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https://www.readbyqxmd.com/read/28811015/multiple-targeted-graphene-based-nanocarrier-for-intracellular-imaging-of-mrnas
#1
Ying Wang, Zhaohui Li, Misha Liu, Jinjin Xu, Dehong Hu, Yuehe Lin, Jinghong Li
Simultaneous detection and imaging of multiple intracellular messenger RNA (mRNAs) hold great significant for early cancer diagnostics and preventive medicine development. Herein, we propose a multiple-targeted graphene oxide (GO) nanocarrier that can simultaneously detect and image different type mRNAs in living cells. First of all, in vitro detection of multiple targets have been realized successfully based on the multiple-targeted GO nanocarrier with linear relationship ranging from 3 nM to 200 nM, as well as sensitive detection limit of 1...
August 29, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28808061/structural-analyses-of-the-bacterial-primosomal-protein-dnab-reveal-that-it-is-a-tetramer-and-forms-a-complex-with-a-primosomal-re-initiation-protein
#2
Yi-Ching Li, Vankadari Naveen, Min-Guan Lin, Chwan-Deng Hsiao
The DnaB primosomal protein from Gram-positive bacteria plays a key role in DNA replication and restart as a loader protein for the recruitment of replisome cascade proteins. Previous investigations have established that DnaB is composed of an N-terminal domain, a middle domain, and a C-terminal domain. However, structural evidence for how DnaB functions at the atomic level is lacking. Here, we report the crystal structure of DnaB, encompassing the N-terminal and middle domains (residues 1-300), from Geobacillus stearothermophilus (GstDnaB1-300) at 2...
August 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28808047/hr-intermediates-can-induce-chromosomal-translocations
#3
(no author information available yet)
Multi-invasions (MI) are HR intermediates formed when a ssDNA invades two dsDNA.
August 14, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28791533/elucidation-of-the-mechanism-of-increased-activity-of-immunostimulatory-dna-by-the-formation-of-polypod-like-structure
#4
Kohta Mohri, Kengo Nagata, Shozo Ohtsuki, Shiori Toyama, Mao Nonomura, Yuki Takahashi, Yoshinobu Takakura, Makiya Nishikawa, Shinji Sakuma
PURPOSE: We previously demonstrated that the immunostimulatory activity of CpG DNA is increased by the formation of polypod-like structures. The present study was designed to elucidate the mechanism underlying this increase. METHODS: Tripodna (three pods) and hexapodna (six pods) were prepared. The cellular uptake of Alexa Fluor 488-labeled DNA samples was examined in several cell lines by measuring the MFI of cells. TNF-α release from RAW264.7 cells was measured after addition of polypodna containing CpG motifs...
August 8, 2017: Pharmaceutical Research
https://www.readbyqxmd.com/read/28782560/glutamate-promotes-ssb-protein-protein-interactions-via-intrinsically-disordered-regions
#5
Alexander G Kozlov, Min Kyung Shinn, Elizabeth A Weiland, Timothy M Lohman
E. coli single strand (ss) DNA binding protein (SSB) is an essential protein that binds to ssDNA intermediates formed during genome maintenance. SSB homotetramers bind ssDNA in several modes that differ in occluded site size and cooperativity. High "unlimited" cooperativity is associated with the 35 site size ((SSB)35) mode at low [NaCl], whereas the 65 site size ((SSB)65) mode formed at higher [NaCl] (> 200mM), where ssDNA wraps completely around the tetramer, displays "limited" cooperativity forming dimers of tetramers...
August 3, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28780638/discrimination-of-adsorbed-double-stranded-and-single-stranded-dna-molecules-on-surfaces-by-fluorescence-emission-spectroscopy-using-acridine-orange-dye
#6
E Hoory, J Budassi, E Pfeffer, N Cho, J Thalappillil, J Andersen, M Rafailovich, J Sokolov
A sensitive and straightforward method for discriminating between surface-adsorbed double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA), based on analysis of the fluorescence emission spectra of DNAs dyed with the metachromatic dye acridine orange, has been developed. Since the degree of discrimination between dsDNA and ssDNA is dependent on dye-base ratio (as has been shown in early studies of DNAs in solution), a specific, reproducible protocol for obtaining good ss-ds discrimination was needed. We studied the emission spectra for DNAs dyed in-situ on two different surfaces, polymethylmethacrylate and poly-l-lysine, using acridine orange solutions of varying concentrations in either 2-(N-morpholino)ethanesulfonic acid (MES) or Tris-Borate EDTA (TBE) buffers...
