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single-stranded DNA binding protein

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https://www.readbyqxmd.com/read/27899607/the-adenovirus-l4-22k-protein-regulates-transcription-and-rna-splicing-via-a-sequence-specific-single-stranded-rna-binding
#1
Susan Lan, Wael Kamel, Tanel Punga, Göran Akusjärvi
The adenovirus L4-22K protein both activates and suppresses transcription from the adenovirus major late promoter (MLP) by binding to DNA elements located downstream of the MLP transcriptional start site: the so-called DE element (positive) and the R1 region (negative). Here we show that L4-22K preferentially binds to the RNA form of the R1 region, both to the double-stranded RNA and the single-stranded RNA of the same polarity as the nascent MLP transcript. Further, L4-22K binds to a 5'-CAAA-3' motif in the single-stranded RNA, which is identical to the sequence motif characterized for L4-22K DNA binding...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27895115/shared-subunits-of-tetrahymena-telomerase-holoenzyme-and-replication-protein-a-have-different-functions-in-different-cellular-complexes
#2
Heather E Upton, Henry Chan, Juli Feigon, Kathleen Collins
In most eukaryotes, telomere maintenance relies on telomeric repeat synthesis by a reverse transcriptase named telomerase. To synthesize telomeric repeats, the catalytic subunit telomerase reverse transcriptase (TERT) uses the RNA subunit (TER) as a template. In the ciliate Tetrahymena thermophila,the telomerase holoenzyme consists of TER, TERT, and eight additional proteins including the telomeric-repeat single-stranded DNA binding protein Teb1 and its heterotrimer partners Teb2 and Teb3. Teb1 is paralogous to the large subunit of the general single-stranded DNA binding heterotrimer Replication Protein A (RPA)...
November 28, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27886600/a-lifetime-sensitive-fluorescence-anisotropy-probe-for-dna-based-bioassays-the-case-of-sybr-green
#3
Benoit Chovelon, Emmanuelle Fiore, Patrice Faure, Eric Peyrin, Corinne Ravelet
In standard steady-state fluorescence anisotropy (FA) DNA-based assays, the ligand binding to a given receptor is typically signalled by the rotational correlation time changes of the tracer. Herein, we report a radically different strategy that relies on the peculiar excited state lifetime features of the SYBR Green (SG) dye. This DNA-binding probe exhibits a drastically short lifetime in solution, leading to a high FA signal. Its complexation to oligonucleotides determines a singular and very large depolarization depending on the concerted effects of extreme lifetime enhancement and resonance energy homotransfer...
November 21, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27885504/plant-dicer-like-proteins-double-stranded-rna-cleaving-enzymes-for-small-rna-biogenesis
#4
Akihito Fukudome, Toshiyuki Fukuhara
Dicer, a double-stranded RNA (dsRNA)-specific endoribonuclease, plays an essential role in triggering both transcriptional and post-transcriptional gene silencing in eukaryotes by cleaving dsRNAs or single-stranded RNAs bearing stem-loop structures such as microRNA precursor transcripts into 21- to 24-nt small RNAs. Unlike animals, plants have evolved to utilize at least four Dicer-like (DCL) proteins. Extensive genetic studies have revealed that each DCL protein participates in a specific gene silencing pathway, with some redundancy...
November 24, 2016: Journal of Plant Research
https://www.readbyqxmd.com/read/27869555/the-influence-of-the-ctip-polymorphism-q418p-on-homologous-recombination-and-predisposition-to-radiation-induced-tumorigenesis-mainly-raml-in-mice
#5
Agata Patel, Jennifer Anderson, Daniela Kraft, Rosemary Finnon, Paul Finnon, Cheryl L Scudamore, Grainne Manning, Robert Bulman, Natalie Brown, Simon Bouffler, Peter O'Neill, Christophe Badie
Exposure to ionizing radiation increases the incidence of acute myeloid leukemia (AML), which has been diagnosed in Japanese atomic bombing survivors, as well as patients treated with radiotherapy. The genetic basis for susceptibility to radiation-induced AML is not well characterized. We previously identified a candidate murine gene for susceptibility to radiation-induced AML (rAML): C-terminal binding protein (CTBP)-interacting protein (CTIP)/retinoblastoma binding protein 8 (RBBP8). This gene is essential for embryonic development, double-strand break (DSB) resection in homologous recombination (HR) and tumor suppression...
