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https://www.readbyqxmd.com/read/28544921/in-situ-formed-copper-nanoparticles-templated-by-tdt-mediated-dna-for-enhanced-spr-sensor-based-dna-assay
#1
Pei-Xin Yuan, Sheng-Yuan Deng, Chen-Yu Zheng, Serge Cosnier, Dan Shan
For the efficient surface plasmon resonance (SPR)-based DNA assay researching, signal amplification tactics were absolutely necessary. In this work, a sensitive SPR-DNA sensor was developed by employing in situ synthesis of copper nanoparticles (CuNPs) templated by poly-T sequences DNA from terminal deoxynucleotidyl transferase (TdT)-mediated extension, and synergistically with nano-effect deposition as the mass relay. The objective of this strategy was manifold: firstly, tDNA hybridized with the optimal designed probes to active the TdT-mediated DNA extension onto the surface of SPR chip, resulted a long poly-T sequences ssDNA chain in dsDNA terminal onto surface of gold chip and characterized by SPR signal amplitudes...
May 18, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28541828/simple-green-production-of-silver-nanoparticles-facilitated-by-bacterial-genomic-dna-and-their-antibacterial-activity
#2
Jiraporn Chumpol, Sineenat Siri
Green synthesis of AgNPs has gained many research interests as a low cost and eco-friendly approach. This work reported on the use of bacterial genomic DNA as the alternative biopolymer for a green production of AgNPs under a neutral pH. Although both ssDNA and dsDNA could function as stabilizing agents during the synthesis process, the ssDNA, generated by pre-heating the dsDNA at 100 °C, was more efficient to produce AgNPs with higher yield as determined by the intensity of the surface plasmon resonance (SPR) peak of silver at 475 nm...
May 25, 2017: Artificial Cells, Nanomedicine, and Biotechnology
https://www.readbyqxmd.com/read/28537750/detection-of-microrna-by-electrocatalytic-amplification-a-general-approach-for-single-particle-biosensing
#3
Alma D Castañeda, Nicholas J Brenes, Aditya Kondajji, Richard M Crooks
Here we report a sensing scheme for detection of microRNA (miRNA) using electrocatalytic amplification (ECA). ECA is a method in which nanoparticles (NPs) that are catalytic for a specific electrochemical reaction collide with an inert electrode surface. Each collision results in a detectable current transient. In the present article, we show that this general approach can be extended to detection of miRNA. Specifically, PtNPs are modified with a single-strand DNA (ssDNA) shell that is complementary to the miRNA target...
May 24, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28534415/sequence-and-structure-dual-dependent-interaction-between-small-molecules-and-dna-for-the-detection-of-residual-silver-ions-in-as-prepared-silver-nanomaterials
#4
Zhaoyin Wang, Jian Zhao, Zijun Li, Jianchun Bao, Zhihui Dai
Investigations on interaction between small molecules and DNA are the basis of designing advanced bioanalytical systems. We herein propose a novel interaction between heterocyclic aromatic compounds (HACs) and single-stranded DNA (ssDNA). Taking methylene blue (MB) as a typical HAC, it is found that MB can interact with cytosine (C)-rich ssDNA in an enthalpy-driven process. The interaction between MB and C-rich ssDNA is sequence and structure dual-dependent: at least three consecutive C and single-stranded structure are necessary...
May 23, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28532103/sensitive-impedimetric-dna-biosensor-based-on-nb-v-codoped-tio2-for-breast-cancer-susceptible-gene-detection
#5
Yu Wang, Xianwei Huang, He Li, Linlang Guo
In this paper, a novel (Nb,V) codoped TiO2 (NVTO) nanoparticle was synthesized, and a novel electrochemical DNA biosensor based on NVTO was first developed for detection of breast cancer susceptible gene detection. The proposed DNA biosensors were fabricated by immobilization of the probe DNA on a nanoporous CHIT-NVTO thin film deposited on an ITO-coated glass plate. The prepared NVTO composite film was characterized by XRD, SEM and FTIR. The results indicated that the synergistic effect of CHIT-NVTO nanocomposite can increase the electroactive surface area and the loading amounts of ssDNA...
August 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28530800/label-free-multiplexed-single-molecule-analysis-of-protein-dna-complexes-with-nanopores
#6
Garbiñe Celaya, Judit Perales-Calvo, Arturo Muga, Fernando Moro, David Rodriguez-Larrea
Protein interactions with specific DNA sequences are crucial in the control of gene expression and the regulation of replication. Single-molecule methods offer excellent capabilities to unravel the mechanism and kinetics of these interactions. Here we develop a nanopore approach where a target DNA sequence is contained in a hairpin followed by a ssDNA. This system allows DNA-protein complexes to be distinguished from bare DNA molecules as they are pulled through a single nanopore detector, providing both equilibrium and kinetic information...
