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https://www.readbyqxmd.com/read/28213234/dna-wrapped-multi-walled-carbon-nanotube-modified-electrochemical-biosensor-for-the-detection-of-escherichia-coli-from-real-samples
#1
Dilsat Ozkan-Ariksoysal, Yasin Ugur Kayran, Fethiye Ferda Yilmaz, Anton Alexandru Ciucu, Iulia Gabriela David, Vasile David, Mine Hosgor-Limoncu, Mehmet Ozsoz
This paper introduces DNA-wrapped multi-walled carbon nanotube (MWCNT)-modified genosensor for the detection of Escherichia coli (E. coli) from polymerase chain reaction (PCR)-amplified real samples while Staphylococcus aureus (S. aureus) was used to investigate the selectivity of the biosensor. The capture probe specifically recognizing E. coli DNA and it was firstly interacted with MWCNTs for wrapping of single-stranded DNA (ssDNA) onto the nanomaterial. DNA-wrapped MWCNTs were then immobilised on the surface of disposable pencil graphite electrode (PGE) for the detection of DNA hybridization...
May 1, 2017: Talanta
https://www.readbyqxmd.com/read/28211680/two-way-gold-nanoparticle-label-free-sensing-of-specific-sequence-and-small-molecule-targets-using-switchable-concatemers
#2
Longjiao Zhu, Xiangli Shao, Yunbo Luo, Kunlun Huang, Wentao Xu
A two-way colorimetric biosensor based on unmodified gold nanoparticles (GNPs) and a switchable double-stranded DNA (dsDNA) concatemer have been demonstrated. Two hairpin probes (H1&H2) were first designed that provided the fuels to assemble the dsDNA concatemers via hybridization chain reaction (HCR). A functional hairpin (FH) was rationally designed to recognize the target sequences. All the hairpins contained single-stranded DNA (ssDNA) loop and sticky-ends to prevent GNPs from salt-induced aggregation. In the presence of target sequence, the capture probe blocked in the FH recognizes the target to form a duplex DNA, which causes the release of the initiator probe by FH conformational change...
February 17, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28211448/cx-5461-is-a-dna-g-quadruplex-stabilizer-with-selective-lethality-in-brca1-2-deficient-tumours
#3
Hong Xu, Marco Di Antonio, Steven McKinney, Veena Mathew, Brandon Ho, Nigel J O'Neil, Nancy Dos Santos, Jennifer Silvester, Vivien Wei, Jessica Garcia, Farhia Kabeer, Daniel Lai, Priscilla Soriano, Judit Banáth, Derek S Chiu, Damian Yap, Daniel D Le, Frank B Ye, Anni Zhang, Kelsie Thu, John Soong, Shu-Chuan Lin, Angela Hsin Chin Tsai, Tomo Osako, Teresa Algara, Darren N Saunders, Jason Wong, Jian Xian, Marcel B Bally, James D Brenton, Grant W Brown, Sohrab P Shah, David Cescon, Tak W Mak, Carlos Caldas, Peter C Stirling, Phil Hieter, Shankar Balasubramanian, Samuel Aparicio
G-quadruplex DNAs form four-stranded helical structures and are proposed to play key roles in different cellular processes. Targeting G-quadruplex DNAs for cancer treatment is a very promising prospect. Here, we show that CX-5461 is a G-quadruplex stabilizer, with specific toxicity against BRCA deficiencies in cancer cells and polyclonal patient-derived xenograft models, including tumours resistant to PARP inhibition. Exposure to CX-5461, and its related drug CX-3543, blocks replication forks and induces ssDNA gaps or breaks...
February 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/28206680/an-ssdna-aptamer-against-mannose-capped-lipoarabinomannan-enhances-anti-tuberculosis-activity-of-macrophages-through-downregulation-of-lipid-sensing-nuclear-receptor-peroxisome-proliferator-activated-receptor-%C3%AE-expression
#4
Qin Pan, Jiamin Yan, Qi Liu, Chunhui Yuan, Xiao-Lian Zhang
Mannose-capped lipoarabinomannan (ManLAM) is an immunomodulatory epitope of Mycobacterium tuberculosis (Mtb). We previously generated an aptamer (ZXL1) that specifically binds to ManLAM from the virulent Mtb H37Rv strain and reported that ZXL1 functioned as an antagonist, inhibiting the ManLAM-induced immunosuppression of dendritic cells (DCs). In the present study, we found that ZXL1 inhibited Mtb entry into murine macrophages. ZXL1 enhanced IL-1β and IL-12 mRNA expression and cytokine production in ManLAM-treated macrophages but decreased IL-10 production...
