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https://www.readbyqxmd.com/read/28917743/selection-of-an-aptamer-against-muscovy-duck-parvovirus-for-highly-sensitive-rapid-visual-detection-by-label-free-aptasensor
#1
Taofeng Lu, Qin Ma, Wenzhuo Yan, Yuanzhi Wang, Yuanyuan Zhang, Lili Zhao, Hongyan Chen
Muscovy duck parvovirus (MDPV) causes high mortality and morbidity in ducks. This study investigated a novel aptamer-based, label-free aptasensor detection of MDPV. In this study, we developed an ssDNA aptamer using the filtration partition and lambda exonuclease method with an affinity-based monitor and counter-screening process. After 15 rounds of SELEX (systematic evolution of ligands by exponential enrichment), the ssDNA aptamer Apt-10, which specifically bound to MDPV with high affinity (Kd = 467nM) was successfully screened, and the aptamer was also found to be good specific to MDPV...
January 1, 2018: Talanta
https://www.readbyqxmd.com/read/28916108/a-eu-iii-doped-metal-organic-framework-conjugated-with-fluorescein-labeled-single-stranded-dna-for-detection-of-cu-ii-and-sulfide
#2
Han Weng, Bing Yan
In this paper, Bio-MOF-1 is prepared as reported and then Eu(3+) is introduced into it via cation exchange method. A FAM-labeled ssDNA is chosen to fabricate with the obtained Eu(3+)@Bio-MOF-1. A luminescent hybrid material is assembled, which can exhibit the fluorescence of Eu(3+) and FAM simultaneously by adjusting the ratio of FAM-ssDNA and Eu(3+)@Bio-MOF-1. The sample is then used for the detecting of metal ions, results shows which has good selectively for Cu(2+) (LOD = 0.14 μM, 0-250 μM). The introduction of Cu(2+) can quench the fluorescence of FAM while the luminescent intensity of Eu(3+) enhancing...
October 2, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28914771/geminiviruses-and-plant-hosts-a-closer-examination-of-the-molecular-arms-race
#3
REVIEW
Shunmugiah V Ramesh, Pranav P Sahu, Manoj Prasad, Shelly Praveen, Hanu R Pappu
Geminiviruses are plant-infecting viruses characterized by a single-stranded DNA (ssDNA) genome. Geminivirus-derived proteins are multifunctional and effective regulators in modulating the host cellular processes resulting in successful infection. Virus-host interactions result in changes in host gene expression patterns, reprogram plant signaling controls, disrupt central cellular metabolic pathways, impair plant's defense system, and effectively evade RNA silencing response leading to host susceptibility...
September 15, 2017: Viruses
https://www.readbyqxmd.com/read/28913768/ionic-effects-on-the-temperature-force-phase-diagram-of-dna
#4
Sitichoke Amnuanpol
Double-stranded DNA (dsDNA) undergoes a structural transition to single-stranded DNA (ssDNA) in many biologically important processes such as replication and transcription. This strand separation arises in response either to thermal fluctuations or to external forces. The roles of ions are twofold, shortening the range of the interstrand potential and renormalizing the DNA elastic modulus. The dsDNA-to-ssDNA transition is studied on the basis that dsDNA is regarded as a bound state while ssDNA is regarded as an unbound state...
September 14, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28912486/the-homologous-recombination-machinery-orchestrates-post-replication-dna-repair-during-self-renewal-of-mouse-embryonic-stem-cells
#5
Eui-Hwan Choi, Seobin Yoon, Kyung-Soon Park, Keun P Kim
Embryonic stem (ES) cells require homologous recombination (HR) to cope with genomic instability caused during self-renewal. Here, we report expression dynamics and localization of endogenous HR factors in DNA break repair of ES cells. In addition, we analyzed gene expression patterns of HR-related factors at the transcript level with RNA-sequencing experiments. We showed that ES cells constitutively expressed diverse HR proteins throughout the cell cycle and that HR protein expression was not significantly changed even in the DNA damaging conditions...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28911316/optimizing-t4-dna-polymerase-conditions-enhances-the-efficiency-of-one-step-sequence-and-ligation-independent-cloning
#6
Mohammad Nazrul Islam, Kyeong Won Lee, Hyung-Soon Yim, Seong Hyuk Lee, Hae Chang Jung, Jung-Hyun Lee, Jae-Yeon Jeong
Previously, we developed a one-step sequence- and ligation-independent cloning (SLIC) method that is simple, fast, and cost-effective. However, although one-step SLIC generally works well, its cloning efficiency is occasionally poor, potentially due to formation of stable secondary structures within the single-stranded DNA (ssDNA) region generated by T4 DNA polymerase during the 2.5 min treatment at room temperature. To overcome this problem, we developed a modified thermo-regulated one-step SLIC approach by testing shorter T4 DNA polymerase treatment durations (5 s-2...
