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https://www.readbyqxmd.com/read/29151205/filamentous-bacteriophage-viruses-preparation-magic-angle-spinning-solid-state-nmr-experiments-and-structure-determination
#1
Omry Morag, Nikolaos G Sgourakis, Gili Abramov, Amir Goldbourt
Filamentous bacteriophages are elongated semi-flexible viruses that infect bacteria. They consist of a circular single-stranded DNA (ssDNA) wrapped by a capsid consisting of thousands of copies of a major coat protein subunit. Given the increasing number of discovered phages and the existence of only a handful of structures, the development of methods for phage structure determination is valuable for biophysics and structural virology. In recent years, we developed and applied techniques to elucidate the 3D atomic-resolution structures of intact bacteriophages using experimental magic-angle spinning (MAS) solid-state NMR data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29150435/biochemical-characterization-of-ints3-and-c9orf80-two-subunits-of-hnabp1-2-heterotrimeric-complex-in-nucleic-acid-binding
#2
Venkatasubramanian Vidhyasagar, Yujiong He, Manhong Guo, Tanu Talwar, Ravi Shankar Singh, Manisha Yadav, George Katselis, Franco J Vizeacoumar, Erique Lukong, Yuliang Wu
Human Nucleic Acid Binding Protein 1 and 2 (hNABP1 and hNABP2, also known as hSSB2 and hSSB1) form two separate and independent complexes with two identical proteins, integrator complex subunit 3 (INTS3) and C9ORF80. We and other groups have demonstrated that hNABP1 and 2 are single stranded (ss) DNA and RNA binding proteins, and function in DNA repair; however, the function of INTS3 and C9OFR80 remains elusive. In this study, we purified recombinant proteins INTS3 and C9ORF80 to near homogeneity. Both proteins exist as a monomer in solution, however C9ORF80 exhibits anomalous behavior on SDS-PAGE and gel filtration because of 48% random coil present in the protein...
November 17, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29145843/development-of-a-crispr-cas9-genome-editing-toolbox-for-corynebacterium-glutamicum
#3
Jiao Liu, Yu Wang, Yujiao Lu, Ping Zheng, Jibin Sun, Yanhe Ma
BACKGROUND: Corynebacterium glutamicum is an important industrial workhorse and advanced genetic engineering tools are urgently demanded. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) have revolutionized the field of genome engineering. The CRISPR/Cas9 system that utilizes NGG as protospacer adjacent motif (PAM) and has good targeting specificity can be developed into a powerful tool for efficient and precise genome editing of C...
November 16, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/29144554/a-sensitive-colorimetric-dna-biosensor-for-specific-detection-of-the-hbv-gene-based-on-silver-coated-glass-slide-and-g-quadruplex-hemin-dnazyme
#4
Yubin Li, Sheng Liu, Qiujuan Deng, Liansheng Ling
A sensitive colorimetric DNA biosensor for specific detection of single stranded oligonucleotide (ssDNA) is proposed in this paper. The biosensor is based on silver-coated glass (SCGS) and G-quadruplex-hemin DNAzyme. Capture DNA is immobilized on the surface of SCGS by Ag-S bond. Signal DNA can be used to hybridize with the target DNA which is selected from the Hepatitis B virus(HBV) gene as target HBV DNA, and the HRP-mimicking G-quadruplex-hemin DNAzyme can be formed through the function of a guanine-rich fragment from signal DNA to catalyze the oxidation of 2,2-azinobis(3-ethylbenzothiozoline)-6-sulfonicacid (ABTS(2-) ) by H2 O2 ...
November 16, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/29143186/identification-of-an-anellovirus-and-genomoviruses-in-ixodid-ticks
#5
Kara Waits, Marten J Edwards, Ilaria N Cobb, Rafaela S Fontenele, Arvind Varsani
Ticks are blood-feeding arachnids that are vectors of several important human and animal pathogens. Little is known about single-stranded DNA (ssDNA) viruses that are associated with these ectoparasites. As part of a pilot study to identify ssDNA viruses present in ticks, female American dog ticks (Dermacentor variabilis) and blacklegged ticks (Ixodes scapularis) were collected in eastern Pennsylvania (USA), and the extracted viral DNA was analyzed using viral metagenomics approaches. Three genomoviruses were recovered from pooled samples of D...
