keyword
MENU ▼
Read by QxMD icon Read
search

single-stranded DNA binding protein

keyword
https://www.readbyqxmd.com/read/28548042/new-insights-into-reovirus-evolution-implications-from-a-newly-characterized-mycoreovirus
#1
Lijiang Liu, Jiasen Cheng, Yanping Fu, Huiquan Liu, Daohong Jiang, Jiatao Xie
We performed molecular cloning and complete genome sequencing of a novel mycoreovirus, Sclerotinia sclerotiorumreovirus 1 (SsReV1), isolated from an isolate of the phytopathogenic fungus Sclerotinia sclerotiorum. SsReV1 has a genome of 28 055 bp and is composed of 11 double-stranded RNA segments. With a combination of unique molecular features, virion shape and composition, and phylogenetic analysis, SsReV1 is significantly distinct from all known reoviruses and defines a novel genus in the family Reoviridae...
May 26, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28546384/systematic-analysis-of-the-dna-damage-response-network-in-telomere-defective-budding-yeast
#2
Eva-Maria Holstein, Greg Ngo, Conor Lawless, Peter Banks, Matthew Greetham, Darren Wilkinson, David Lydall
Functional telomeres are critically important to eukaryotic genetic stability. Scores of proteins and pathways are known to affect telomere function. Here, we report a series of related genome-wide genetic interaction screens performed on budding yeast cells with acute or chronic telomere defects. Genetic interactions were examined in cells defective in Cdc13 and Stn1, affecting two components of CST, a single stranded DNA (ssDNA) binding complex that binds telomeric DNA. For comparison, genetic interactions were also examined in cells with defects in Rfa3, affecting the major ssDNA binding protein, RPA, which has overlapping functions with CST at telomeres...
May 25, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28544018/next-generation-nucleic-acid-aptamers-with-two-base-modified-nucleotides-improve-the-binding-affinity-and-potency
#3
Rakesh Naduvile Veedu, Hadi AlShamaileh
Aptamers are single-stranded oligonucleotides (RNA or DNA) that can bind to their targets with high affinities and specificities because of their ability to adopt three-dimensional shapes in solution. Traditionally, aptamers are developed by SELEX (Systematic Evolution of Ligands by Exponential enrichment), a reiterative process involving selection by target molecule incubation with an oligonucleotide library and enrichment of the selected oligonucleotides by amplification. One drawback of current aptamer selection approach is the lack of diversity in the nucleic acid library with only four nucleobases compositions...
May 24, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28542368/in-vivo-and-in-vitro-characterization-of-ddrc-a-dna-damage-response-protein-in-deinococcus-radiodurans-bacterium
#4
Claire Bouthier de la Tour, Martine Mathieu, Laura Meyer, Pauline Dupaigne, Fanny Passot, Pascale Servant, Suzanne Sommer, Eric Le Cam, Fabrice Confalonieri
The bacterium Deinococcus radiodurans possesses a set of Deinococcus-specific genes highly induced after DNA damage. Among them, ddrC (dr0003) was recently re-annotated, found to be in the inverse orientation and called A2G07_00380. Here, we report the first in vivo and in vitro characterization of the corrected DdrC protein to better understand its function in irradiated cells. In vivo, the ΔddrC null mutant is sensitive to high doses of UV radiation and the ddrC deletion significantly increases UV-sensitivity of ΔuvrA or ΔuvsE mutant strains...
2017: PloS One
https://www.readbyqxmd.com/read/28534707/type-ia-topoisomerases-can-be-magicians-for-both-dna-and-rna-in-all-domains-of-life
#5
Muzammil Ahmad, Dongyi Xu, Weidong Wang
Topoisomerases solve critical topological problems in DNA metabolism and have long been regarded as the "magicians" of the DNA world. Here we present views from two of our recent studies indicating that Type IA topoisomerases from all domains of life often possess dual topoisomerase activities for both DNA and RNA. In animals, one of the two Type IA topoisomerases, Top3β, contains an RNA-binding domain, possesses RNA topoisomerase activity, binds mRNAs, interacts with mRNA-binding proteins, and associates with active mRNA translation machinery...