November 21, 2016: Radiation Research
https://www.readbyqxmd.com/read/27869169/critical-role-of-the-pot1-ob-domain-in-maintaining-genomic-stability
#6
T K Pandita
Oligonucleotide/oligosaccharide-binding (OB) domain-containing proteins have been identified as critical for telomere maintenance, DNA repair, transcription and other DNA metabolism processes. Protection of telomere 1 (POT1), a telomere binding protein, has an OB domain like single-strand binding protein (SSB1). In this issue of Oncogene, Gu et al. present evidence that POT1, like SSB1, is required to maintain genomic stability. This work, in conjunction with results from previous investigators, highlights the importance of POT1 in telomere metabolism...
November 21, 2016: Oncogene
https://www.readbyqxmd.com/read/27867009/a-polar-and-nucleotide-dependent-mechanism-of-action-for-rad51-paralogs-in-rad51-filament-remodeling
#7
Martin R G Taylor, Mário Špírek, Chu Jian Ma, Raffaella Carzaniga, Tohru Takaki, Lucy M Collinson, Eric C Greene, Lumir Krejci, Simon J Boulton
Central to homologous recombination in eukaryotes is the RAD51 recombinase, which forms helical nucleoprotein filaments on single-stranded DNA (ssDNA) and catalyzes strand invasion with homologous duplex DNA. Various regulatory proteins assist this reaction including the RAD51 paralogs. We recently discovered that a RAD51 paralog complex from C. elegans, RFS-1/RIP-1, functions predominantly downstream of filament assembly by binding and remodeling RAD-51-ssDNA filaments to a conformation more proficient for strand exchange...
December 1, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27865995/g-quadruplex-based-aptamers-against-protein-targets-in-therapy-and-diagnostics
#8
REVIEW
Chiara Platella, Claudia Riccardi, Daniela Montesarchio, Giovanni N Roviello, Domenica Musumeci
Nucleic acid aptamers are single-stranded DNA or RNA molecules identified to recognize with high affinity specific targets including proteins, small molecules, ions, whole cells and even entire organisms, such as viruses or bacteria. They can be identified from combinatorial libraries of DNA or RNA oligonucleotides by SELEX technology, an in vitro iterative selection procedure consisting of binding (capture), partitioning and amplification steps. Remarkably, many of the aptamers selected against biologically relevant protein targets are G-rich sequences that can fold into stable G-quadruplex (G4) structures...
November 16, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27857998/a-parp1-erk2-synergism-is-required-for-stimulation-induced-expression-of-immediate-early-genes
#9
M Cohen-Armon
A PARP1-Erk2 synergism was required to generate synaptic long-term potentiation in the CA3-CA1 hippocampal connections. This molecular mechanism was associated with the recently identified pivotal role of polyADP-ribosylation in learning. High frequency electrical stimulation of cortical and hippocampal neurons induced binding of phosphorylated Erk2 (transported into the nucleus) to the nuclear protein PARP1. PARP1-Erk2 binding induced PARP1 activation and polyADP-ribosylation of its prominent substrate, linker histone H1...
2016: Gene & Translational Bioinformatics
https://www.readbyqxmd.com/read/27846560/molecular-force-spectroscopy-with-a-dna-origami-based-nanoscopic-force-clamp
#10
Philipp C Nickels, Bettina Wünsch, Phil Holzmeister, Wooli Bae, Luisa M Kneer, Dina Grohmann, Philip Tinnefeld, Tim Liedl
Forces in biological systems are typically investigated at the single-molecule level with atomic force microscopy or optical and magnetic tweezers, but these techniques suffer from limited data throughput and their requirement for a physical connection to the macroscopic world. We introduce a self-assembled nanoscopic force clamp built from DNA that operates autonomously and allows massive parallelization. Single-stranded DNA sections of an origami structure acted as entropic springs and exerted controlled tension in the low piconewton range on a molecular system, whose conformational transitions were monitored by single-molecule Förster resonance energy transfer...
