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https://www.readbyqxmd.com/read/28430587/parkin-regulates-translesion-dna-synthesis-in-response-to-uv-radiation
#1
Xuefei Zhu, Xiaolu Ma, Yingfeng Tu, Min Huang, Hongmei Liu, Fengli Wang, Juanjuan Gong, Jiuqiang Wang, Xiaoling Li, Qian Chen, Hongyan Shen, Shu Zhu, Yun Wang, Yang Liu, Caixia Guo, Tie-Shan Tang
Deficiency of Parkin is a major cause of early-onset Parkinson's disease (PD). Notably, PD patients also exhibit a significantly higher risk in melanoma and other skin tumors, while the mechanism remains largely unknown. In this study, we show that depletion of Parkin causes compromised cell viability and genome stability after ultraviolet (UV) radiation. We demonstrate that Parkin promotes efficient Rad18-dependent proliferating cell nuclear antigen (PCNA) monoubiquitination by facilitating the formation of Replication protein A (RPA)-coated ssDNA upon UV radiation...
April 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28422238/3d-single-molecule-tracking-enables-direct-hybridization-kinetics-measurement-in-solution
#2
Cong Liu, Judy M Obliosca, Yen-Liang Liu, Yu-An Chen, Ning Jiang, Hsin-Chih Yeh
Single-molecule measurements of DNA hybridization kinetics are mostly performed on a surface or inside a trap. Here we demonstrate a time-resolved, 3D single-molecule tracking (3D-SMT) method that allows us to follow a freely diffusing ssDNA molecule in solution for hundreds of milliseconds or even seconds and observe multiple annealing and melting events taking place on the same molecule. This is achieved by combining confocal-feedback 3D-SMT with time-domain fluorescence lifetime measurement, where fluorescence lifetime serves as the indicator of hybridization...
April 19, 2017: Nanoscale
https://www.readbyqxmd.com/read/28416680/using-microsecond-single-molecule-fret-to-determine-the-assembly-pathways-of-t4-ssdna-binding-protein-onto-model-dna-replication-forks
#3
Carey Phelps, Brett Israels, Davis Jose, Morgan C Marsh, Peter H von Hippel, Andrew H Marcus
DNA replication is a core biological process that occurs in prokaryotic cells at high speeds (∼1 nucleotide residue added per millisecond) and with high fidelity (fewer than one misincorporation event per 10(7) nucleotide additions). The ssDNA binding protein [gene product 32 (gp32)] of the T4 bacteriophage is a central integrating component of the replication complex that must continuously bind to and unbind from transiently exposed template strands during DNA synthesis. We here report microsecond single-molecule FRET (smFRET) measurements on Cy3/Cy5-labeled primer-template (p/t) DNA constructs in the presence of gp32...
April 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28416612/a-biochemical-and-biophysical-model-of-g-quadruplex-dna-recognition-by-positive-coactivator-of-transcription-4
#4
Wezley C Griffin, Jun Gao, Alicia K Byrd, Shubeena Chib, Kevin D Raney
DNA sequences that are guanine-rich have received considerable attention due to their potential to fold into a secondary, four-stranded DNA structure termed G-quadruplex (G4) which has been implicated in genomic instability and some human diseases. We have previously identified positive coactivator of transcription (PC4), a single-stranded DNA (ssDNA) binding protein, as a novel G4 interactor. Here, to expand on these previous observations, we biochemically and biophysically characterized the interaction between PC4 and G4DNA...
April 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28414900/precision-templated-bottom-up-multiprotein-nanoassembly-through-defined-click-chemistry-linkage-to-dna
#5
Gabriella Marth, Andrew M Hartley, Samuel C Reddington, Lauren L Sargisson, Marlène Parcollet, Katherine E Dunn, D Dafydd Jones, Eugen Stulz
We demonstrate an approach that allows attachment of single-stranded DNA (ssDNA) to a defined residue in a protein of interest (POI) so as to provide optimal and well-defined multicomponent assemblies. Using an expanded genetic code system, azido-phenylalanine (azF) was incorporated at defined residue positions in each POI; copper-free click chemistry was used to attach exactly one ssDNA at precisely defined residues. By choosing an appropriate residue, ssDNA conjugation had minimal impact on protein function, even when attached close to active sites...
