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single-stranded DNA binding protein

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https://www.readbyqxmd.com/read/28928411/reca-ssb-interaction-modulates-reca-nucleoprotein-filament-formation-on-ssb-wrapped-dna
#1
Hung-Yi Wu, Chih-Hao Lu, Hung-Wen Li
E. coli RecA recombinase catalyzes the homology pairing and strand exchange reactions in homologous recombinational repair. RecA must compete with single-stranded DNA binding proteins (SSB) for single-stranded DNA (ssDNA) substrates to form RecA nucleoprotein filaments, as the first step of this repair process. It has been suggested that RecA filaments assemble mainly by binding and extending onto the free ssDNA region not covered by SSB, or are assisted by mediators. Using the tethered particle motion (TPM) technique, we monitored individual RecA filament assembly on SSB-wrapped ssDNA in real-time...
September 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28926145/a-crispr-reimagining-new-twists-and-turns-of-crispr-beyond-the-genome-engineering-revolution
#2
Robert J Plummer, Yi Guo, Ying Peng
Despite its explosive applications in genome engineering, CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) has been developed into a versatile tool beyond its well-known nuclease function. In this prospect article, we summarize a few exciting "off-label" applications of CRISPR including manipulating DNA sequences, visualizing chromosomal loci in living cells, and modulating transcription and chromatin structures. These novel applications will likely elevate CRISPR tools into yet another level of sophistication and diversity, leading to many more exciting cell biological discoveries...
September 19, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28923950/single-molecule-visualization-of-saccharomyces-cerevisiae-leading-strand-synthesis-reveals-dynamic-interaction-between-mtc-and-the-replisome
#3
Jacob S Lewis, Lisanne M Spenkelink, Grant D Schauer, Flynn R Hill, Roxanna E Georgescu, Michael E O'Donnell, Antoine M van Oijen
The replisome, the multiprotein system responsible for genome duplication, is a highly dynamic complex displaying a large number of different enzyme activities. Recently, the Saccharomyces cerevisiae minimal replication reaction has been successfully reconstituted in vitro. This provided an opportunity to uncover the enzymatic activities of many of the components in a eukaryotic system. Their dynamic behavior and interactions in the context of the replisome, however, remain unclear. We use a tethered-bead assay to provide real-time visualization of leading-strand synthesis by the S...
September 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28922417/lingering-single-strand-breaks-trigger-rad51-independent-homology-directed-repair-of-collapsed-replication-forks-in-the-polynucleotide-kinase-phosphatase-mutant-of-fission-yeast
#4
Arancha Sanchez, Mariana C Gadaleta, Oliver Limbo, Paul Russell
The DNA repair enzyme polynucleotide kinase/phosphatase (PNKP) protects genome integrity by restoring ligatable 5'-phosphate and 3'-hydroxyl termini at single-strand breaks (SSBs). In humans, PNKP mutations underlie the neurological disease known as MCSZ, but these individuals are not predisposed for cancer, implying effective alternative repair pathways in dividing cells. Homology-directed repair (HDR) of collapsed replication forks was proposed to repair SSBs in PNKP-deficient cells, but the critical HDR protein Rad51 is not required in PNKP-null (pnk1Δ) cells of Schizosaccharomyces pombe...
September 18, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28916391/zika-virus-structural-biology-and-progress-in-vaccine-development
#5
REVIEW
Hsiao-Han Lin, Bak-Sau Yip, Li-Min Huang, Suh-Chin Wu
The growing number of zika virus (ZIKV) infections plus a 20-fold increase in neonatal microcephaly in newborns in Brazil have raised alarms in many countries regarding the threat to pregnant women. Instances of microcephaly and central nervous system malformations continue to increase in ZIKV outbreak regions. ZIKV is a small enveloped positive-strand RNA virus belonging to the Flavivirus genus of the Flaviviridae family. High-resolution ZIKV structures recently identified by cryo-electron microscopy indicate that the overall ZIKV structure is similar to those of other flaviviruses...