May 23, 2017: RNA Biology
https://www.readbyqxmd.com/read/28531371/wing-1-of-protein-hop2-is-as-important-as-helix-3-in-dna-binding-by-md-simulation
#6
Hem Moktan, Donghua H Zhou
The repair of programmed DNA double-strand breaks through recombination is required for proper association and disjunction of the meiotic homologous chromosomes. Meiosis specific protein HOP2 plays essential roles in recombination by promoting recombinase activities. The N-terminal domain of HOP2 interacts with DNA through helix 3 (H3) and wing 1 (W1). Mutations in wing 1 (Y65A/K67A/Q68A) slightly weakened the binding but mutations in helices 2 and 3 (Q30A/K44A/K49A) nearly abolished the binding. To better understand such differential effects at atomic level, molecular dynamics simulations were employed...
May 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28530298/aptabody-aptatope-interactions-in-aptablotting-assays
#7
Simranjeet Singh Sekhon, Hyun-Ju Um, Woo-Ri Shin, Sang-Hee Lee, Jiho Min, Ji-Young Ahn, Yang-Hoon Kim
We demonstrate an aptablotting assay method that involves direct and indirect aptabody recognition. Nanoscale single-stranded DNA aptamers against GST and DIG-tags are utilized as aptabodies (GST-2 and DIG-1, respectively), and the GST-2 aptabody binding site, or aptatope, as predicted by a MOE-docking simulation of the protein-aptamer complex, shows the interaction of the GST-2 aptabody at the catalytically active region. The aptabody-aptatope interaction was evaluated by an in vitro enzyme inhibitory analysis...
May 22, 2017: Nanoscale
https://www.readbyqxmd.com/read/28529734/differential-regulation-of-mouse-and-human-mu-opioid-receptor-gene-depends-on-the-single-stranded-dna-structure-of-its-promoter-and-%C3%AE-complex-protein-1
#8
Dong-Sun Lee, Ping-Yee Law, Wei Ln, Horace H Loh, Kyu Young Song, Hack Sun Choi
The Mu opioid receptor (MOR) mediates various functions of opioid-induced analgesia, euphoria and respiratory depression, and is a major target of opioid analgesics. Understanding of MOR gene expression among species is important for understanding its analgesic function in humans. In the current study, the polypyrimidine/polypurine (PPy/u) region, a key element of MOR gene expression, was compared in humans and mice. The mouse PPy/u element is highly homologous to its human element (84%), and the mouse MOR (mMOR) reporter drives luciferase activity 35-fold more effectively than the human MOR (hMOR) reporter...
May 2017: Biomedical Reports
https://www.readbyqxmd.com/read/28521053/compaction-and-condensation-of-dna-mediated-by-the-c-terminal-domain-of-hfq
#9
Antoine Malabirade, Kai Jiang, Krzysztof Kubiak, Alvaro Diaz-Mendoza, Fan Liu, Jeroen A van Kan, Jean-François Berret, Véronique Arluison, Johan R C van der Maarel
Hfq is a bacterial protein that is involved in several aspects of nucleic acids metabolism. It has been described as one of the nucleoid associated proteins shaping the bacterial chromosome, although it is better known to influence translation and turnover of cellular RNAs. Here, we explore the role of Escherichia coli Hfq's C-terminal domain in the compaction of double stranded DNA. Various experimental methodologies, including fluorescence microscopy imaging of single DNA molecules confined inside nanofluidic channels, atomic force microscopy, isothermal titration microcalorimetry and electrophoretic mobility assays have been used to follow the assembly of the C-terminal and N-terminal regions of Hfq on DNA...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28520746/dna-recognition-by-an-rna-guided-bacterial-argonaute
#10
Kevin W Doxzen, Jennifer A Doudna
Argonaute (Ago) proteins are widespread in prokaryotes and eukaryotes and share a four-domain architecture capable of RNA- or DNA-guided nucleic acid recognition. Previous studies identified a prokaryotic Argonaute protein from the eubacterium Marinitoga piezophila (MpAgo), which binds preferentially to 5'-hydroxylated guide RNAs and cleaves single-stranded RNA (ssRNA) and DNA (ssDNA) targets. Here we present a 3.2 Å resolution crystal structure of MpAgo bound to a 21-nucleotide RNA guide and a complementary 21-nucleotide ssDNA substrate...