April 20, 2017: ACS Nano
https://www.readbyqxmd.com/read/28414417/graphene-nanoprobes-for-real-time-monitoring-of-isothermal-nucleic-acid-amplification
#6
Fan Li, Xiaoguo Liu, Bin Zhao, Juan Yan, Qian Li, Ali Aldalbahi, Jiye Shi, Shiping Song, Chunhai Fan, Lihua Wang
Isothermal amplification is an efficient way to amplify DNA with high accuracy, however, the real-time monitoring for quantification analysis mostly relied on expensive and precisely designed probes. In the present study, Graphene oxide (GO)-based nano probe was used to real-time monitor the isothermal amplification process. The interaction between GO and different DNA structures was systematically investigated, including single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), DNA 3-helix, and long rolling circle amplification (RCA) and hybridization chain reaction (HCR) products, which existed in one-, two- and three-dimensional structures...
April 17, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28412544/phosphorylation-of-whirly1-by-cipk14-shifts-its-localization-and-dual-functions-in-arabidopsis
#7
Yujun Ren, Yanyun Li, Youqiao Jiang, Binghua Wu, Ying Miao
Plastid-to-nucleus retrograde signaling is critical for normal growth and development in plants. The dual-function and dual-located ssDNA binding protein WHIRLY1 (WHY1) has been supposed to coordinate the retrograde signaling from plastids to the nucleus. However, the regulatory mechanism governing the functional switch of WHY1 for mediating plastid-to-nucleus retrograde signaling remains unknown. Here we report that the Calcineurin B-Like-Interacting Protein Kinase14 (CIPK14) interacts with and phosphorylates WHY1 in Arabidopsis...
April 12, 2017: Molecular Plant
https://www.readbyqxmd.com/read/28411822/label-free-and-sensitive-assay-for-deoxyribonuclease-i-activity-based-on-enzymatically-polymerized-superlong-poly-thymine-hosted-fluorescent-copper-nanoparticles
#8
Lan Luo, Fengzhou Xu, Hui Shi, Xiaoxiao He, Taiping Qing, Yanli Lei, Jinlu Tang, Dinggeng He, Kemin Wang
Deoxyribonuclease I (DNase I) is an important physiological indicator and diagnostic biomarker, but traditional methods for assessing its activity are time-consuming, laborious, and usually radioactive. Herein, by effectively combining the special functions of DNase I and terminal deoxynucleotidyl transferase (TdT), a simple, green, cost-effective, label-free and ultrasensitive assay for DNase I activity has been constructed based on superlong poly(thymine)-hosted copper nanoparticles (poly T-CuNPs). In this strategy, a 3'-phosphorylated DNA primer is designed to block TdT polymerization...
July 1, 2017: Talanta
https://www.readbyqxmd.com/read/28411218/the-conjugative-relaxase-trwc-promotes-integration-of-foreign-dna-in-the-human-genome
#9
Coral González-Prieto, Richard Gabriel, Christoph Dehio, Manfred Schmidt, Matxalen Llosa
Bacterial conjugation is a mechanism of horizontal DNA transfer. The relaxase TrwC of the conjugative plasmid R388 cleaves one strand of the transferred DNA at the oriT, covalently attaches to it and leads the ssDNA into the recipient cell. In addition, TrwC catalyzes site-specific integration of the transferred DNA into its target sequence present in the genome of the recipient bacterium. Here, we report the analysis of the efficiency and specificity of the integrase activity of TrwC in human cells, using the Type IV Secretion System of the human pathogen Bartonella henselae to introduce relaxase-DNA complexes...
April 14, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28408432/1-n-6-%C3%AE-hydroxypropanoadenine-the-acrolein-adduct-to-adenine-is-a-substrate-for-alkb-dioxygenase
#10
Małgorzata Dylewska, Jarosław Tomasz Kuśmierek, Tomasz Pilzys, Jarosław Poznański, Agnieszka Monika Maciejewska
1,N(6)-α-hydroxypropanoadenine (HPA) is an exocyclic DNA adduct of acrolein - an environmental pollutant and endocellular oxidative stress product. E. coli AlkB dioxygenase belongs to the superfamily of α-ketoglutarate (αKG)- and iron-dependent dioxygenases which remove alkyl lesions from bases via an oxidative mechanism, thereby restoring native DNA structure. Here, we provide in vivo and in vitro evidence that HPA is mutagenic and is effectively repaired by AlkB dioxygenase. HPA generated in plasmid DNA caused A→C and A→T transversions and, less frequently, A→G transitions...