August 5, 2017: Journal of Fluorescence
https://www.readbyqxmd.com/read/28756274/biophysical-characterization-of-the-association-of-histones-with-single-stranded-dna
#7
Ying Wang, Luis van Merwyk, Katja Tönsing, Volker Walhorn, Dario Anselmetti, Xavier Fernàndez-Busquets
BACKGROUND: Despite the profound current knowledge of the architecture and dynamics of nucleosomes, little is known about the structures generated by the interaction of histones with single-stranded DNA (ssDNA), which is widely present during replication and transcription. METHODS: Non-denaturing gel electrophoresis, transmission electron microscopy, atomic force microscopy, magnetic tweezers. RESULTS: Histones have a high affinity for ssDNA in 0...
July 27, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28743747/the-ul8-subunit-of-the-helicase-primase-complex-of-herpes-simplex-virus-promotes-dna-annealing-and-has-a-high-affinity-for-replication-forks
#8
Oya Bermek, Sandra K Weller, Jack D Griffith
During lytic infection, herpes simplex virus (HSV) DNA is replicated by a mechanism involving DNA recombination. For instance, replication of the HSV-1 genome produces X- and Y-branched structures, reminiscent of recombination intermediates. HSV-1's replication machinery includes a trimeric helicase/primase is composed of helicase (UL5) and primase (UL52) subunits and a third subunit, UL8. UL8 has been reported to stimulate the helicase and primase activities of the complex in the presence of ICP8, an HSV-1 protein that functions as an annealase, a protein that binds complementary single-stranded (ss)DNA and facilitates its annealing to duplex DNA...
July 25, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28741345/direct-detection-of-nucleic-acid-with-minimizing-background-and-improving-sensitivity-based-on-a-conformation-discriminating-indicator
#9
Lixuan Zhu, Zhihe Qing, Lina Hou, Sheng Yang, Zhen Zou, Zhong Cao, Ronghua Yang
As well known, the nucleic acid indicator-based strategy is one of the major approaches to monitor the nucleic acid hybridization-mediated recognition events in biochemical analysis, displaying obvious advantages including simplicity, low-cost, convenience and generality. However, conventional indicators either hold strong self-fluorescence or can be lighted by both ssDNA and dsDNA, lacking absolute selectivity for a certain conformation, always with high-background interference and low sensitivity in sensing; and additional processing (e...
July 25, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28738593/boron-nitride-nanosheets-as-a-platform-for-fluorescence-sensing
#10
Yuanjin Zhan, Jingjing Yan, Mei Wu, Longhua Guo, Zhenyu Lin, Bin Qiu, Guonan Chen, Kwok-Yin Wong
Hexagonal boron nitride nanosheets (BNNS), one kind of inorganic graphene analogue, exhibit high fluorescence quenching ability via the photo-induced electron transfer (PET) and different affinity toward single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). As a proof of concept, the BNNS was first used as a sensing platform for the rapid detection of DNA and small molecules with high sensitivity and selectivity in this study. This strategy is versatile and quick fluorescence sensing of DNA and extensive DNA related analytes such as metal cations and small molecules...
November 1, 2017: Talanta
https://www.readbyqxmd.com/read/28738244/dna-binding-and-unwinding-by-hel308-helicase-requires-dual-functions-of-a-winged-helix-domain
#11
Sarah J Northall, Ryan Buckley, Nathan Jones, J Carlos Penedo, Panos Soultanas, Edward L Bolt
Hel308 helicases promote genome stability linked to DNA replication in archaea, and have homologues in metazoans. In the crystal structure of archaeal Hel308 bound to a tailed DNA duplex, core helicase domains encircle single-stranded DNA (ssDNA) in a "ratchet" for directional translocation. A winged helix domain (WHD) is also present, but its function is mysterious. We investigated the WHD in full-length Hel308, identifying that mutations in a solvent exposed α-helix resulted in reduced DNA binding and unwinding activities...