February 16, 2017: Microbiology and Immunology
https://www.readbyqxmd.com/read/28202543/nucleosome-like-ssdna-histone-octamer-complexes-and-the-implication-for-dna-double-strand-break-repair
#5
Nicholas L Adkins, Sarah G Swygert, Parminder Kaur, Hengyao Niu, Sergei A Grigoryev, Patrick Sung, Hong Wang, Craig L Peterson
Repair of DNA double strand breaks (DSBs) is key for maintenance of genome integrity. When DSBs are repaired by homologous recombination, DNA ends can undergo extensive processing, producing long stretches of single-stranded DNA (ssDNA). In vivo, DSB processing occurs in the context of chromatin, and studies indicate that histones may remain associated with processed DSBs. Here we demonstrate that histones are not evicted from ssDNA after in vitro chromatin resection. In addition, we reconstitute histone-ssDNA complexes (termed ssNucs) with ssDNA and recombinant histones and analyze these particles by a combination of native gel electrophoresis, sedimentation velocity, electron microscopy, and a recently developed electrostatic force microscopy technique, DREEM (Dual-Resonance-frequency-Enhanced Electrostatic force Microscopy)...
February 15, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28193151/extraction-of-ultrashort-dna-molecules-from-herbarium-specimens
#6
Rafal M Gutaker, Ella Reiter, Anja Furtwängler, Verena J Schuenemann, Hernán A Burbano
DNA extracted from herbarium specimens is highly fragmented; therefore, it is crucial to use extraction protocols that retrieve short DNA molecules. Improvements in extraction and DNA library preparation protocols for animal remains have allowed efficient retrieval of molecules shorter than 50 bp. Here, we applied these improvements to DNA extraction protocols for herbarium specimens and evaluated extraction performance by shotgun sequencing, which allows an accurate estimation of the distribution of DNA fragment lengths...
February 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28192924/revealing-and-resolving-the-restrained-enzymatic-cleavage-of-dna-self-assembled-monolayers-on-gold-electrochemical-quantitation-and-esi-ms-confirmation
#7
Xiaoyi Gao, Mingxi Geng, Yunchao Li, Xinglin Wang, Hua-Zhong Yu
Herein, we report a combined electrochemical and ESI-MS study of the enzymatic hydrolysis efficiency of DNA self-assembled monolayers (SAMs) on gold, platform systems for understanding nucleic acid surface chemistry, and for constructing DNA-based biosensors. Our electrochemical approach is based on the comparison of the amounts of surface-tethered DNA nucleotides before and after exonuclease I (Exo I) incubation using electrostatically bound [Ru(NH3)6](3+) as redox indicators. It is surprising to reveal that the hydrolysis efficiency of ssDNA SAMs does not depend on the packing density and base sequence, and that the cleavage ends with surface-bound shorter strands (9-13 mers)...
February 9, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28188145/structural-studies-of-rfc-c-tf18-reveal-a-novel-chromatin-recruitment-role-for-dcc1
#8
Benjamin O Wade, Hon Wing Liu, Catarina P Samora, Frank Uhlmann, Martin R Singleton
Replication factor C complexes load and unload processivity clamps from DNA and are involved in multiple DNA replication and repair pathways. The RFC(C)(tf18) variant complex is required for activation of the intra-S-phase checkpoint at stalled replication forks and aids the establishment of sister chromatid cohesion. Unlike other RFC complexes, RFC(C)(tf18) contains two non-Rfc subunits, Dcc1 and Ctf8. Here, we present the crystal structure of the Dcc1-Ctf8 heterodimer bound to the C-terminus of Ctf18. We find that the C-terminus of Dcc1 contains three-winged helix domains, which bind to both ssDNA and dsDNA We further show that these domains are required for full recruitment of the complex to chromatin, and correct activation of the replication checkpoint...
February 10, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28182975/fluorescent-on-off-on-switching-sensor-based-on-cdte-quantum-dots-coupled-with-multiwalled-carbon-nanotubes-graphene-oxide-nanoribbons-for-simultaneous-monitoring-of-dual-foreign-dnas-in-transgenic-soybean
#9
Yaqi Li, Li Sun, Jing Qian, Lingliang Long, Henan Li, Qian Liu, Jianrong Cai, Kun Wang
With the increasing concern of potential health and environmental risk, it is essential to develop reliable methods for transgenic soybean detection. Herein, a simple, sensitive and selective assay was constructed based on homogeneous fluorescence resonance energy transfer (FRET) between CdTe quantum dots (QDs) and multiwalled carbon nanotubes@graphene oxide nanoribbons (MWCNTs@GONRs) to form the fluorescent "on-off-on" switching for simultaneous monitoring dual target DNAs of promoter cauliflower mosaic virus 35s (P35s) and terminator nopaline synthase (TNOS) from transgenic soybean...