September 12, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28911227/a-fluorescence-assay-for-ribonuclease-h-based-on-non-labeled-substrate-and-dnazyme-assisted-cascade-amplification
#6
Lanbo Wang, Hongyan Zhou, Bin Liu, Chuan Zhao, Jialong Fan, Wei Wang, Chunyi Tong
As a highly conserved damage repair protein, RNase H can specifically hydrolyze RNA in DNA-RNA chimeric strands. DNAzyme, a synthetic single-stranded DNA consisting of binding and catalytic sites, can cleave RNA in the presence of cofactors. In this study, we establish a highly sensitive RNase H assay assisted with DNAzyme's cleavage property. A DNA-RNA chimeric strand, which contains DNAzyme sequences, is used as the hydrolysis substrate of RNase H. The RNase H hydrolysis of the chimeric substrate results in the release of DNAzyme...
September 15, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28905214/mir-217-5p-induces-apoptosis-by-directly-targeting-prkci-bag3-itgav-and-mapk1-in-colorectal-cancer-cells
#7
Marion Flum, Michael Kleemann, Helga Schneider, Benjamin Weis, Simon Fischer, René Handrick, Kerstin Otte
Apoptosis is a genetically directed process of programmed cell death. A variety of microRNAs (miRNAs), endogenous single-stranded non-coding RNAs of about 22 nucleotides in length have been shown to be involved in the regulation of the intrinsic or extrinsic apoptotic pathways. There is increasing evidence that the aberrant expression of miRNAs plays a causal role in the development of diseases such as cancer. This makes miRNAs promising candidate molecules as therapeutic targets or agents. MicroRNA (miR)-217-5p has been implicated in carcinogenesis of various cancer entities, including colorectal cancer...
September 14, 2017: Journal of Cell Communication and Signaling
https://www.readbyqxmd.com/read/28902926/down-regulation-of-single-stranded-dna-binding-protein-1-expression-induced-by-hcmv-infection-promotes-lipid-accumulation-in-cells
#8
N Guo, N Zhang, L Yan, X Cao, F Lv, J Wang, Y Wang, H Cong
The objective of this study was to observe the infection of human cytomegalovirus (HCMV) to human umbilical vein endothelial cells, and its effect on the expression of single-stranded DNA-binding protein (SSBP1) and on lipid metabolism in endothelial cells. We screened the differential expression of mRNAs after HCMV infection by suppression subtractive hybridization and the expression levels of SSBP1 mRNA and protein after HCMV infection by real-time PCR and western blot. After verification of successful infection by indirect immunofluorescent staining and RT-PCR, we found a differential expression of lipid metabolism-related genes including LDLR, SCARB, CETP, HMGCR, ApoB and LPL induced by HCMV infection...
September 12, 2017: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
https://www.readbyqxmd.com/read/28882222/role-of-the-trna-derived-small-rnas-in-cancer-new-potential-biomarkers-and-target-for-therapy
#9
Veronica Balatti, Yuri Pekarsky, Carlo M Croce
Noncoding RNAs are untranslated RNA molecules that can be divided into two main types: infrastructural, including transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), and regulatory, including long ncRNAs (lncRNAs) and small ncRNAs (sRNA). Among small ncRNA, the role of microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs) in cancer is well documented. Recently, other small ncRNAs have been described. In particular, tRNA-derived small RNAs (tsRNA) have been found to be frequently dysregulated in cancer. Since tsRNAs can be considered unique sequences and are able to bind both Argonaute proteins (like miRNAs) and Piwi proteins (like piRNAs), their dysregulation could play a critical role in cancer by interfering with gene expression regulation at different levels...
2017: Advances in Cancer Research
https://www.readbyqxmd.com/read/28881087/organometallic-dna-b12-conjugates-as-potential-oligonucleotide-vectors-synthesis-structural-and-binding-studies-with-human-cobalamin-transport-proteins
#10
Elena Mutti, Miriam Hunger, Sergey Fedosov, Ebba Nexo, Bernhard Kräutler
We report on the synthesis and structural characterization of Co-(dN)25-Cbl and Co-(dN)39-Cbl, organometallic DNA-B12-conjugates with single DNA-strands consisting of 25 and 39 deoxy-nucleotides, respectively, and on binding studies of these two DNA-cobalamin (DNA-Cbl) conjugates to the three homologous human Cbl transporting proteins transcobalamin (TC), intrinsic factor (IF) and haptocorrin (HC). This investigation tests the suitability of such DNA-Cbls for the task of eventual in-vivo oligonucleotide delivery...