April 13, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28407412/adsorption-and-desorption-of-single-stranded-dna-from-single-walled-carbon-nanotubes
#11
Cameron James Shearer, LePing Yu, Renzo Fenati, Alex Sibley, Jamie Scott Quinton, Christopher Thomas Gibson, Amanda Vera Ellis, Gunther Andersson, Joseph George Shapter
The chemical affinity of single stranded DNA (ssDNA) to adsorb to the surface of single walled carbon nanotubes (SWCNTs) is used for SWCNT purification, separation and in bio-devices. Despite the popularity of research on SWCNT-ssDNA conjugates, very little work has been dedicated to study the removal of adsorbed ssDNA on SWCNTs. This paper reports a comprehensive study of biological, physical and chemical treatments for the removal of ssDNA from SWCNT-ssDNA suspensions. These include enzymatic cleavage, heat treatment under vacuum up to 400 oC, chemical treatments with high or low pH, oxidising conditions, and high ionic strength solvents...
April 13, 2017: Chemistry, An Asian Journal
https://www.readbyqxmd.com/read/28406641/quenching-of-single-walled-carbon-nanotube-fluorescence-by-dissolved-oxygen-reveals-selective-single-stranded-dna-affinities
#12
Yu Zheng, Sergei M Bachilo, R Bruce Weisman
The selective interactions between short oligomers of single-stranded DNA (ssDNA) and specific structures of single-walled carbon nanotubes have been exploited in powerful methods for nanotube sorting. We report here that nanotubes coated with ssDNA also display selective interactions through the selective quenching of nanotube fluorescence by dissolved oxygen. In aqueous solutions equilibrated under 1 atm of O2, emission intensity from semiconducting nanotubes is reduced by between 9 and 40%, varying with the combination of ssDNA sequence and nanotube structure...
April 13, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28403156/direct-fluorescence-detection-of-vire2-secretion-by-agrobacterium-tumefaciens
#13
Noga Yaakov, Yoav Barak, Idan Pereman, Peter J Christie, Michael Elbaum
VirE2 is a ssDNA binding protein essential for virulence in Agrobacterium tumefaciens. A tetracysteine mutant (VirE2-TC) was prepared for in vitro and in vivo fluorescence imaging based on the ReAsH reagent. VirE2-TC was found to be biochemically active as it binds both ssDNA and the acidic secretion chaperone VirE1. It was also biologically functional in complementing virE2 null strains transforming Arabidopsis thaliana roots and Nicotiana tabacum leaves. In vitro experiments demonstrated a two-color fluorescent complex using VirE2-TC/ReAsH and Alexa Fluor 488 labeled ssDNA...
2017: PloS One
https://www.readbyqxmd.com/read/28396594/human-primpol-activity-is-enhanced-by-rpa
#14
María I Martínez-Jiménez, Antonio Lahera, Luis Blanco
Human PrimPol is a primase belonging to the AEP superfamily with the unique ability to synthesize DNA primers de novo, and a non-processive DNA polymerase able to bypass certain DNA lesions. PrimPol facilitates both mitochondrial and nuclear replication fork progression either acting as a conventional TLS polymerase, or repriming downstream of blocking lesions. In vivo assays have shown that PrimPol is rapidly recruited to sites of DNA damage by interaction with the human replication protein A (RPA). In agreement with previous findings, we show here that the higher affinity of RPA for ssDNA inhibits PrimPol activities in short ssDNA templates...
April 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28393515/aptamer-protein-proximity-binding-triggered-molecular-machine-for-amplified-electrochemical-sensing-of-thrombin
#15
Jianmei Yang, Baoting Dou, Ruo Yuan, Yun Xiang
The development of convenient and sensitive methods without involving any enzymes or complex nanomaterials for the monitoring of proteins is of great significance in disease diagnostics. In this work, we describe the validation of a new aptamer/protein proximity binding-triggered molecular machinery amplification strategy for sensitive electrochemical assay of thrombin in complex serum samples. The sensing interface is prepared by self-assembly of three-stranded DNA complexes on the gold electrode. The association of two distinct functional aptamers with different sites of thrombin triggers proximity binding-induced displacement of one of the short single-stranded DNAs (ssDNAs) from the surface-immobilized three-stranded DNA complexes, exposing a prelocked toehold domain to hybridize with a methylene blue (MB)-tagged fuel ssDNA strand (MB-DNA)...