January 28, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28177605/replication-protein-a-prohibits-diffusion-of-the-pcna-sliding-clamp-along-single-stranded-dna
#10
Mark Hedglin, Stephen J Benkovic
The replicative polymerases cannot accommodate distortions to the native DNA sequence such as modifications (lesions) to the native template bases from exposure to reactive metabolites and environmental mutagens. Consequently, DNA synthesis on an afflicted template abruptly stops upon encountering these lesions but the replication fork progresses onward, exposing long stretches of the damaged template before eventually stalling. Such arrests may be overcome by translesion DNA synthesis where a specialized TLS polymerases binds to the resident PCNA and replicates the damaged DNA...
February 8, 2017: Biochemistry
https://www.readbyqxmd.com/read/28176452/overlooking-the-smallest-matter-viruses-impact-biological-invasions
#11
REVIEW
Cara A Faillace, Nicholas S Lorusso, Siobain Duffy
Parasites and pathogens have recently received considerable attention for their ability to affect biological invasions, however, researchers have largely overlooked the distinct role of viruses afforded by their unique ability to rapidly mutate and adapt to new hosts. With high mutation and genomic substitution rates, RNA and single-stranded DNA (ssDNA) viruses may be important constituents of invaded ecosystems, and could potentially behave quite differently from other pathogens. We review evidence suggesting that rapidly evolving viruses impact invasion dynamics in three key ways: (1) Rapidly evolving viruses may prevent exotic species from establishing self-sustaining populations...
February 8, 2017: Ecology Letters
https://www.readbyqxmd.com/read/28168694/the-optimization-of-electrophoresis-on-a-glass-microfluidic-chip-and-its-application-in-forensic-science
#12
Jun P Han, Jing Sun, Le Wang, Peng Liu, Bin Zhuang, Lei Zhao, Yao Liu, Cai X Li
Microfluidic chips offer significant speed, cost, and sensitivity advantages, but numerous parameters must be optimized to provide microchip electrophoresis detection. Experiments were conducted to study the factors, including sieving matrices (the concentration and type), surface modification, analysis temperature, and electric field strengths, which all impact the effectiveness of microchip electrophoresis detection of DNA samples. Our results showed that the best resolution for ssDNA was observed using 4...
February 7, 2017: Journal of Forensic Sciences
https://www.readbyqxmd.com/read/28167766/genome-wide-transcription-coupled-repair-in-escherichia-coli-is-mediated-by-the-mfd-translocase
#13
Ogun Adebali, Yi-Ying Chiou, Jinchuan Hu, Aziz Sancar, Christopher P Selby
We used high-throughput sequencing of short, cyclobutane pyrimidine dimer-containing ssDNA oligos generated during repair of UV-induced damage to study that process at both mechanistic and systemic levels in Escherichia coli Numerous important insights on DNA repair were obtained, bringing clarity to the respective roles of UvrD helicase and Mfd translocase in repair of UV-induced damage. Mechanistically, experiments showed that the predominant role of UvrD in vivo is to unwind the excised 13-mer from dsDNA and that mutation of uvrD results in remarkable protection of that oligo from exonuclease activity as it remains hybridized to the dsDNA...
February 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28161951/selection-and-application-of-ssdna-aptamers-against-clenbuterol-hydrochloride-based-on-ssdna-library-immobilized-selex
#14
Nuo Duan, Wenhui Gong, Shijia Wu, Zhouping Wang
Clenbuterol Hydrochloride (CLB) is often abused as additive feed for livestock to decrease adipose tissue deposition and increase growth rate. It raised a potential risk to human health through the animal product consume. In this study, aptamers with higher affinity and specificity was screened through sixteen selection rounds based on ssDNA library immobilized systematic evolution of ligands by exponential enrichment (SELEX) technique. After cloning and sequencing, five aptamer candidates were picked out for affinity and specificity assays based on graphene oxide (GO) adsorption method...
February 6, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28159667/a-novel-method-for-detection-of-h9n2-influenza-viruses-by-an-aptamer-real-time-pcr
#15
Issam Hmila, Manoosak Wongphatcharachai, Nacira Laamiri, Rim Aouini, Boutheina Marnissi, Marwa Arbi, Srinand Sreevatsan, Abdeljelil Ghram
H9N2 Influenza subtype has emerged in Tunisia causing epidemics in poultry and resulting in major economic losses. New mutations in their hemagglutinin and neuraminidase proteins were acquired, suggesting their potential to directly infect humans. Effective surveillance tools should be implemented to help prevent potential spillover of the virus across species. We have developed a highly sensitive real time immuno-polymerase chain reaction (RT-I-PCR) method for detecting H9N2 virus. The assay applies aptamers as ligands to capture and detect the virus...