October 21, 2016: Science
https://www.readbyqxmd.com/read/27846236/disruption-of-higher-order-dna-structures-in-friedreich-s-ataxia-gaa-n-repeats-by-pna-or-lna-targeting
#11
Helen Bergquist, Cristina S J Rocha, Rubén Álvarez-Asencio, Chi-Hung Nguyen, Mark W Rutland, C I Edvard Smith, Liam Good, Peter E Nielsen, Rula Zain
Expansion of (GAA)n repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich's ataxia. (GAA)n expansions form non-canonical structures, including intramolecular triplex (H-DNA), and R-loops and are associated with epigenetic modifications. With the aim of interfering with higher order H-DNA (like) DNA structures within pathological (GAA)n expansions, we examined sequence-specific interaction of peptide nucleic acid (PNA) with (GAA)n repeats of different lengths (short: n=9, medium: n=75 or long: n=115) by chemical probing of triple helical and single stranded regions...
2016: PloS One
https://www.readbyqxmd.com/read/27844433/probing-single-helicase-dynamics-on-long-nucleic-acids-through-fluorescence-force-measurement
#12
Chang-Ting Lin, Taekjip Ha
Helicases are nucleic acid-dependent ATPases which can bind and remodel nucleic acids, protein-nucleic acid complexes, or both. They are involved in almost every step in cells related to nucleic acid metabolisms, including DNA replication and repair, transcription, RNA maturation and splicing, and nuclear export processes. Using single-molecule fluorescence-force spectroscopy, we have previously directly observed helicase translocation on long single-stranded DNA and revealed that two monomers of UvrD helicase are required for the initiation of unwinding function...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27830676/-replication-protein-a-as-a-major-eukaryotic-single-stranded-dna-binding-protein-and-its-role-in-dna-repair
#13
Y S Krasikova, N I Rechkunova, O I Lavrik
Replication protein A (RPA) is a key regulator of eukaryotic DNA metabolism. RPA is a highly conserved heterotrimeric protein and contains multiple oligonucleotide/oligosaccharide-binding folds. The major RPA function is binding to single-stranded DNA (ssDNA) intermediates forming in DNA replication, repair, and recombination. Although binding ssDNA with high affinity, RPA can rapidly diffuse along ssDNA and destabilizes the DNA secondary structure. A highly dynamic RPA binding to ssDNA allows other proteins to access ssDNA and to displace RPA from the RPA-ssDNA complex...
September 2016: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/27830193/human-norovirus-aptamer-exhibits-high-degree-of-target-conformation-dependent-binding-similar-to-that-of-receptors-and-discriminates-particle-functionality
#14
Matthew D Moore, Benjamin G Bobay, Brittany Mertens, Lee-Ann Jaykus
Although two in vitro cultivation methods have been reported, discrimination of infectious human norovirus particles for study of viral inactivation is still a challenge, as both rely on reverse transcriptase quantitative PCR. Histo-blood group antigen (HBGA) binding assays serve as a proxy for estimation of infectious particles; however, they are costly and difficult to purify/modify. Some evidence suggests that certain nucleic acid aptamers only bind intact target proteins, thus displaying a high degree of conformation-dependent binding...
November 2016: MSphere
https://www.readbyqxmd.com/read/27825805/humanku70-protein-binds-hairpin-rna-and-double-stranded-dna-through-two-different-sites
#15
Andrey N Anisenko, Ekaterina S Knyazhanskaya, Timofey S Zatsepin, Marina B Gottikh
Human protein Ku usually functions in the cell as a complex of two subunits, Ku70 and Ku80. The Ku heterodimer plays a key role in the non-homologous end joining DNA repair pathway by specifically recognizing the DNA ends at the site of the lesion. The binding of the Ku heterodimer to DNA has been well-studied, and its interactions with RNA have been also described. However, Ku70 subunit is known to have independent DNA binding capability, which is less characterized. RNA binding properties of Ku70 have not been yet specially studied...