November 15, 2017: Virus Genes
https://www.readbyqxmd.com/read/29138440/structural-basis-for-dna-recognition-of-a-single-stranded-dna-binding-protein-from-enterobacter-phage-enc34
#6
Elina Cernooka, Janis Rumnieks, Kaspars Tars, Andris Kazaks
Modern DNA sequencing capabilities have led to the discovery of a large number of new bacteriophage genomes, which are a rich source of novel proteins with an unidentified biological role. The genome of Enterobacter cancerogenus bacteriophage Enc34 contains several proteins of unknown function that are nevertheless conserved among distantly related phages. Here, we report the crystal structure of a conserved Enc34 replication protein ORF6 which contains a domain of unknown function DUF2815. Despite the low (~15%) sequence identity, the Enc34 ORF6 structurally resembles the gene 2...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29136862/stimulus-response-click-chemistry-based-aptamer-functionalized-mesoporous-silica-nanoparticles-for-fluorescence-detection-of-thrombin
#7
Zhonghui Chen, Mi Sun, Fang Luo, Kefeng Xu, Zhenyu Lin, Lan Zhang
In most aptamer based stimulus response mesoporous silica nanoparticles (MSN) systems, the aptamer is modified on the MSN via electrostatic interaction, however leakage might exist after a certain time in the system and hence the stability is not good. In this study, the pores of MSN were capped by aptamer through click chemistry reaction for the first time and the system was then employed to develop a fluorescence biosensor. Specifically, the aptamer of the target (thrombin in this study) was hybridized with its complementary DNA (which was initially modified with alkyne at the terminal) to form a double strand DNA (dsDNA) firstly, and then this dsDNA was modified on N3 modified MSN via Cu(I) catalyzed alkyne-azide cycloaddition reaction...
February 1, 2018: Talanta
https://www.readbyqxmd.com/read/29136243/structure-and-electrical-properties-of-dna-nanotubes-embedded-in-lipid-bilayer-membranes
#8
Himanshu Joshi, Prabal K Maiti
Engineering the synthetic nanopores through lipid bilayer membrane to access the interior of a cell is a long persisting challenge in biotechnology. Here, we demonstrate the stability and dynamics of a tile-based 6-helix DNA nanotube (DNT) embedded in POPC lipid bilayer using the analysis of 0.2 μs long equilibrium MD simulation trajectories. We observe that the head groups of the lipid molecules close to the lumen cooperatively tilt towards the hydrophilic sugar-phosphate backbone of DNA and form a toroidal structure around the patch of DNT protruding in the membrane...
November 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29133916/brca2-antagonizes-classical-and-alternative-nonhomologous-end-joining-to-prevent-gross-genomic-instability
#9
Jinhua Han, Chunyan Ruan, Michael S Y Huen, Jiadong Wang, Anyong Xie, Chun Fu, Ting Liu, Jun Huang
BRCA2-deficient cells exhibit gross genomic instability, but the underlying mechanisms are not fully understood. Here we report that inactivation of BRCA2 but not RAD51 destabilizes RPA-coated single-stranded DNA (ssDNA) structures at resected DNA double-strand breaks (DSBs) and greatly enhances the frequency of nuclear fragmentation following cell exposure to DNA damage. Importantly, these BRCA2-associated deficits are fueled by the aberrant activation of classical (c)- and alternative (alt)- nonhomologous end-joining (NHEJ), and rely on the well-defined DNA damage signaling pathway involving the pro-c-NHEJ factor 53BP1 and its downstream effector RIF1...