January 31, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28155197/revisiting-the-taxonomy-of-the-family-circoviridae-establishment-of-the-genus-cyclovirus-and-removal-of-the-genus-gyrovirus
#16
Karyna Rosario, Mya Breitbart, Balázs Harrach, Joaquim Segalés, Eric Delwart, Philippe Biagini, Arvind Varsani
The family Circoviridae contains viruses with covalently closed, circular, single-stranded DNA (ssDNA) genomes, including the smallest known autonomously replicating, capsid-encoding animal pathogens. Members of this family are known to cause fatal diseases in birds and pigs and have been historically classified in one of two genera: Circovirus, which contains avian and porcine pathogens, and Gyrovirus, which includes a single species (Chicken anemia virus). However, over the course of the past six years, viral metagenomic approaches as well as degenerate PCR detection in unconventional hosts and environmental samples have elucidated a broader host range, including fish, a diversity of mammals, and invertebrates, for members of the family Circoviridae...
February 2, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28153300/a-colorimetric-fluorescent-dual-mode-sensor-for-ultra-sensitive-detection-of-hg-2
#17
Tao Yu, Ting-Ting Zhang, Wei Zhao, Jing-Juan Xu, Hong-Yuan Chen
A highly sensitive colorimetric/fluorescent dual-mode sensor based on hybridization chain reaction (HCR) combining multifunctional Au NPs is presented for the detection of Hg(2+) in aqueous solution. In Hg(2+) absent solution, the surface of Au NPs was covered by hairpin auxiliary DNAs and a single strand DNA (ssDNA), which prevented Au NPs from salt-induced aggregation. At the same time, the fluorescence intensity of the dye-labeled hairpin probes was significantly quenched by Au NPs. In the presence of Hg(2+), T-Hg(2+)-T coordination chemistry between helper DNA and the hairpin probes was induced which triggered the formation of extended double-stranded DNA (dsDNA) polymers via HCR...
April 1, 2017: Talanta
https://www.readbyqxmd.com/read/28148987/gene-specific-impedimetric-bacterial-dna-sensor-for-rheumatic-heart-disease
#18
Swati Singh, Ankur Kaushal, Sunil Gupta, Ashok Kumar
An impedimetric mga gene specific DNA sensor was developed by immobilization of single stranded DNA probe onto the screen printed modified gold-dendrimer nanohybrid composite electrode for early and rapid detection of S. pyogenes in human throat swab samples causing rheumatic heart disease. Electrochemical impedance response was measured after hybridization with bacterial single stranded genomic DNA (ssG-DNA) with probe. The sensor was found highly specific to S. pyogenes and can detect as low as 0.01 ng ssDNA in 6 µL sample only in 30 min...
March 2017: Indian Journal of Microbiology
https://www.readbyqxmd.com/read/28147483/a-dna-bubble-mediated-gene-regulation-system-based-on-thrombin-bound-dna-aptamers
#19
Jing Wang, Le Yang, Xun Cui, Zhe Zhang, Lichun Dong, Ningzi Guan
We describe here a novel approach to enhance the transcription of target gene in cell-free systems by symmetrically introducing duplex aptamers upstream to T7 promoter in both the sense and antisense strands of double-stranded plasmids, which leads to the formation of a DNA bubble due to the none-complementary state of the ssDNA region harboring the aptamer sequences. With the presence of thrombins, the DNA bubble would be enlarged due to the binding of aptamers with thrombins. Consequently, the recognition region of the promoter contained in the DNA bubble can be more easily recognized and bound by RNA polymerases, and the separation efficiency of the unwinding region can also be significantly improved, leading to the enhanced expression of the target gene at the transcriptional level...
February 1, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28134253/specialized-interfaces-of-smc5-6-control-hinge-stability-and-dna-association
#20
Aaron Alt, Hung Q Dang, Owen S Wells, Luis M Polo, Matt A Smith, Grant A McGregor, Thomas Welte, Alan R Lehmann, Laurence H Pearl, Johanne M Murray, Antony W Oliver
The Structural Maintenance of Chromosomes (SMC) complexes: cohesin, condensin and Smc5/6 are involved in the organization of higher-order chromosome structure-which is essential for accurate chromosome duplication and segregation. Each complex is scaffolded by a specific SMC protein dimer (heterodimer in eukaryotes) held together via their hinge domains. Here we show that the Smc5/6-hinge, like those of cohesin and condensin, also forms a toroidal structure but with distinctive subunit interfaces absent from the other SMC complexes; an unusual 'molecular latch' and a functional 'hub'...
January 30, 2017: Nature Communications
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