May 22, 2017: ACS Nano
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
#7
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/28525848/an-amplified-comparative-fluorescence-resonance-energy-transfer-immunosensing-of-ca125-tumor-marker-and-ovarian-cancer-cells-using-green-and-economic-carbon-dots-for-bio-applications-in-labeling-imaging-and-sensing
#8
Somayeh Hamd-Ghadareh, Abdollah Salimi, Fardin Fathi, Saman Bahrami
CA125, is a marker in the clinical diagnosis of several cancers and currently is the best serum-based tumor marker for ovarian cancer. Here, we developed an ultrasensitive antibody-ssDNA aptamer sandwich-type fluorescence immunosensor for CA125 detection. Based on a novel signal amplification strategy the carbon dots (CDs) functionalized with aptamer (CD-aptamer) used as detection probe and PAMAM-Dendrimers/AuNPs was used for covalent attachment of CA125-antibody and completing the sandwich assay method. By measuring of fluorescence resonance energy transfer (FRET) signals between CDs and AuNPs as nanoquenchers, the fluorescence signal quenched during sandwich complex formed between anti-CA125, CA125 and CDs-Aptamer and decreasing of fluorescence response signal is related to CA125 concentrations...
May 4, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28523919/editing-plants-for-virus-resistance-using-crispr-cas
#9
J C Green, J S Hu
This minireview summarizes recent advancements using the clustered regularly interspaced palindromic repeats-associated nuclease systems (CRISPR-Cas) derived from prokaryotes to breed plants resistant to DNA and RNA viruses. The CRISPR-Cas system represents a powerful tool able to edit and insert novel traits into plants precisely at chosen loci offering enormous advantages to classical breeding. Approaches to engineering plant virus resistance in both transgenic and non-transgenic plants are discussed. Iterations of the CRISPR-Cas system, FnCas9 and C2c2 capable of editing RNA in eukaryotic cells offer a particular advantage for providing resistance to RNA viruses which represent the great majority of known plant viruses...
2017: Acta Virologica
https://www.readbyqxmd.com/read/28522818/efficient-modification-of-%C3%AE-dna-substrates-for-single-molecule-studies
#10
Yoori Kim, Armando de la Torre, Andrew A Leal, Ilya J Finkelstein
Single-molecule studies of protein-nucleic acid interactions frequently require site-specific modification of long DNA substrates. The bacteriophage λ is a convenient source of high quality long (48.5 kb) DNA. However, introducing specific sequences, tertiary structures, and chemical modifications into λ-DNA remains technically challenging. Most current approaches rely on multi-step ligations with low yields and incomplete products. Here, we describe a molecular toolkit for rapid preparation of modified λ-DNA...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28522308/development-of-a-ssdna-aptamer-for-detection-of-residual-benzylpenicillin
#11
A-Young Lee, Na-Reum Ha, In-Pil Jung, Sang-Heon Kim, A-Ru Kim, Moon-Young Yoon
Antibiotics are useful for improving the living conditions of livestock. However, residual antibiotics induce several human diseases such as food-borne illness and infection of carbapenem-resistant Enterobacteriaceae (CRE). In this study, the identification of a benzylpenicillin-specific aptamer was selected by rGO-SELEX (reduced Graphene Oxide-Systematic Evolution of Ligands by EXponential enrichment). A random ssDNA library was incubated with rGO for adsorption and eluted with benzylpenicillin. As a result of the selection process, a DNA aptamer was found that specifically bound to benzylpenicillin with high binding affinity, Kd = 383...
May 15, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28521363/a-cisplatin-derivative-tetra-pt-bpy-as-an-oncotherapeutic-agent-for-targeting-alt-cancer
#12
Xiao-Hui Zheng, Xin Nie, Yiming Fang, Zepeng Zhang, Yingnan Xiao, Zongwan Mao, Haiying Liu, Jian Ren, Feng Wang, Lixin Xia, Junjiu Huang, Yong Zhao
Background: In approximately 15% of human cancers, telomere length is maintained independently of telomerase by the homologous recombination (HR)-mediated alternative lengthening of telomeres (ALT) pathway. Whether the ALT pathway can be exploited for therapeutic treatment remains unknown. The purpose of this study is to develop oncotherapeutic agent to target ALT cancers. Methods: Surface plasmon resonance assay, antibody to G-quadruplex, and fluorescence in situ hybridization (FISH) were used to discover Tetra-Pt(bpy), a cisplatin derivative that specifically targets telomeric G-quadruplex...
October 1, 2017: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/28520746/dna-recognition-by-an-rna-guided-bacterial-argonaute
#13
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/28515154/progerin-sequestration-of-pcna-promotes-replication-fork-collapse-and-mislocalization-of-xpa-in-laminopathy-related-progeroid-syndromes
#14
Benjamin A Hilton, Ji Liu, Brian M Cartwright, Yiyong Liu, Maya Breitman, Youjie Wang, Rowdy Jones, Hui Tang, Antonio Rusinol, Phillip R Musich, Yue Zou
Hutchinson-Gilford progeria syndrome (HGPS) is a rare genetic disorder that is caused by a point mutation in the LMNA gene resulting in production of a truncated farnesylated-prelamin A protein (progerin). We previously reported that XPA mislocalized to the progerin-induced DNA double-strand break (DSB) sites, blocking DSB repair, which led to DSB accumulation, DNA damage responses, and early replication arrest in HGPS. In this study, the XPA mislocalization to DSBs occurred at stalled or collapsed replication forks, concurrent with a significant loss of PCNA at the forks, whereas PCNA efficiently bound to progerin...