November 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29131586/single-walled-carbon-nanotubes-probed-with-insulator-based-dielectrophoresis
#10
Mohammad Towshif Rabbani, Christoph F Schmidt, Alexandra Ros
Single-walled carbon nanotubes (SWNTs) offer unique electrical and optical properties. Common synthesis processes yield SWNTs with large length polydispersity (several tens of nanometers up to centimeters) and heterogeneous electrical and optical properties. Applications often require suitable selection and purification. Dielectrophoresis is one manipulation method for separating SWNTs based on dielectric properties and geometry. Here, we present a study of surfactant and ssDNA wrapped SWNTs suspended in aqueous solutions manipulated by insulator-based dielectrophoresis (iDEP)...
November 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29130087/polyethylenimine-coated-fe3o4-nanoparticles-effectively-quench-fluorescent-dna-which-can-be-developed-as-a-novel-platform-for-protein-detection
#11
Long Ma, Nana Sun, Jinyan Zhang, Chunhao Tu, Xiuqi Cao, Demin Duan, Aipo Diao, Shuli Man
We report a novel assembly of polyethyleneimine (PEI)-coated Fe3O4 nanoparticles (NPs) with single-stranded DNA (ssDNA), and the fluorescence of the dye labeled in the DNA is remarkably quenched. In the presence of a target protein, the protein-DNA aptamer mutual interaction releases the ssDNA from this assembly and hence restores the fluorescence. This feature could be adopted to develop an aptasensor for protein detection. As a proof-of-concept, for the first time, we have used this proposed sensing strategy to detect thrombin selectively and sensitively...
November 13, 2017: Nanoscale
https://www.readbyqxmd.com/read/29126473/a-luminescent-probe-of-mismatched-dna-hybridization-location-and-number-of-mismatches
#12
Amira F El-Yazbi, Alysha Wong, Glen R Loppnow
The human genome is susceptible to change; base mismatches can arise from damaged DNA, replication errors, and spontaneous mutation, and have the potential to cause apoptosis, carcinogenesis, and mutagenesis. Many techniques have been developed for DNA mismatch detection, but many of these methods have complex, time-consuming procedures and are limited to the detection of specific types of DNA mismatches. In this work, we present a general method for the simple and sensitive nucleobase-sensitized luminescent detection of mismatches in double-stranded DNA (dsDNA) using terbium ions...
November 22, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29124689/xeroderma-pigmentosa-group-a-xpa-nucleotide-excision-repair-and-regulation-by-atr-in-response-to-ultraviolet-irradiation
#13
Phillip R Musich, Zhengke Li, Yue Zou
The sensitivity of Xeroderma pigmentosa (XP) patients to sunlight has spurred the discovery and genetic and biochemical analysis of the eight XP gene products (XPA-XPG plus XPV) responsible for this disorder. These studies also have served to elucidate the nucleotide excision repair (NER) process, especially the critical role played by the XPA protein. More recent studies have shown that NER also involves numerous other proteins normally employed in DNA metabolism and cell cycle regulation. Central among these is ataxia telangiectasia and Rad3-related (ATR), a protein kinase involved in intracellular signaling in response to DNA damage, especially DNA damage-induced replicative stresses...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29124021/allele-specific-lamp-gold-nanoparticle-for-characterization-of-single-nucleotide-polymorphisms
#14
Fábio Ferreira Carlos, Bruno Veigas, Ana S Matias, Gonçalo Doria, Orfeu Flores, Pedro V Baptista
Due to their relevance as disease biomarkers and for diagnostics, screening of single nucleotide polymorphism (SNPs) requires simple and straightforward strategies capable to provide results in medium throughput settings. Suitable approaches relying on isothermal amplification techniques have been evolving to substitute the cumbersome and highly specialized PCR amplification detection schemes. Nonetheless, identification of an individual's genotype still requires sophisticated equipment and laborious methods...
December 2017: Biotechnology Reports
https://www.readbyqxmd.com/read/29120623/aptamer-based-elisa-assay-for-highly-specific-and-sensitive-detection-of-zika-ns1-protein
#15
Kyung Hyun Lee, Huaqiang Zeng
We report here a few Zika NS1-binding ssDNA aptamers selected using the conventional SELEX protocol, and their application in an ELISA assay for sensitive diagnosis of Zika NS1 protein. Among the aptamers identified, aptamers 2 and 10 could recognize different binding epitopes of Zika NS1 protein. This complementary in binding site, when coupled with an extraordinarily high binding affinity by 2 (41-nt, KD = 45 pM) and high specificity by 10, was used successfully to construct an ELISA-based assay where 2 and 10 serve as the capture and detection agents, respectively, giving rise to a highly specific detection of Zika NS1 with a detection limit of 100 ng/mL in buffer...
