanism in dynamic DNA nanotechnology. Here we show that the large parameter space that is accessible by single-molecule FRET is ideal for the simultaneous monitoring of multiple reactants and products of DNA strand exchange reactions. We monitored the strand displacement from double-stranded DNA (dsDNA) by single-stranded DNA (ssDNA) at 37 °C; the data were modelled as a second-order reaction approaching equilibrium, with a rate constant of ca. 10 M-1 s-1...
January 5, 2018: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Abdur Rahman Ansari, Ning-Ya Li, Zhi-Jian Sun, Hai-Bo Huang, Xing Zhao, Lei Cui, Ya-Fang Hu, Ju-Ming Zhong, Niel A Karrow, Hua-Zhen Liu
We investigated the mechanisms that induce atrophy of the chicken bursa of Fabricius (BF) upon lipopolysaccharide (LPS) treatment in young chicks. LPS treatment resulted in ∼36% decrease in bursal weight within 36 h (P < 0.01). Histological analysis showed infiltration of eosinophilic heterophils and nucleated oval shaped RBCs in or near blood vessels of the BF from LPS-treated chicks. Scanning electron micrographs showed severe erosion and breaks in the mucosal membrane at 12 h and complete exuviation of bursal mucosal epithelial cells at 36 h...
December 12, 2017: Oncotarget
Shao-Hua Wen, Yi Wang, Yan-Hong Yuan, Ru-Ping Liang, Jian-Ding Qiu
An electrochemical sensor was fabricated for arsenite detection using graphene oxide-assisted generation of prussian blue nanoparticles as enhanced redox signal label. The 5'-thiolate-labeled (GT)21-ssDNA was first self-assembled on a gold electrode surface via Au-S bond. Graphene oxide can interact with ssDNA through π-π stacking interaction and facilitate the generation of prussian blue nanoparticles on its surface as an electrochemically active indicator. In the absence of arsenite, plenty of graphene oxide/prussian blue nanoparticles can be adsorbed on the electrode surface to produce a stronger redox signal of prussian blue nanoparticles...
March 9, 2018: Analytica Chimica Acta
Jinchuan Liu, Xiaohong Zhou, Hanchang Shi
Monitoring and controlling of toxic cyanobacterial strains, which can produce microcystins, is critical to protect human and ecological health. We herein reported an optical biosensor-based quantification of microcystin synthetase A (mcyA) gene so as to discriminate microcystins-producing from non-producing strains. In this assay, the mcyA-specific ssDNA probes were designed in silico with an online tool and then synthesized to be covalently immobilized on an optical fiber surface. Production of fluorescently modified target DNA fragment amplicons was accomplished through the use of Cy5-tagged deoxycytidine triphosphates (dCTPs) in the polymerase chain reaction (PCR) method, which resulted in copies with internally labelled multiple sites per DNA molecule and delivered the great sensitivity...
January 5, 2018: Analytical Chemistry
Molly C Kottemann, Brooke A Conti, Francis P Lach, Agata Smogorzewska
The protection and efficient restart of stalled replication forks is critical for the maintenance of genome integrity. Here, we identify a regulatory pathway that promotes stalled forks recovery from replication stress. We show that the mammalian replisome component C20orf43/RTF2 (homologous to S. pombe Rtf2) must be removed for fork restart to be optimal. We further show that the proteasomal shuttle proteins DDI1 and DDI2 are required for RTF2 removal from stalled forks. Persistence of RTF2 at stalled forks results in fork restart defects, hyperactivation of the DNA damage signal, accumulation of single-stranded DNA (ssDNA), sensitivity to replication drugs, and chromosome instability...
January 4, 2018: Molecular Cell
Matthew D Moore, Brittany S Mertens, Lee-Ann Jaykus
Human norovirus exacts considerable public health and economic losses worldwide. Emerging in vitro cultivation advances are not yet applicable for routine detection of the virus. The current detection and quantification techniques, which rely primarily on nucleic acid amplification, do not discriminate infectious from non-infectious viral particles. The purpose of this article is to present specific details on recent advances in techniques used together in order to acquire further information on the infectivity status of viral particles...
November 16, 2017: Journal of Visualized Experiments: JoVE
Ka L Hong, Letha J Sooter
Fipronil is a commonly used insecticide that has been shown to have environmental and human health risks. The current standard methods of detection for fipronil and its metabolites, such as GC-MS, are time consuming and labor intensive. In this study, a variant of systematic evolution of ligands by exponential enrichment (SELEX), was utilized to identify the first single-stranded DNA (ssDNA) molecular recognition element (MRE) that binds to fipronil with high affinity (Kd = 48 ± 8 nM). The selected MRE displayed low cross binding activity on various environmentally relevant, structurally unrelated herbicides and pesticides, in addition to broad-spectrum binding activity on major metabolites of fipronil and a structurally similar pesticide in prepared river samples...
December 28, 2017: International Journal of Molecular Sciences
Jia-Yu Huang, Hong-Ting Lin, Tzu-Heng Chen, Chung-An Chen, Huan-Tsung Chang, Chien-Fu Chen
In this work, we report a highly sensitive colorimetric sensing strategy for cancer biomarker diagnosis using gold nanoparticles (AuNPs) labelled with biotinylated poly-adenine ssDNA sequences and streptavidin-horseradish peroxidase for enzymatic signal enhancement. By adopting this DNA-AuNP nanoconjugate sensing strategy, we were able to eliminate the complicated and costly thiol-binding process typically used to modify AuNP surfaces with ssDNA. In addition, different antibodies can be introduced to the AuNP surfaced via electrostatic interactions to provide highly specific recognition sites for biomolecular sensing...
December 28, 2017: ACS Sensors
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