September 7, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28878086/metsv-a-novel-archaeal-lytic-virus-targeting-methanosarcina-strains
#11
Katrin Weidenbach, Lisa Nickel, Horst Neve, Omer S Alkhnbashi, Sven Künzel, Anne Kupczok, Thorsten Bauersachs, Liam Cassidy, Andreas Tholey, Rolf Backofen, Ruth A Schmitz
A novel archaeal lytic virus targeting species of the genus Methanosarcina was isolated using Methanosarcina mazei strain Gö1 as host. Due to its spherical morphology the virus was designated Methanosarcinaspherical virus (MetSV). Molecular analysis demonstrated that MetSV contains double stranded linear DNA with a genome size of 10,567 bp containing 22 open reading frames (ORFs) all oriented in the same direction. Functions were predicted for some of these ORFs, i. e. like DNA polymerase, ATPase, DNA-binding protein, as well as envelope (structural) protein...
September 6, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28875174/improved-base-excision-repair-inhibition-and-bacteriophage-mu-gam-protein-yields-c-g-to-t-a-base-editors-with-higher-efficiency-and-product-purity
#12
Alexis C Komor, Kevin T Zhao, Michael S Packer, Nicole M Gaudelli, Amanda L Waterbury, Luke W Koblan, Y Bill Kim, Ahmed H Badran, David R Liu
We recently developed base editing, the programmable conversion of target C:G base pairs to T:A without inducing double-stranded DNA breaks (DSBs) or requiring homology-directed repair using engineered fusions of Cas9 variants and cytidine deaminases. Over the past year, the third-generation base editor (BE3) and related technologies have been successfully used by many researchers in a wide range of organisms. The product distribution of base editing-the frequency with which the target C:G is converted to mixtures of undesired by-products, along with the desired T:A product-varies in a target site-dependent manner...
August 2017: Science Advances
https://www.readbyqxmd.com/read/28874457/correction-for-chenail-et-al-borrelia-burgdorferi-cp32-bpab-modulates-expression-of-the-prophage-nucp-nuclease-and-ssbp-single-stranded-dna-binding-protein
#13
Alicia M Chenail, Brandon L Jutras, Claire A Adams, Logan H Burns, Amy Bowman, Ashutosh Verma, Brian Stevenson
No abstract text is available yet for this article.
October 1, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28867292/single-molecule-imaging-reveals-how-mre11-rad50-nbs1-initiates-dna-break-repair
#14
Logan R Myler, Ignacio F Gallardo, Michael M Soniat, Rajashree A Deshpande, Xenia B Gonzalez, Yoori Kim, Tanya T Paull, Ilya J Finkelstein
DNA double-strand break (DSB) repair is essential for maintaining our genomes. Mre11-Rad50-Nbs1 (MRN) and Ku70-Ku80 (Ku) direct distinct DSB repair pathways, but the interplay between these complexes at a DSB remains unclear. Here, we use high-throughput single-molecule microscopy to show that MRN searches for free DNA ends by one-dimensional facilitated diffusion, even on nucleosome-coated DNA. Rad50 binds homoduplex DNA and promotes facilitated diffusion, whereas Mre11 is required for DNA end recognition and nuclease activities...
September 7, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28863186/fusion-of-taq-dna-polymerase-with-single-stranded-dna-binding-like-protein-of-nanoarchaeum-equitans-expression-and-characterization
#15
Marcin Olszewski, Marta Śpibida, Maciej Bilek, Beata Krawczyk
DNA polymerases are present in all organisms and are important enzymes that synthesise DNA molecules. They are used in various fields of science, predominantly as essential components for in vitro DNA syntheses, known as PCR. Modern diagnostics, molecular biology and genetic engineering need DNA polymerases which demonstrate improved performance. This study was aimed at obtaining a new NeqSSB-TaqS fusion DNA polymerase from the Taq DNA Stoffel domain and a single-stranded DNA binding-like protein of Nanoarchaeum equitans in order to significantly improve the properties of DNA polymerase...