November 9, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29114244/phage-and-nucleocytoplasmic-large-viral-sequences-dominate-coral-viromes-from-the-arabian-gulf
#16
Huda Mahmoud, Liny Jose
Corals that naturally thrive under extreme conditions are gaining increasing attention due to their importance as living models to understand the impact of global warming on world corals. Here, we present the first metagenomic study of viral communities in corals thriving in a thermally variable water body in which the temperature fluctuates between 11 and 39°C in different seasons. The viral assemblages of two of the most abundant massive (Porites harrisoni) and branching (Acropora downingi) corals in offshore and inshore reef systems in the northern Arabian Gulf were investigated...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29111738/binary-superlattice-design-by-controlling-dna-mediated-interactions
#17
Minseok Song, Yajun Ding, Hasan Zerze, Mark A Snyder, Jeetain Mittal
Most binary superlattices created using DNA functionalization rely on particle size differences to achieve compositional order and structural diversity. Here we study two-dimensional (2D) assembly of DNA-functionalized micron- sized particles (DFPs), and employ a strategy that leverages the tunable disparity in interparticle interactions, and thus enthalpic driving forces, to open new avenues for design of binary superlattices that do not rely on the ability to tune particle size (i.e., entropic driving forces)...
November 7, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29107578/facile-detection-of-microrna-based-on-phosphorescence-resonance-energy-transfer-and-duplex-specific-nuclease-assisted-signal-amplification
#18
Jia-Jia Yang, Zhi-Feng Zhang, Gui-Qin Yan
MicroRNAs (miRNAs) play an important role in many biological processes, and its level in plasma and other biological fluids is closely related to many diseases. In this work, a selective room-temperature phosphorescence (RTP) detection method for miRNA was developed based on a duplex-specific nuclease (DSN) -assisted signal amplification strategy and phosphorescence resonance energy transfer (PRET) between poly-diallyldimethylammonium chloride-modified quantum dots (QDs@PDDA) and 6-carboxy-X-rhodamine-modified miRNA sequences complementary oligonucleotide (ROX-ssDNA)...
October 28, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/29104981/mechanism-of-the-formation-of-the-reca-ssdna-nucleoprotein-filament-structure-a-coarse-grained-approach
#19
Goutam Mukherjee, Arumay Pal, Yaakov Levy
In prokaryotes, the RecA protein catalyzes the repair and strand exchange of double-stranded DNA. RecA binds to single-stranded DNA (ssDNA) and forms a presynaptic complex in which the protein polymerizes around the ssDNA to form a right-handed helical nucleoprotein filament structure. In the present work, the mechanism for the formation of the RecA-ssDNA filament structure is modeled using coarse-grained molecular dynamics simulations. Information from the X-ray structure was used to model the protein itself but not its interactions; the interactions between the protein and the ssDNA were modeled solely by electrostatic, aromatic, and repulsive energies...
November 6, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/29099837/using-long-ssdna-polynucleotides-to-amplify-strs-loci-in-degraded-dna-samples
#20
Martín E Mautner, Agustín Pérez Santángelo, Rodrigo M Corti Bielsa, Andrea Sala, Santiago Ginart, Daniel Corach
Obtaining informative short tandem repeat (STR) profiles from degraded DNA samples is a challenging task usually undermined by locus or allele dropouts and peak-high imbalances observed in capillary electrophoresis (CE) electropherograms, especially for those markers with large amplicon sizes. We hereby show that the current STR assays may be greatly improved for the detection of genetic markers in degraded DNA samples by using long single stranded DNA polynucleotides (ssDNA polynucleotides) as surrogates for PCR primers...
2017: PloS One
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