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single-stranded DNA binding protein

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https://www.readbyqxmd.com/read/28345032/agrobacterium-delivers-vire2-protein-into-host-cells-via-clathrin-mediated-endocytosis
#1
Xiaoyang Li, Shen Q Pan
Agrobacterium tumefaciens can cause crown gall tumors on a wide range of host plants. As a natural genetic engineer, the bacterium can transfer both single-stranded DNA (ssDNA) [transferred DNA (T-DNA)] molecules and bacterial virulence proteins into various recipient cells. Among Agrobacterium-delivered proteins, VirE2 is an ssDNA binding protein that is involved in various steps of the transformation process. However, it is not clear how plant cells receive the T-DNA or protein molecules. Using a split-green fluorescent protein approach, we monitored the VirE2 delivery process inside plant cells in real time...
March 2017: Science Advances
https://www.readbyqxmd.com/read/28334825/the-impact-of-base-stacking-on-the-conformations-and-electrostatics-of-single-stranded-dna
#2
Alex Plumridge, Steve P Meisburger, Kurt Andresen, Lois Pollack
Single-stranded DNA (ssDNA) is notable for its interactions with ssDNA binding proteins (SSBs) during fundamentally important biological processes including DNA repair and replication. Previous work has begun to characterize the conformational and electrostatic properties of ssDNA in association with SSBs. However, the conformational distributions of free ssDNA have been difficult to determine. To capture the vast array of ssDNA conformations in solution, we pair small angle X-ray scattering with novel ensemble fitting methods, obtaining key parameters such as the size, shape and stacking character of strands with different sequences...
February 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334742/recognition-but-no-repair-of-abasic-site-in-single-stranded-dna-by-human-ribosomal-us3-protein-residing-within-intact-40s-subunit
#3
Anastasia S Grosheva, Dmitry O Zharkov, Joachim Stahl, Alexander V Gopanenko, Alexey E Tupikin, Marsel R Kabilov, Dmitri M Graifer, Galina G Karpova
Isolated human ribosomal protein uS3 has extra-ribosomal functions including those related to base excision DNA repair, e.g. AP lyase activity that nicks double-stranded (ds) DNA 3΄ to the abasic (AP) site. However, the ability of uS3 residing within ribosome to recognize and cleave damaged DNA has never been addressed. Here, we compare interactions of single-stranded (ss) DNA and dsDNA bearing AP site with human ribosome-bound uS3 and with the isolated protein, whose interactions with ssDNA were not yet studied...
January 30, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28331958/nucleic-acid-sensing-with-enzyme-dna-binding-protein-conjugates-cascade-and-simple-dna-nanostructures
#4
Gülsen Betül Aktas, Vasso Skouridou, Lluis Masip
A versatile and universal DNA sensing platform is presented based on enzyme-DNA binding protein tags conjugates and simple DNA nanostructures. Two enzyme conjugates were thus prepared, with horseradish peroxidase linked to the dimeric single-chain bacteriophage Cro repressor protein (HRP-scCro) and glucose oxidase linked to the dimeric headpiece domain of Escherichia coli LacI repressor protein (GOx-dHP), and used in conjunction with a hybrid ssDNA-dsDNA detection probe. This probe served as a simple DNA nanostructure allowing first for target recognition through its target-complementary single-stranded DNA (ssDNA) part and then for signal generation after conjugate binding on the double-stranded DNA (dsDNA) containing the specific binding sites for the dHP and scCro DNA binding proteins...
March 22, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28328200/fluorescence-resonance-energy-transfer-based-dna-tetrahedron-nano-tweezer-for-highly-reliable-detection-of-tumor-related-mrna-in-living-cells
#5
Lei He, Dan-Qing Lu, Hao Liang, Sitao Xie, Can Luo, Miaomiao Hu, Liujun Xu, Xiaobing Zhang, Weihong Tan
Accurate detection and imaging of tumor-related mRNA in living cells hold great promise for early cancer detection. However, currently, most probes designed to image intracellular mRNA confront intrinsic interferences arising from complex biological matrices and resulting in inevitable false-positive signals. To circumvent this problem, a new class of intracellular DNA nanoprobe, termed DNA tetrahedron nano-tweezer (DTNT), was developed to reliably image tumor-related mRNA in living cells based on the FRET (fluorescence resonance energy transfer) "off" to "on" signal readout mode...