2017: PloS One
https://www.readbyqxmd.com/read/28513534/unraveling-prion-protein-interactions-with-aptamers-and-other-prp-binding-nucleic-acids
#11
REVIEW
Bruno Macedo, Yraima Cordeiro
Transmissible spongiform encephalopathies (TSEs) are a group of neurodegenerative disorders that affect humans and other mammals. The etiologic agents common to these diseases are misfolded conformations of the prion protein (PrP). The molecular mechanisms that trigger the structural conversion of the normal cellular PrP (PrP(C)) into the pathogenic conformer (PrP(Sc)) are still poorly understood. It is proposed that a molecular cofactor would act as a catalyst, lowering the activation energy of the conversion process, therefore favoring the transition of PrP(C) to PrP(Sc)...
May 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28505149/distinct-dna-binding-surfaces-in-the-atpase-and-linker-domains-of-mutl%C3%AE-determine-its-substrate-specificities-and-exert-separable-functions-in-meiotic-recombination-and-mismatch-repair
#12
Corentin Claeys Bouuaert, Scott Keeney
Mlh1-Mlh3 (MutLγ) is a mismatch repair factor with a central role in formation of meiotic crossovers, presumably through resolution of double Holliday junctions. MutLγ has DNA binding, nuclease, and ATPase activities, but how these relate to one another and to in vivo functions are unclear. Here, we combine biochemical and genetic analyses to characterize Saccharomyces cerevisiae MutLγ. Limited proteolysis and atomic force microscopy showed that purified recombinant MutLγ undergoes ATP-driven conformational changes...
May 15, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28489024/the-role-of-the-n-terminal-domains-of-bacterial-initiator-dnaa-in-the-assembly-and-regulation-of-the-bacterial-replication-initiation-complex
#13
REVIEW
Anna Zawilak-Pawlik, Małgorzata Nowaczyk, Jolanta Zakrzewska-Czerwińska
The primary role of the bacterial protein DnaA is to initiate chromosomal replication. The DnaA protein binds to DNA at the origin of chromosomal replication (oriC) and assembles into a filament that unwinds double-stranded DNA. Through interaction with various other proteins, DnaA also controls the frequency and/or timing of chromosomal replication at the initiation step. Escherichia coli DnaA also recruits DnaB helicase, which is present in unwound single-stranded DNA and in turn recruits other protein machinery for replication...
May 10, 2017: Genes
https://www.readbyqxmd.com/read/28486639/dna-synthesis-determines-the-binding-mode-of-the-human-mitochondrial-single-stranded-dna-binding-protein
#14
José A Morin, Fernando Cerrón, Javier Jarillo, Elena Beltran-Heredia, Grzegorz L Ciesielski, J Ricardo Arias-Gonzalez, Laurie S Kaguni, Francisco J Cao, Borja Ibarra
Single-stranded DNA-binding proteins (SSBs) play a key role in genome maintenance, binding and organizing single-stranded DNA (ssDNA) intermediates. Multimeric SSBs, such as the human mitochondrial SSB (HmtSSB), present multiple sites to interact with ssDNA, which has been shown in vitro to enable them to bind a variable number of single-stranded nucleotides depending on the salt and protein concentration. It has long been suggested that different binding modes might be used selectively for different functions...
May 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28485576/new-lanthanide-tag-for-the-generation-of-pseudocontact-shifts-in-dna-by-site-specific-ligation-to-a-phosphorothioate-group
#15
Zuyan Wu, Michael D Lee, Thomas J Carruthers, Monika Szabo, Matthew L Dennis, James D Swarbrick, Bim Graham, Gottfried Otting
Pseudocontact shifts (PCS) generated by paramagnetic lanthanides provide a rich source of long-range structural restraints that can readily be measured by nuclear magnetic resonance (NMR) spectroscopy. Many different lanthanide-binding tags have been designed for site-specific tagging of proteins, but established routes for tagging DNA with a single metal ion rely on difficult chemical synthesis. Here we present a simple and practical strategy for site-specific tagging of inexpensive phosphorothioate (PT) oligonucleotides...