September 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28911117/structure-based-domain-assignment-in-leishmania-infantum-endog-characterization-of-a-ph-dependent-regulatory-switch-and-a-c-terminal-extension-that-largely-dictates-dna-substrate-preferences
#7
Cristina Oliva, Pedro A Sánchez-Murcia, Eva Rico, Ana Bravo, Margarita Menéndez, Federico Gago, Antonio Jiménez-Ruiz
Mitochondrial endonuclease G from Leishmania infantum (LiEndoG) participates in the degradation of double-stranded DNA (dsDNA) during parasite cell death and is catalytically inactive at a pH of 8.0 or above. The presence, in the primary sequence, of an acidic amino acid-rich insertion exclusive to trypanosomatids and its spatial position in a homology-built model of LiEndoG led us to postulate that this peptide stretch might act as a pH sensor for self-inhibition. We found that a LiEndoG variant lacking residues 145-180 is indeed far more active than its wild-type counterpart at pH values >7...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28911099/bacillus-subtilis-reca-with-dpra-ssba-antagonizes-recx-function-during-natural-transformation
#8
Shimin Le, Ester Serrano, Ryo Kawamura, Begoña Carrasco, Jie Yan, Juan C Alonso
Bacillus subtilis DprA and RecX proteins, which interact with RecA, are crucial for efficient chromosomal and plasmid transformation. We showed that RecA, in the rATP·Mg2+ bound form (RecA·ATP), could not compete with RecX, SsbA or SsbB for assembly onto single-stranded (ss)DNA, but RecA·dATP partially displaced these proteins from ssDNA. RecX promoted reversible depolymerization of preformed RecA·ATP filaments. The two-component DprA-SsbA mediator reversed the RecX negative effect on RecA filament extension, but not DprA or DprA and SsbB...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28905626/dna-assisted-dispersion-of-carbon-nanotubes-and-comparison-with-other-dispersing-agents
#9
Debabrata Pramanik, Prabal K K Maiti
Separation and sorting of pristine carbon nanotubes (CNTs) from bundle geometry is a very challenging task due to non-soluble and non-dispersive nature of CNTs in aqueous medium. Recently many studies have been performed to address this problem using various organic and inorganic solutions, surfactant molecules and biomolecules as dispersing agents. Recent experimental studies have reported the DNA to be highly efficient in dispersion of CNTs from bundle geometry. But there is no microscopic study and also quantitative estimation of the dispersion efficiency of the DNA...
September 14, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28905055/the-c-terminal-cytidine-deaminase-domain-of-apobec3g-itself-undergoes-intersegmental-transfer-for-a-target-search-as-revealed-by-real-time-nmr-monitoring
#10
Keisuke Kamba, Takashi Nagata, Masato Katahira
APOBEC3G (A3G), an anti-human immunodeficiency virus 1 factor, deaminates cytidines. We examined deamination of two cytidines located separately on substrate ssDNA by the C-terminal domain (CTD) of A3G using real-time NMR monitoring. The deamination preference between the two cytidines was lost when either the substrate or non-substrate ssDNA concentration increased. When the non-substrate ssDNA concentration increased, the deamination activity first increased, but then decreased. This indicates that even a single domain, A3G-CTD, undergoes intersegmental transfer for a target search...
September 14, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28900093/-synthesis-of-circular-dna-templates-with-t4-rna-ligase-for-rolling-circle-amplification
#11
A R Sakhabutdinova, M A Maksimova, R R Garafutdinov
Currently, isothermal methods of nucleic acid amplification have been well established; in particular, rolling circle amplification is of great interest. In this approach, circular ssDNA molecules have been used as a target that can be obtained by the intramolecular template-dependent ligation of an oligonucleotide C-probe. Here, a new method of synthesizing small circular DNA molecules via the cyclization of ssDNA based on T4 RNA ligase has been proposed. Circular ssDNA is further used as the template for the rolling circle amplification...
July 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28898802/nucleases-activities-during-french-bean-leaf-aging-and-dark-induced-senescence
#12
Rocío Lambert, Francisco Antonio Quiles, Gregorio Gálvez-Valdivieso, Pedro Piedras
During leaf senescence resources are managed, with nutrients mobilized from older leaves to new sink tissues. The latter implies a dilemma in terms of resource utilization, the leaf senescence should increase seed quality whereas delay in senescence should improve the seed yield. Increased knowledge about nutrient recycling during leaf senescence could lead to advances in agriculture and improved seed quality. Macromolecules mobilized during leaf senescence include proteins and nucleic acids. Although nucleic acids have been less well studied than protein degradation, they are possible reservoirs of nitrogen and phosphorous...
September 7, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28895249/salt-responsive-morphologies-of-ssdna-based-triblock-polyelectrolytes-in-semi-dilute-regime-effect-of-volume-fractions-and-polyelectrolyte-length
#13
Nan K Li, Huihui Kuang, William H Fuss, Stefan Zauscher, Efrosini Kokkoli, Yaroslava G Yingling
A comprehensive study is reported on the effect of salt concentration, polyelectrolyte block length, and polymer concentration on the morphology and structural properties of nanoaggregates self-assembled from BAB single-strand DNA (ssDNA) triblock polynucleotides in which A represents polyelectrolyte blocks and B represents hydrophobic neutral blocks. A morphological phase diagram above the gelation point is developed as a function of solvent ionic strength and polyelectrolyte block length utilizing an implicit solvent ionic strength method for dissipative particle dynamics simulations...