April 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28390322/simple-and-highly-selective-detection-of-arsenite-based-on-the-assembly-induced-fluorescence-enhancement-of-dna-quantum-dots
#16
Li Zhang, Xiu-Zhi Cheng, Lan Kuang, Ai-Zhen Xu, Ru-Ping Liang, Jian-Ding Qiu
Novel fluorescent DNA quantum dots (QDs) were synthesized by hydrothermal treatment of G-/T-rich ssDNA at relatively low reaction temperature. The obtained DNA QDs demonstrate unique optical properties, maintain the basic structure and biological activities of ssDNA precursors, which makes the DNA QDs able to specifically bind with arsenite, driving the (GT)29 region suffer conformation evolution and form well-ordered assembly rather than random aggregations. We speculate that the strong inter-molecule interaction and efficient stacking of base pairs stiffen the assembly structure, block the nonradiative relaxation channels, populate the radiative decay, and thus making the assembly be highly emissive as a new fluorescence center...
March 30, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28386108/structural-insight-into-the-specific-dna-template-binding-to-dnag-primase-in-bacteria
#17
Yingqin Zhou, Hao Luo, Zhongchuan Liu, Mu Yang, Xiaoyun Pang, Fei Sun, Ganggang Wang
Bacterial primase initiates the repeated synthesis of short RNA primers that are extended by DNA polymerase to synthesize Okazaki fragments on the lagging strand at replication forks. It remains unclear how the enzyme recognizes specific initiation sites. In this study, the DnaG primase from Bacillus subtilis (BsuDnaG) was characterized and the crystal structure of the RNA polymerase domain (RPD) was determined. Structural comparisons revealed that the tethered zinc binding domain plays an important role in the interactions between primase and specific template sequence...
April 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28385527/saccharomyces-cerevisiae-hrq1-helicase-activity-is-affected-by-the-sequence-but-not-the-length-of-single-stranded-dna
#18
Cody M Rogers, Matthew L Bochman
Mutations in the human RecQ4 DNA helicase are associated with three different diseases characterized by genomic instability. To gain insight into how RecQ4 dysfunction leads to these pathologies, several groups have used the Saccharomyces cerevisiae RecQ4 homolog Hrq1 as an experimental model. Hrq1 displays many of the same functions as RecQ4 in vivo and in vitro. However, there is some disagreement in the literature about the effects of single-stranded DNA (ssDNA) length on Hrq1 helicase activity and the ability of Hrq1 to anneal complementary ssDNA oligonucleotides into duplex DNA...
April 3, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28381576/dna-binding-properties-of-the-african-swine-fever-virus-pa104r-a-histone-like-protein-involved-in-viral-replication-and-transcription
#19
Gonçalo Frouco, Ferdinando B Freitas, João Coelho, Alexandre Leitão, Carlos Martins, Fernando Ferreira
African swine fever virus (ASFV) codes for a putative histone-like protein (pA104R) with extensive sequence homology to bacterial proteins that are implicated in genome replication and packaging. Functional characterization of purified recombinant pA104R revealed that it binds to ssDNA and dsDNA over a wide range of temperatures, pH values, salt concentrations and in an ATP-independent manner, with an estimated binding site size of about 14-16 nucleotides. Using site-directed mutagenesis, the arginine located in pA104R's DNA-binding domain, at position 69, was found to be relevant for an efficient DNA-binding activity...
April 5, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28381554/dna-mutagenic-activity-and-capacity-for-hiv-1-restriction-of-the-cytidine-deaminase-apobec3g-depends-on-whether-dna-or-rna-binds-to-tyrosine-315
#20
Bogdan Polevoda, Rebecca Joseph, Alan E Friedman, Ryan P Bennett, Rebecca Greiner, Thareendra De Zoysa, Ryan A Stewart, Harold C Smith
APOBEC3G (A3G) belongs to the AID/APOBEC protein family of cytidine deaminases (CDA) that bind to nucleic acids. A3G mutates the HIV genome by deamination of dC to dU, leading to accumulation of virus-inactivating mutations. Binding to cellular RNAs inhibits A3G binding to substrate single-stranded (ss) DNA and CDA activity. RNA and ssDNA bind to the same three A3G tryptic peptides (amino acids 181-194, 314-320, and 345-374) that form parts of a continuously exposed protein surface extending from the catalytic domain in the C-terminus of A3G to its N-terminus...
April 5, 2017: Journal of Biological Chemistry
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