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single-stranded DNA binding protein

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https://www.readbyqxmd.com/read/28431230/structural-basis-for-guide-rna-processing-and-seed-dependent-dna-targeting-by-crispr-cas12a
#1
Daan C Swarts, John van der Oost, Martin Jinek
The CRISPR-associated protein Cas12a (Cpf1), which has been repurposed for genome editing, possesses two distinct nuclease activities: endoribonuclease activity for processing its own guide RNAs and RNA-guided DNase activity for target DNA cleavage. To elucidate the molecular basis of both activities, we determined crystal structures of Francisella novicida Cas12a bound to guide RNA and in complex with an R-loop formed by a non-cleavable guide RNA precursor and a full-length target DNA. Corroborated by biochemical experiments, these structures reveal the mechanisms of guide RNA processing and pre-ordering of the seed sequence in the guide RNA that primes Cas12a for target DNA binding...
April 20, 2017: Molecular Cell
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
#2
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
#3
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/28402520/a-non-canonical-multisubunit-rna-polymerase-encoded-by-the-ar9-phage-recognizes-the-template-strand-of-its-uracil-containing-promoters
#4
Maria Sokolova, Sergei Borukhov, Daria Lavysh, Tatjana Artamonova, Mikhail Khodorkovskii, Konstantin Severinov
AR9 is a giant Bacillus subtilis phage whose uracil-containing double-stranded DNA genome encodes distant homologs of β and β' subunits of bacterial RNA polymerase (RNAP). The products of these genes are thought to assemble into two non-canonical multisubunit RNAPs - a virion RNAP (vRNAP) that is injected into the host along with phage DNA to transcribe early phage genes, and a non-virion RNAP (nvRNAP), which is synthesized during the infection and transcribes late phage genes. We purified the AR9 nvRNAP from infected B...
April 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28401569/influences-on-viral-replication-and-sensitivity-to-gls4-a-hap-compound-of-naturally-occurring-t109-v124-mutations-in-hepatitis-b-virus-core-protein
#5
Jianghua Wang, Haiying Zhang, Yingjun Zhang, Dong Jiang, Jing Li, Siegfried Goldmann, Qingyun Ren, Ran Fei, Xueyan Wang, Lai Wei
Heteroaryldihydropyrimidine (HAP) compounds inhibit HBV replication by binding to a hydrophobic pocket at the interface between hepatitis B virus core protein (HBcAg) dimer, which interrupts capsid assembly by changing the kinetics and thermodynamics during this process. Structure biological studies have identified several amino acids in HBcAg crucial for compound binding. Here we investigated the polymorphisms of T109 and V124 amino acids in HBV sequences submitted to GenBank database. Naturally occurring T109 and V124 and/or possible compensatory mutations in neighbored amino acids were introduced into HBV-expressing plasmids...
April 12, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28383499/eukaryotic-replicative-helicase-subunit-interaction-with-dna-and-its-role-in-dna-replication
#6
REVIEW
Matthew P Martinez, Amanda L Wacker, Irina Bruck, Daniel L Kaplan
The replicative helicase unwinds parental double-stranded DNA at a replication fork to provide single-stranded DNA templates for the replicative polymerases. In eukaryotes, the replicative helicase is composed of the Cdc45 protein, the heterohexameric ring-shaped Mcm2-7 complex, and the tetrameric GINS complex (CMG). The CMG proteins bind directly to DNA, as demonstrated by experiments with purified proteins. The mechanism and function of these DNA-protein interactions are presently being investigated, and a number of important discoveries relating to how the helicase proteins interact with DNA have been reported recently...
April 6, 2017: Genes
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
#7
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
https://www.readbyqxmd.com/read/28377493/roles-of-leu28-side-chain-intercalation-in-the-interaction-between-cren7-and-dna
#8
Zhenfeng Zhang, Mohan Zhao, Li Wang, Yuanyuan Chen, Yuhui Dong, Yong Gong, Li Huang
Crenarchaeal chromatin protein Cren7 binds double-stranded DNA in the minor groove, introducing a sharp single-step DNA kink. The side chain of Leu28, a residue conserved among all Cren7 homologues, intercalates into the kink DNA step. In this study, we replaced Leu28 with a residue containing a hydrophobic side chain of different sizes (i.e., L28A, L28V, L28I, L28M and L28F). Both the stability of the Cren7-DNA complex and the ability of Cren7 to constrain DNA supercoils correlated well with the size of the intercalated side chain...