November 4, 2016: Biochimie
https://www.readbyqxmd.com/read/27813001/computer-aided-design-of-rna-origami-structures
#16
Steffen L Sparvath, Cody W Geary, Ebbe S Andersen
RNA nanostructures can be used as scaffolds to organize, combine, and control molecular functionalities, with great potential for applications in nanomedicine and synthetic biology. The single-stranded RNA origami method allows RNA nanostructures to be folded as they are transcribed by the RNA polymerase. RNA origami structures provide a stable framework that can be decorated with functional RNA elements such as riboswitches, ribozymes, interaction sites, and aptamers for binding small molecules or protein targets...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27809499/dna-binding-and-cleavage-by-human-parvovirus-b19-ns1-nuclease-domain
#17
Jonathan L Sanchez, Zachary Romero, Angelica Quinones, Kristiane R Torgeson, Nancy C Horton
Infection with human parvovirus B19 (B19V) has been associated with a myriad of illnesses, including erythema infectiosum (Fifth disease), hydrops fetalis, arthropathy, hepatitis, cardiomyopathy and also possibly the triggering of any number of different autoimmune diseases. B19V NS1 is a multi-domain protein that plays a critical role in viral replication, with predicted nuclease, helicase, and gene transactivation activities. Herein we investigate the biochemical activities of the nuclease domain (residues 2-176) of B19V NS1 (NS1-nuc) in sequence-specific DNA binding of the viral origin of replication sequences, as well as those of promoter sequences including the viral p6 and the human p21, TNFα, and IL-6 promoters previously identified in NS1-dependent transcriptional transactivation...
November 4, 2016: Biochemistry
https://www.readbyqxmd.com/read/27775344/single-stranded-nucleic-acids-bind-to-the-tetramer-interface-of-samhd1-and-prevent-formation-of-the-catalytic-homotetramer
#18
Kyle J Seamon, Namandje N Bumpus, James T Stivers
Sterile Alpha Motif and HD Domain Protein 1 (SAMHD1) is a unique enzyme that has important roles in nucleic acid metabolism, viral restriction, and the pathogenesis of autoimmune diseases and cancer. Although much attention has been focused on its dNTP triphosphohydrolase activity in viral restriction and disease, SAMHD1 also binds to single-stranded RNA and DNA. Here we utilize a UV crosslinking method using 5-bromodeoxyuridine-substituted oligonucleotides coupled with high-resolution mass spectrometry (HRMS) to identify the binding site for single-stranded nucleic acids (ssNA) on SAMHD1...
October 24, 2016: Biochemistry
https://www.readbyqxmd.com/read/27767195/replication-of-a-pathogenic-non-coding-rna-increases-dna-methylation-in-plants-associated-with-a-bromodomain-containing-viroid-binding-protein
#19
Dian-Qiu Lv, Shang-Wu Liu, Jian-Hua Zhao, Bang-Jun Zhou, Shao-Peng Wang, Hui-Shan Guo, Yuan-Yuan Fang
Viroids are plant-pathogenic molecules made up of single-stranded circular non-coding RNAs. How replicating viroids interfere with host silencing remains largely unknown. In this study, we investigated the effects of a nuclear-replicating Potato spindle tuber viroid (PSTVd) on interference with plant RNA silencing. Using transient induction of silencing in GFP transgenic Nicotiana benthamiana plants (line 16c), we found that PSTVd replication accelerated GFP silencing and increased Virp1 mRNA, which encodes bromodomain-containing viroid-binding protein 1 and is required for PSTVd replication...
October 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27766959/screening-for-clusters-of-charge-in-human-virus-proteomes
#20
Najla Kharrat, Sabrine Belmabrouk, Rania Abdelhedi, Riadh Benmarzoug, Mourad Assidi, Mohammed H Al Qahtani, Ahmed Rebai
BACKGROUND: The identification of charge clusters (runs of charged residues) in proteins and their mapping within the protein structure sequence is an important step toward a comprehensive analysis of how these particular motifs mediate, via electrostatic interactions, various molecular processes such as protein sorting, translocation, docking, orientation and binding to DNA and to other proteins. Few algorithms that specifically identify these charge clusters have been designed and described in the literature...
October 17, 2016: BMC Genomics
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