2017: PloS One
https://www.readbyqxmd.com/read/28862774/deinococcus-radiodurans-dr1088-is-a-novel-recf-interacting-protein-that-stimulates-single-stranded-dna-annealing
#16
Kaiying Cheng, Guangzhi Xu, Hong Xu, Ye Zhao, Yuejin Hua
RecF, together with the recombination mediators RecO and RecR, is required in the RecFOR homologous recombination repair pathway in bacteria. In this study, a recF-dr1088 operon, which is highly conserved in the Deinococcus-Thermus phylum, was identified in Deinococcus radiodurans. Interaction between DRRecF and DR1088 was confirmed by yeast two-hybrid and pull-down assays. DR1088 exhibited some RecO-like biochemical properties including single/double-stranded DNA binding activity, ssDNA binding protein (SSB) replacement ability and ssDNA (with or without SSB) annealing activity...
September 1, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28860187/analysis-of-dna-binding-by-human-factor-xeroderma-pigmentosum-complementation-group-a-xpa-provides-insight-into-its-interactions-with-nucleotide-excision-repair-substrates
#17
Norie Sugitani, Markus W Voehler, Michelle S Roh, Agnieszka M Topolska-Woś, Walter J Chazin
Xeroderma pigmentosum (XP) complementation group A (XPA) is an essential scaffolding protein in the multi-protein nucleotide excision repair (NER) machinery. The interaction of XPA with DNA is a core function of this protein; a number of mutations in the DNA binding domain (DBD) are associated with XP disease. Although structures of the central globular domain of human XPA and data on binding of DNA substrates have been reported, the structural basis for XPAs DNA binding activity remains unknown. X-ray crystal structures of the central globular domain of yeast XPA (Rad14) with lesion-containing DNA duplexes have provided valuable insights, but the DNA substrates used for this study do not correspond to the substrates of XPA as it functions within the NER machinery...
August 31, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28854736/the-role-of-poly-adp-ribosylation-in-the-first-wave-of-dna-damage-response
#18
Chao Liu, Aditi Vyas, Muzaffer A Kassab, Anup K Singh, Xiaochun Yu
Poly ADP-ribose polymerases (PARPs) catalyze massive protein poly ADP-ribosylation (PARylation) within seconds after the induction of DNA single- or double-strand breaks. PARylation occurs at or near the sites of DNA damage and promotes the recruitment of DNA repair factors via their poly ADP-ribose (PAR) binding domains. Several novel PAR-binding domains have been recently identified. Here, we summarize these and other recent findings suggesting that PARylation may be the critical event that mediates the first wave of the DNA damage response...
August 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28854734/amide-linkages-mimic-phosphates-in-rna-interactions-with-proteins-and-are-well-tolerated-in-the-guide-strand-of-short-interfering-rnas
#19
Daniel Mutisya, Travis Hardcastle, Samwel K Cheruiyot, Pradeep S Pallan, Scott D Kennedy, Martin Egli, Melissa L Kelley, Anja van Brabant Smith, Eriks Rozners
While the use of RNA interference (RNAi) in molecular biology and functional genomics is a well-established technology, in vivo applications of synthetic short interfering RNAs (siRNAs) require chemical modifications. We recently found that amides as non-ionic replacements for phosphodiesters may be useful modifications for optimization of siRNAs. Herein, we report a comprehensive study of systematic replacement of a single phosphate with an amide linkage throughout the guide strand of siRNAs. The results show that amides are surprisingly well tolerated in the seed and central regions of the guide strand and increase the silencing activity when placed between nucleosides 10 and 12, at the catalytic site of Argonaute...
August 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28854357/neil3-repairs-telomere-damage-during-s-phase-to-secure-chromosome-segregation-at-mitosis
#20
Jia Zhou, Jany Chan, Marie Lambelé, Timur Yusufzai, Jason Stumpff, Patricia L Opresko, Markus Thali, Susan S Wallace
Oxidative damage to telomere DNA compromises telomere integrity. We recently reported that the DNA glycosylase NEIL3 preferentially repairs oxidative lesions in telomere sequences in vitro. Here, we show that loss of NEIL3 causes anaphase DNA bridging because of telomere dysfunction. NEIL3 expression increases during S phase and reaches maximal levels in late S/G2. NEIL3 co-localizes with TRF2 and associates with telomeres during S phase, and this association increases upon oxidative stress. Mechanistic studies reveal that NEIL3 binds to single-stranded DNA via its intrinsically disordered C terminus in a telomere-sequence-independent manner...
August 29, 2017: Cell Reports
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