September 12, 2017: Macromolecular Rapid Communications
https://www.readbyqxmd.com/read/28886359/the-trex1-dinosaur-bites-the-brain-through-the-line
#14
José Luis García Pérez, Marta E Alarcón-Riquelme
In this issue of Cell Stem Cell, Thomas et al. (2017) define the nature of accumulated ssDNA present in the neuron and astrocyte cytoplasm of TREX1 mutated stem cell-derived organoids. Accumulated ssDNAs are derived from LINE-1 endogenous retroelements, providing new clues as to the development of Aicardi-Goutières syndrome in the neural system.
September 7, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28885140/xenogenic-rolling-circle-replication-of-a-synthetic-beak-and-feather-disease-virus-genomic-clone-in-293tt-mammalian-cells-and-nicotiana-benthamiana
#15
Guy L Regnard, Warren R J de Moor, Inga I Hitzeroth, Anna-Lise Williamson, Edward P Rybicki
The preparation of infectious beak and feather disease circovirus virions (BFDV) has until now relied on the extraction of virus from whole tissue of deceased or euthanized parrots known to be infected with the virus. Extraction from diseased tissue is necessary, as the virus has yet to be grown in vitro using tissue-cultured cells from any source. While infectious DNA clones have been synthesized for porcine and duck circoviruses, and both replicate in host cells and result in active viral infection in animals, this has not been shown for BFDV...
September 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28882207/a-polymerase-with-potential-the-fe-s-cluster-in-human-dna-primase
#16
Marilyn E Holt, Lauren E Salay, Walter J Chazin
Replication of DNA in eukaryotes is primarily executed by the combined action of processive DNA polymerases δ and ɛ. These enzymes cannot initiate synthesis of new DNA without the presence of a primer on the template ssDNA. The primers on both the leading and lagging strands are generated by DNA polymerase α-primase (pol-prim). DNA primase is a DNA-dependent RNA polymerase that synthesizes the first ~10 nucleotides and then transfers the substrate to polymerase α to complete primer synthesis. The mechanisms governing the coordination and handoff between primase and polymerase α are largely unknown...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28872145/synthesis-of-infectious-bacteriophages-in-an-e-coli-based-cell-free-expression-system
#17
Mark Rustad, Allen Eastlund, Ryan Marshall, Paul Jardine, Vincent Noireaux
A new generation of cell-free transcription-translation (TXTL) systems, engineered to have a greater versatility and modularity, provide novel capabilities to perform basic and applied sciences in test tube reactions. Over the past decade, cell-free TXTL has become a powerful technique for a broad range of novel multidisciplinary research areas related to quantitative and synthetic biology. The new TXTL platforms are particularly useful to construct and interrogate biochemical systems through the execution of synthetic or natural gene circuits...
August 17, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28869283/review-article-the-human-intestinal-virome-in-health-and-disease
#18
REVIEW
S R Carding, N Davis, L Hoyles
BACKGROUND: The human virome consists of animal-cell viruses causing transient infections, bacteriophage (phage) predators of bacteria and archaea, endogenous retroviruses and viruses causing persistent and latent infections. High-throughput, inexpensive, sensitive sequencing methods and metagenomics now make it possible to study the contribution dsDNA, ssDNA and RNA virus-like particles make to the human virome, and in particular the intestinal virome. AIM: To review and evaluate the pioneering studies that have attempted to characterise the human virome and generated an increased interest in understanding how the intestinal virome might contribute to maintaining health, and the pathogenesis of chronic diseases...
September 4, 2017: Alimentary Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/28865923/rapid-and-label-free-electrochemical-dna-biosensor-for-detecting-hepatitis-a-virus
#19
Marisa Manzano, Sara Viezzi, Sandra Mazerat, Robert S Marks, Jasmina Vidic
Diagnostic systems that can deliver highly specific and sensitive detection of hepatitis A virus (HAV) in food and water are of particular interest in many fields including food safety, biosecurity and control of outbreaks. Our aim was the development of an electrochemical method based on DNA hybridization to detect HAV. A ssDNA probe specific for HAV (capture probe) was designed and tested on DNAs from various viral and bacterial samples using Nested-Reverse Transcription Polymerase Chain Reaction (nRT-PCR)...
August 19, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28864184/reduced-graphene-oxide-as-a-resonance-light-scattering-probe-for-thrombin-detection-using-dual-aptamer-based-dsdna
#20
Feng Chen, Yi Liu, Rong Liao, Hang Gong, Chunyan Chen, Xiaoming Chen, Changqun Cai
This paper describes a reduced graphene oxide (RGO)-based resonance light-scattering (RLS) method for thrombin detection by using double strand DNA (dsDNA) as a binding element. dsDNA is obtained by hybridizing DNA1 and DNA2, which respectively consist of one aptamer of thrombin and the complementary strand of the other aptamer of thrombin. When thrombin is added, the specific binding of two aptamers to thrombin results in a complex (DNA1-thrombin-DNA2) and triggers the release of the complementary strand of two aptamers from dsDNA...
September 8, 2017: Analytica Chimica Acta
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