May 17, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28515022/sos-response-in-bacteria-inhibitory-activity-of-lichen-secondary-metabolites-against-escherichia-coli-reca-protein
#15
Pierangelo Bellio, Letizia Di Pietro, Alisia Mancini, Marisa Piovano, Marcello Nicoletti, Fabrizia Brisdelli, Donatella Tondi, Laura Cendron, Nicola Franceschini, Gianfranco Amicosante, Mariagrazia Perilli, Giuseppe Celenza
BACKGROUND: RecA is a bacterial multifunctional protein essential to genetic recombination, error-prone replicative bypass of DNA damages and regulation of SOS response. The activation of bacterial SOS response is directly related to the development of intrinsic and/or acquired resistance to antimicrobials. Although recent studies directed towards RecA inactivation via ATP binding inhibition described a variety of micromolar affinity ligands, inhibitors of the DNA binding site are still unknown...
June 15, 2017: Phytomedicine: International Journal of Phytotherapy and Phytopharmacology
https://www.readbyqxmd.com/read/28511701/easi-crispr-a-robust-method-for-one-step-generation-of-mice-carrying-conditional-and-insertion-alleles-using-long-ssdna-donors-and-crispr-ribonucleoproteins
#16
Rolen M Quadros, Hiromi Miura, Donald W Harms, Hisako Akatsuka, Takehito Sato, Tomomi Aida, Ronald Redder, Guy P Richardson, Yutaka Inagaki, Daisuke Sakai, Shannon M Buckley, Parthasarathy Seshacharyulu, Surinder K Batra, Mark A Behlke, Sarah A Zeiner, Ashley M Jacobi, Yayoi Izu, Wallace B Thoreson, Lisa D Urness, Suzanne L Mansour, Masato Ohtsuka, Channabasavaiah B Gurumurthy
BACKGROUND: Conditional knockout mice and transgenic mice expressing recombinases, reporters, and inducible transcriptional activators are key for many genetic studies and comprise over 90% of mouse models created. Conditional knockout mice are generated using labor-intensive methods of homologous recombination in embryonic stem cells and are available for only ~25% of all mouse genes. Transgenic mice generated by random genomic insertion approaches pose problems of unreliable expression, and thus there is a need for targeted-insertion models...
May 17, 2017: Genome Biology
https://www.readbyqxmd.com/read/28510759/an-intact-mcm10-coiled-coil-interaction-surface-is-important-for-origin-melting-helicase-assembly-and-the-recruitment-of-pol-%C3%AE-to-mcm2-7
#17
Patricia Perez-Arnaiz, Irina Bruck, Max K Colbert, Daniel L Kaplan
Mcm10 is an essential eukaryotic factor required for DNA replication. The replication fork helicase is composed of Cdc45, Mcm2-7 and GINS (CMG). DDK is an S-phase-specific kinase required for replication initiation, and the DNA primase-polymerase in eukaryotes is pol α. Mcm10 forms oligomers in vitro, mediated by the coiled-coil domain at the N-terminal region of the protein. We characterized an Mcm10 mutant at the N-terminal Domain (NTD), Mcm10-4A, defective for self-interaction. We found that the Mcm10-4A mutant was defective for stimulating DDK phosphorylation of Mcm2, binding to eighty-nucleotide ssDNA, and recruiting pol α to Mcm2-7 in vitro...
May 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28508913/digitally-encoded-silica-microparticles-for-multiplexed-nucleic-acid-detection
#18
Weiwei Xu, Chao Chen, Xiaodong Ma, Lihua Yuan, Shenquan Liu, Kexiao Zheng, Jiong Li
A robust high throughput suspension array was proposed to analyze biomolecules. To exploit its capacity for nucleic acid detection, we designed a multiplex nested asymmetric PCR (MNAS PCR) that can produce single stranded DNA (ssDNA) efficiently without complicated optimization. Multiplexed HPV genotyping was demonstrated with high selectivity, high sensitivity and rapid hybridization within 20 minutes.
May 16, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28507156/rna-primer-primase-complexes-serve-as-the-signal-for-polymerase-recycling-and-okazaki-fragment-initiation-in-t4-phage-dna-replication
#19
Michelle M Spiering, Philip Hanoian, Swathi Gannavaram, Stephen J Benkovic
The opposite strand polarity of duplex DNA necessitates that the leading strand is replicated continuously whereas the lagging strand is replicated in discrete segments known as Okazaki fragments. The lagging-strand polymerase sometimes recycles to begin the synthesis of a new Okazaki fragment before finishing the previous fragment, creating a gap between the Okazaki fragments. The mechanism and signal that initiate this behavior-that is, the signaling mechanism-have not been definitively identified. We examined the role of RNA primer-primase complexes left on the lagging ssDNA from primer synthesis in initiating early lagging-strand polymerase recycling...
May 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
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
#20
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
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