March 22, 2017: ACS Nano
https://www.readbyqxmd.com/read/28322928/a-temperature-responsive-gene-in-sorghum-encodes-a-glycine-rich-protein-that-interacts-with-calmodulin
#6
Supreet Singh, Amardeep Singh Virdi, Rajdeep Jaswal, Mrinalini Chawla, Sanjay Kapoor, Samar B Mohapatra, Narayanan Manoj, Ashwani Pareek, Sanjay Kumar, Prabhjeet Singh
Imposition of different biotic and abiotic stress conditions results in an increase in intracellular levels of Ca(2+) which is sensed by various sensor proteins. Calmodulin (CaM) is one of the best studied transducers of Ca(2+) signals. CaM undergoes conformational changes upon binding to Ca(2+) and interacts with different types of proteins, thereby, regulating their activities. The present study reports the cloning and characterization of a sorghum cDNA encoding a protein (SbGRBP) that shows homology to glycine-rich RNA-binding proteins...
March 18, 2017: Biochimie
https://www.readbyqxmd.com/read/28316233/dna-linkers-and-diluents-for-ultrastable-gold-nanoparticle-bioconjugates-in-multiplexed-assay-development
#7
Samuel S Hinman, Kristy S McKeating, Quan Cheng
A novel bioconjugation strategy leading to ultrastable gold nanoparticles (AuNPs), utilizing DNA linkers and diluents in place of traditional self-assembled monolayers, is reported. The protective capacity of DNA confers straightforward biomolecular attachment and multistep derivatization capabilities to these nanoparticles and, more significantly, substantially enhances their stability in demanding and complex sensing environments. The DNA/AuNPs were assembled through pH-assisted thiol-gold bonding of single stranded DNA and salt aging, with preconjugated biotin moieties facing outward from the gold surface...
March 24, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28288277/direct-comparison-of-amino-acid-and-salt-interactions-with-double-stranded-and-single-stranded-dna-from-explicit-solvent-molecular-dynamics-simulations
#8
Casey Tyler Andrews, Brady A Campbell, Adrian Hamilton Elcock
Given the ubiquitous nature of protein-DNA interactions, it is important to understand the interaction thermodynamics of individual amino acid sidechains for DNA. One way to assess these preferences is to perform molecular dynamics (MD) simulations. Here we report MD simulations of twenty amino acid sidechain analogs interacting simultaneously with both a 70-base pair double-stranded DNA and with a 70-nucleotide single-stranded DNA. The relative preferences of the amino acid sidechains for dsDNA and ssDNA match well with values deduced from crystallographic analyses of protein-DNA complexes...
March 13, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28282044/predatory-behaviour-in-synthetic-protocell-communities
#9
Yan Qiao, Mei Li, Richard Booth, Stephen Mann
Recent progress in the chemical construction of colloidal objects comprising integrated biomimetic functions is paving the way towards rudimentary forms of artificial cell-like entities (protocells). Although several new types of protocells are currently available, the design of synthetic protocell communities and investigation of their collective behaviour has received little attention. Here we demonstrate an artificial form of predatory behaviour in a community of protease-containing coacervate microdroplets and protein-polymer microcapsules (proteinosomes) that interact via electrostatic binding...
February 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28280637/selection-of-dna-aptamers-for-ovarian-cancer-biomarker-ca125-using-one-pot-selex-and-high-throughput-sequencing
#10
Delia J Scoville, Tae Kyu Brian Uhm, Jamie A Shallcross, Rebecca J Whelan
CA125 is a mucin glycoprotein whose concentration in serum correlates with a woman's risk of developing ovarian cancer and also indicates response to therapy in diagnosed patients. Accurate detection of this large, complex protein in patient samples is of great clinical relevance. We suggest that powerful new diagnostic tools may be enabled by the development of nucleic acid aptamers with affinity for CA125. Here, we report on our use of One-Pot SELEX to isolate single-stranded DNA aptamers with affinity for CA125, followed by high-throughput sequencing of the selected oligonucleotides...
2017: Journal of Nucleic Acids
https://www.readbyqxmd.com/read/28276514/the-human-mitochondrial-transcription-factor-a-is-a-versatile-g-quadruplex-binding-protein
#11
Sébastien Lyonnais, Aleix Tarrés-Soler, Anna Rubio-Cosials, Anna Cuppari, Reicy Brito, Joaquim Jaumot, Raimundo Gargallo, Marta Vilaseca, Cristina Silva, Anton Granzhan, Marie-Paule Teulade-Fichou, Ramon Eritja, Maria Solà
The ability of the guanine-rich strand of the human mitochondrial DNA (mtDNA) to form G-quadruplex structures (G4s) has been recently highlighted, suggesting potential functions in mtDNA replication initiation and mtDNA stability. G4 structures in mtDNA raise the question of their recognition by factors associated with the mitochondrial nucleoid. The mitochondrial transcription factor A (TFAM), a high-mobility group (HMG)-box protein, is the major binding protein of human mtDNA and plays a critical role in its expression and maintenance...