April 4, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28369637/nmr-based-method-of-small-changes-reveals-how-dna-mutator-apobec3a-interacts-with-its-single-stranded-dna-substrate
#9
Stefan Harjes, Geoffrey B Jameson, Vyacheslav V Filichev, Patrick J B Edwards, Elena Harjes
APOBEC3 proteins are double-edged swords. They deaminate cytosine to uracil in single-stranded DNA and provide protection, as part of our innate immune system, against viruses and retrotransposons, but they are also involved in cancer evolution and development of drug resistance. We report a solution-state model of APOBEC3A interaction with its single-stranded DNA substrate obtained with the 'method of small changes'. This method compares pairwise the 2D 15N-1H NMR spectra of APOBEC3A bearing a deactivating mutation E72A in the presence of 36 slightly different DNA substrates...
March 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28369586/uracil-dna-glycosylase-udg-activities-in-bradyrhizobium-diazoefficiens-characterization-of-a-new-class-of-udg-with-broad-substrate-specificity
#10
Ullas Valiya Chembazhi, Vinod Vikas Patil, Shivjee Sah, Wayne Reeve, Ravi P Tiwari, Euijeon Woo, Umesh Varshney
Repair of uracils in DNA is initiated by racil NA lycosylases (UDGs). Family 1 UDGs (Ung) are the most efficient and ubiquitous proteins having an exquisite specificity for uracils in DNA. Ung are characterized by motifs A (GQDPY) and B (HPSPLS) sequences. We report a novel dimeric UDG, Blr0248 ( Bdi Ung) from Bradyrhizobium diazoefficiens . Although Bdi Ung contains the motif A (GQDPA), it has low sequence identity to known UDGs. Bdi Ung prefers single stranded DNA and excises uracil, 5-hydroxymethyl-uracil or xanthine from it...
March 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28367958/generation-of-aptamers-from-a-primer-free-randomized-ssdna-library-using-magnetic-assisted-rapid-aptamer-selection
#11
Shih-Ming Tsao, Ji-Ching Lai, Horng-Er Horng, Tu-Chen Liu, Chin-Yih Hong
Aptamers are oligonucleotides that can bind to specific target molecules. Most aptamers are generated using random libraries in the standard systematic evolution of ligands by exponential enrichment (SELEX). Each random library contains oligonucleotides with a randomized central region and two fixed primer regions at both ends. The fixed primer regions are necessary for amplifying target-bound sequences by PCR. However, these extra-sequences may cause non-specific bindings, which potentially interfere with good binding for random sequences...
April 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28358012/suppression-of-foxm1-transcriptional-activities-via-a-single-stranded-dna-aptamer-generated-by-selex
#12
Qin Xiang, Guixiang Tan, Xia Jiang, Kuangpei Wu, Weihong Tan, Yongjun Tan
The transcription factor FOXM1 binds to its consensus sequence at promoters through its DNA binding domain (DBD) and activates proliferation-associated genes. The aberrant overexpression of FOXM1 correlates with tumorigenesis and progression of many cancers. Inhibiting FOXM1 transcriptional activities is proposed as a potential therapeutic strategy for cancer treatment. In this study, we obtained a FOXM1-specific single stranded DNA aptamer (FOXM1 Apt) by SELEX with a recombinant FOXM1 DBD protein as the target of selection...
March 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28345032/agrobacterium-delivers-vire2-protein-into-host-cells-via-clathrin-mediated-endocytosis
#13
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
#14
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...
April 20, 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
#15
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...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28331958/nucleic-acid-sensing-with-enzyme-dna-binding-protein-conjugates-cascade-and-simple-dna-nanostructures
#16
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-nanotweezer-for-highly-reliable-detection-of-tumor-related-mrna-in-living-cells
#17
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, an intracellular DNA nanoprobe, termed DNA tetrahedron nanotweezer (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 30, 2017: ACS Nano
https://www.readbyqxmd.com/read/28322928/a-temperature-responsive-gene-in-sorghum-encodes-a-glycine-rich-protein-that-interacts-with-calmodulin
#18
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
#19
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
#20
Casey T Andrews, Brady A Campbell, Adrian H Elcock
Given the ubiquitous nature of protein-DNA interactions, it is important to understand the interaction thermodynamics of individual amino acid side chains for DNA. One way to assess these preferences is to perform molecular dynamics (MD) simulations. Here we report MD simulations of 20 amino acid side chain 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 side chains for dsDNA and ssDNA match well with values deduced from crystallographic analyses of protein-DNA complexes...
April 11, 2017: Journal of Chemical Theory and Computation
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