May 15, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28475766/sak-and-sak4-recombinases-are-required-for-bacteriophage-replication-in-staphylococcus-aureus
#16
Maan M Neamah, Ignacio Mir-Sanchis, María López-Sanz, Sonia Acosta, Ignacio Baquedano, Andreas F Haag, Alberto Marina, Silvia Ayora, José R Penadés
DNA-single strand annealing proteins (SSAPs) are recombinases frequently encoded in the genome of many bacteriophages. As SSAPs can promote homologous recombination among DNA substrates with an important degree of divergence, these enzymes are involved both in DNA repair and in the generation of phage mosaicisms. Here, analysing Sak and Sak4 as representatives of two different families of SSAPs present in phages infecting the clinically relevant bacterium Staphylococcus aureus, we demonstrate for the first time that these enzymes are absolutely required for phage reproduction...
May 5, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28475327/development-of-dna-nanostructures-for-high-affinity-binding-to-human-serum-albumin
#17
Aurélie Lacroix, Thomas G W Edwardson, Mark A Hancock, Michael D Dore, Hanadi F Sleiman
The development of nucleic acid therapeutics has been hampered by issues associated with their stability and in vivo delivery. To address these challenges, we describe a new strategy to engineer DNA structures with strong binding affinity to human serum albumin (HSA). HSA is the most abundant protein in the blood and has a long circulation half-life (19 days). It has been shown to hinder phagocytosis, is retained in tumors, and aids in cellular penetration. Indeed, HSA has already been successfully used for the delivery of small-molecule drugs and nanoparticles...
May 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28472517/the-rna-binding-protein-npl3-promotes-resection-of-dna-double-strand-breaks-by-regulating-the-levels-of-exo1
#18
Chiara Vittoria Colombo, Camilla Trovesi, Luca Menin, Maria Pia Longhese, Michela Clerici
Eukaryotic cells preserve genome integrity upon DNA damage by activating a signaling network that promotes DNA repair and controls cell cycle progression. One of the most severe DNA damage is the DNA double-strand break (DSB), whose 5΄ ends can be nucleolitically resected by multiple nucleases to create 3΄-ended single-stranded DNA tails that trigger DSB repair by homologous recombination. Here, we identify the Saccharomyces cerevisiae RNA binding protein Npl3 as a new player in DSB resection. Npl3 is related to both the metazoan serine-arginine-rich and the heterogeneous nuclear ribonucleo-proteins...
May 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28471366/structure-of-the-family-b-dna-polymerase-from-the-hyperthermophilic-archaeon-pyrobaculum-calidifontis
#19
Jingxu Guo, Wenling Zhang, Alun R Coker, Steve P Wood, Jonathan B Cooper, Shazeel Ahmad, Syed Ali, Naeem Rashid, Muhummad Akhtar
The family B DNA polymerase from Pyrobaculum calidifontis (Pc-polymerase) consists of 783 amino acids and is magnesium-ion dependent. It has an optimal pH of 8.5, an optimal temperature of 75°C and a half-life of 4.5 h at 95°C, giving it greater thermostability than the widely used Taq DNA polymerase. The enzyme is also capable of PCR-amplifying larger DNA fragments of up to 7.5 kb in length. It was shown to have functional, error-correcting 3'-5' exonuclease activity, as do the related high-fidelity DNA polymerases from Pyrococcus furiosus, Thermococcus kodakarensis KOD1 and Thermococcus gorgonarius, which have extensive commercial applications...
May 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28468824/the-dead-box-protein-ddx43-hage-is-a-dual-rna-dna-helicase-and-has-a-k-homology-domain-required-for-full-nucleic-acid-unwinding-activity
#20
Talwar Tanu, Venkatasubramanian Vidhyasagar, Jennifer Qing, Manhong Guo, Ahmad Kariem, Yi Lu, Ravi Shankar Singh, Kiven Erique Lukong, Yuliang Wu
The K-homology (KH) domain is a nucleic acid-binding domain present in many proteins, but has not been reported in helicases. DDX43, also known as HAGE (helicase antigen gene), is a member of the DEAD-box protein family. It contains a helicase core domain in its C-terminus and a potential KH domain in its N-terminus. DDX43 is highly expressed in many tumors, and is therefore considered a potential target for immunotherapy. Despite its potential as a therapeutic target, little is known about its activities. Here, we purified recombinant DDX43 protein to near homogeneity and found that it exists as a monomer in solution...
May 3, 2017: Journal of Biological Chemistry
keyword
keyword
68801
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"