March 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28270450/ssb1-and-ssb2-cooperate-to-regulate-mouse-hematopoietic-stem-and-progenitor-cells-by-resolving-replicative-stress
#12
Wei Shi, Therese Vu, Didier Boucher, Anna Biernacka, Jules Nde, Raj K Pandita, Jasmin Straube, Glen M Boyle, Fares Al-Ejeh, Purba Nag, Jessie Jeffery, Janelle L Harris, Amanda L Bain, Marta Grzelak, Magdalena Skrzypczak, Abhishek Mitra, Norbert Dojer, Nicola Crosetto, Nicole Cloonan, Olivier J Becherel, John Finnie, Jeffrey R Skaar, Carl R Walkley, Tej K Pandita, Maga Rowicka, Krzysztof Ginalski, Steven W Lane, Kum Kum Khanna
Hematopoietic stem and progenitor cells (HSPCs) are vulnerable to endogenous damage and defects in DNA repair can limit their function. The two single-stranded DNA binding proteins SSB1 and SSB2 are crucial regulators of the DNA damage response; however their overlapping roles during normal physiology are incompletely understood. We generated mice where both Ssb1 and Ssb2 were constitutively or conditionally deleted. Constitutive Ssb1/Ssb2 double knockout (DKO) caused early embryonic lethality, while conditional Ssb1/Ssb2 double knockout (cDKO) in adult mice resulted in acute lethality due to bone marrow failure and intestinal atrophy featuring stem and progenitor cell depletion, a phenotype unexpected from the previously reported single knockout models of Ssb1 or Ssb2 Mechanistically, cDKO HSPCs showed altered replication fork dynamics, massive accumulation of DNA damage, genome-wide double strand breaks (DSBs) enriched at Ssb binding regions and CpG islands, together with the accumulation of R-loops and cytosolic ssDNA...
March 7, 2017: Blood
https://www.readbyqxmd.com/read/28267323/a-dna-templated-aptamer-probe-for-identification-of-target-proteins
#13
Wenjing Bi, Xue Bai, Fan Gao, Congcong Lu, Ye Wang, Guijin Zhai, Shanshan Tian, Enguo Fan, YuKui Zhang, Kai Zhang
Using aptamers as molecular probes for biomarker discovery has attracted a great deal of attention in recent years. However, it is still a big challenge to accurately identify those protein markers that are targeted by aptamers under physiological conditions due to weak and non-covalent aptamer-protein interactions. Herein, we developed an aptamer based dual-probe using DNA-templated chemistry and photo-crosslinking technique for the identification of target proteins that are recognized by aptamers. In this system, the aptamer was modified by a single strand DNA as binding probe (BP), and another comple-mentary DNA with a photo-active group and reporter group was modified as capture probe (CP)...
March 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28265089/reconstitution-of-saccharomyces-cerevisiae-dna-polymerase-%C3%AE%C2%B5-dependent-mismatch-repair-with-purified-proteins
#14
Nikki Bowen, Richard D Kolodner
Mammalian and Saccharomyces cerevisiae mismatch repair (MMR) proteins catalyze two MMR reactions in vitro. In one, mispair binding by either the MutS homolog 2 (Msh2)-MutS homolog 6 (Msh6) or the Msh2-MutS homolog 3 (Msh3) stimulates 5' to 3' excision by exonuclease 1 (Exo1) from a single-strand break 5' to the mispair, excising the mispair. In the other, Msh2-Msh6 or Msh2-Msh3 activate the MutL homolog 1 (Mlh1)-postmeiotic segregation 1 (Pms1) endonuclease in the presence of a mispair and a nick 3' to the mispair, to make nicks 5' to the mispair, allowing Exo1 to excise the mispair...
March 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28265063/deep-sea-vent-phage-dna-polymerase-specifically-initiates-dna-synthesis-in-the-absence-of-primers
#15
Bin Zhu, Longfei Wang, Hitoshi Mitsunobu, Xueling Lu, Alfredo J Hernandez, Yukari Yoshida-Takashima, Takuro Nunoura, Stanley Tabor, Charles C Richardson
A DNA polymerase is encoded by the deep-sea vent phage NrS-1. NrS-1 has a unique genome organization containing genes that are predicted to encode a helicase and a single-stranded DNA (ssDNA)-binding protein. The gene for an unknown protein shares weak homology with the bifunctional primase-polymerases (prim-pols) from archaeal plasmids but is missing the zinc-binding domain typically found in primases. We show that this gene product has efficient DNA polymerase activity and is processive in DNA synthesis in the presence of the NrS-1 helicase and ssDNA-binding protein...