July 16, 2017: DNA Repair
https://www.readbyqxmd.com/read/28736786/an-enzyme-free-flow-cytometric-bead-assay-for-the-sensitive-detection-of-micrornas-based-on-click-nucleic-acid-ligation-mediated-signal-amplification
#12
Yan Qi, Liying Qiu, Wenjiao Fan, Chenghui Liu, Zhengping Li
A versatile flow cytometric bead assay (FCBA) coupled with a completely enzyme-free signal amplification mechanism is developed for the sensitive detection of microRNAs (miRNAs). This new strategy integrates click chemistry-mediated ligation chain reaction (CLCR) with hybridization chain reaction (HCR) for enzyme-free signal amplification on magnetic beads (MBs), and a flow cytometer for the robust fluorescence readout of the MBs. Firstly, target miRNA can initiate CLCR on the surface of MBs based on the click chemical ligation between dibenzocyclooctyne (DBCO)- and azide-modified single-stranded DNA (ssDNA) probes, and the amount of ligated ssDNA sequences on the MBs will be proportional to the dosage of target miRNA...
August 7, 2017: Analyst
https://www.readbyqxmd.com/read/28726394/human-cst-prefers-g-rich-but-not-necessarily-telomeric-sequences
#13
Robert A Hom, Deborah S Wuttke
The human CST (CTC1-STN1-TEN1) heterotrimeric complex plays roles in both telomere maintenance and DNA replication through its ability to interact with single-stranded DNA (ssDNA) of a variety of sequences. The precise sequence specificity required to execute these functions is unknown. Telomere-binding proteins have been shown to specifically recognize key telomeric sequence motifs within ssDNA while accommodating nonspecifically recognized sequences through conformationally plastic interfaces. To better understand the role CST plays in these processes, we have produced a highly purified heterotrimer and elucidated the sequence requirements for CST recognition of ssDNA in vitro...
August 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/28726373/ultrasensitive-homogeneous-electrochemical-detection-of-transcription-factor-by-coupled-isothermal-cleavage-reaction-and-cycling-amplification-based-on-exonuclease-iii
#14
Lihua Lu, Huijuan Su, Feng Li
The assay and monitoring of transcription factors (TFs) has attracted extensive attention due to their important roles in regulation of gene expressions. Herein, a simple, low cost, rapid, and highly sensitive homogeneous electrochemical method utilizing the coupled isothermal cleavage reaction and cycling amplification based on exonuclease III (Exo III) was explored for the analysis of transcription factor NF-κB p50 in aqueous solution. In the assay, a 3'-methylene blue (MB)-labeled hairpin probe is designed, which can be opened up by the single stranded DNA (ssDNA) protected by NF-κB p50 from the Exo III cleavage, to trigger the subsequent Exo III-assisted digestion, thus a large amount of MB-labeled mononucleotides are liberated to result in the greatly amplified electrochemical signal...
August 3, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28716906/virus-found-in-a-boreal-lake-links-ssdna-and-dsdna-viruses
#15
Elina Laanto, Sari Mäntynen, Luigi De Colibus, Jenni Marjakangas, Ashley Gillum, David I Stuart, Janne J Ravantti, Juha T Huiskonen, Lotta-Riina Sundberg
Viruses have impacted the biosphere in numerous ways since the dawn of life. However, the evolution, genetic, structural, and taxonomic diversity of viruses remain poorly understood, in part because sparse sampling of the virosphere has concentrated mostly on exploring the abundance and diversity of dsDNA viruses. Furthermore, viral genomes are highly diverse, and using only the current sequence-based methods for classifying viruses and studying their phylogeny is complicated. Here we describe a virus, FLiP (Flavobacterium-infecting, lipid-containing phage), with a circular ssDNA genome and an internal lipid membrane enclosed in the icosahedral capsid...