March 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28257700/functions-of-replication-protein-a-as-a-sensor-of-r-loops-and-a-regulator-of-rnaseh1
#16
Hai Dang Nguyen, Tribhuwan Yadav, Sumanprava Giri, Borja Saez, Timothy A Graubert, Lee Zou
R loop, a transcription intermediate containing RNA:DNA hybrids and displaced single-stranded DNA (ssDNA), has emerged as a major source of genomic instability. RNaseH1, which cleaves the RNA in RNA:DNA hybrids, plays an important role in R loop suppression. Here we show that replication protein A (RPA), an ssDNA-binding protein, interacts with RNaseH1 and colocalizes with both RNaseH1 and R loops in cells. In vitro, purified RPA directly enhances the association of RNaseH1 with RNA:DNA hybrids and stimulates the activity of RNaseH1 on R loops...
March 2, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28254886/tex19-paralogs-are-new-members-of-the-pirna-pathway-controlling-retrotransposon-suppression
#17
Yara Tarabay, Mayada Achour, Marius Teletin, Tao Ye, Aurélie Teissandier, Manuel Mark, Déborah Bourc'his, Stéphane Viville
Tex19 genes are mammalian specific and duplicated in Tex19.1 and Tex19.2 in some species, such as the mouse and rat. It has been demonstrated that mutant Tex19.1 males display a variable degree of infertility whereas they all upregulate MMERVK10C transposons in their germ line. In order to study the function of both paralogs in the mouse, we generated and studied double knockout (Tex19DKO) mutant mice. Adult Tex19DKO males exhibited a fully penetrant phenotype, similar to the most severe phenotype observed in single Tex19...
March 2, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28242466/elucidation-of-trna-cytochrome-c-interactions-through-hydrogen-deuterium-exchange-mass-spectrometry
#18
Yi-Ting Lo, Hung-Wei Huang, Yi-Chuan Huang, Jui-Fen Chan, Yuan-Hao Howard Hsu
Cytochrome c (cyt c) is a mitochondrial protein responsible for transferring electrons between electron transport chain complexes III and IV. The release of cyt c from the mitochondria has been considered as a commitment step in intrinsic apoptosis. Transfer RNA (tRNA) has recently been found to interact with the released cyt c to prevent the formation of the apoptosome complex, thus preventing cell apoptosis. To understand the molecular basis of tRNA-cyt c interactions, we applied hydrogen/deuterium exchange mass spectrometry (HDXMS) to analyze the interactions between tRNA and cyt c...
February 27, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28212352/rta-occupancy-of-the-origin-of-lytic-replication-during-murine-gammaherpesvirus-68-reactivation-from-b-cell-latency
#19
Alexis L Santana, Darby G Oldenburg, Varvara Kirillov, Laraib Malik, Qiwen Dong, Roman Sinayev, Kenneth B Marcu, Douglas W White, Laurie T Krug
RTA, the viral Replication and Transcription Activator, is essential for rhadinovirus lytic gene expression upon de novo infection and reactivation from latency. Lipopolysaccharide (LPS)/toll-like receptor (TLR)4 engagement enhances rhadinovirus reactivation. We developed two new systems to examine the interaction of RTA with host NF-kappaB (NF-κB) signaling during murine gammaherpesvirus 68 (MHV68) infection: a latent B cell line (HE-RIT) inducible for RTA-Flag expression and virus reactivation; and a recombinant virus (MHV68-RTA-Bio) that enabled in vivo biotinylation of RTA in BirA transgenic mice...
February 16, 2017: Pathogens
https://www.readbyqxmd.com/read/28210897/upregulated-single-stranded-dna-binding-protein-1-induces-cell-chemoresistance-to-cisplatin-in-lung-cancer-cell-lines
#20
Xiang Zhao, Rong He, Yu Liu, Yongkai Wu, Leitao Kang
Cisplatin and its analogues are widely used as anti-tumor drugs in lung cancer but many cisplatin-resistant lung cancer cases have been identified in recent years. Single-stranded DNA-binding protein 1 (SSDBP1) can effectively induce H69 cell resistance to cisplatin in our previous identification; thus, it is necessary to explore the mechanism underlying the effects of SSDBP1-induced resistance to cisplatin. First, SSDBP1-overexpressed or silent cell line was constructed and used to analyze the effects of SSDBP1 on chemoresistance of lung cancer cells to cisplatin...
February 16, 2017: Molecular and Cellular Biochemistry
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