August 1, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28714285/dynamic-cooperation-of-hydrogen-binding-and-%C3%AF-stacking-in-ssdna-adsorption-on-graphene-oxide
#16
Zhen Xu, Xiaoling Lei, Yusong Tu, Zhi-Jie Tan, Bo Song, Haiping Fang
Functional nanoscale structures consisting of a DNA molecule coupled to graphene or graphene oxide (GO) have great potential for applications in biosensors, biomedicine, nanotechnology, and materials science. Extensive studies using the most sophisticated experimental techniques and theoretical methods have still not clarified the dynamic process of single-stranded DNA (ssDNA) adsorbed on a GO surface. Based on a molecular dynamics simulation, this work shows that an ssDNA segment could be stably adsorbed on a GO surface through hydrogen bonding and a π-π stacking interaction, with preferential binding to an oxidized region rather than to an unoxidized region of the GO surface...
July 16, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28710290/3-terminated-overhangs-regulate-dna-double-strand-break-processing-in-escherichia-coli
#17
Edyta Đermić, Davor Zahradka, Dušica Vujaklija, Siniša Ivanković, Damir Đermić
Double-strand breaks (DSBs) are lethal DNA lesions, which are repaired by homologous recombination in Escherichia coli To study DSB processing in vivo, we induced DSBs into the E. coli chromosome by gamma irradiation and measured chromosomal degradation. We show that the DNA degradation is regulated by RecA protein concentration and its rate of association with ssDNA. RecA decreased DNA degradation in wild-type, recB and recD strains, indicating that it is a general phenomenon in E. coli On the other hand, DNA degradation was greatly reduced and unaffected by RecA in the recB1080 mutant (which produces long overhangs) and in a strain devoid of four exonucleases that degrade a 3' tail (ssExos)...
July 14, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28707271/identification-and-genetic-characterization-of-a-novel-circular-single-stranded-dna-virus-in-a-human-upper-respiratory-tract-sample
#18
Lunbiao Cui, Binyao Wu, Xiaojuan Zhu, Xiling Guo, Yiyue Ge, Kangchen Zhao, Xian Qi, Zhiyang Shi, Fengcai Zhu, Lixin Sun, Minghao Zhou
Metagenomic analysis through high-throughput sequencing is a tool for detecting both known and novel viruses. Using this technique, a novel circular single-stranded DNA (ssDNA) virus genome was discovered in respiratory secretions from a febrile traveler. The virus, named human respiratory-associated PSCV-5-like virus (HRAPLV), has a genome comprising 3,018 bases, with two major putative ORFs inversely encoding capsid (Cap) and replicase (Rep) protein and separated by two intergenic regions. One stem-loop structure was predicted in the larger intergenic region (LIR)...
July 13, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28696187/dpra-from-neisseria-meningitidis-properties-and-role-in-natural-competence-for-transformation
#19
Eirik Hovland, Getachew Tesfaye Beyene, Stephan A Frye, Håvard Homberset, Seetha V Balasingham, Marta Gómez-Muñoz, Jeremy P Derrick, Tone Tønjum, Ole H Ambur
DNA processing chain A (DprA) is a DNA-binding protein that is ubiquitous in bacteria and expressed in some archaea. DprA is active in many bacterial species that are competent for transformation of DNA, but its role in Neisseriameningitidis (Nm) is not well characterized. An Nm mutant lacking DprA was constructed, and the phenotypes of the wild-type and ΔdprA mutant were compared. The salient feature of the phenotype of dprA null cells is the total lack of competence for genetic transformation shown by all of the donor DNA substrates tested in this study...
July 12, 2017: Microbiology
https://www.readbyqxmd.com/read/28690254/mno2-nanosheet-based-fluorescence-sensing-platform-for-sensitive-detection-of-endonuclease
#20
Chao Hu, Xiang Juan Kong, Ru Qin Yu, Ting Ting Chen, Xia Chu
A novel fluorescence sensing platform for ultrasensitive detection of S1 nuclease activity has been constructed based on MnO2 nanosheets and FAM labeled single-stranded DNA (FAM-ssDNA). In this system, MnO2 nanosheets were found to have different adsorbent ability toward ssDNA and mono- or oligonucleotide fragments. FAM-ssDNA could adsorb on MnO2 nanosheets and resulted in significant fluorescence quenching through fluorescence resonance energy transfer (FRET), while mono- or oligonucleotide fragments could not adsorb on MnO2 nanosheets and still retained strong fluorescence emission...
2017: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
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