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https://www.readbyqxmd.com/read/29627731/triple-helix-molecular-switch-based-aptasensors-and-dna-sensors
#1
REVIEW
Elnaz Bagheri, Khalil Abnous, Mona Alibolandi, Mohammad Ramezani, Seyed Mohammad Taghdisi
Utilization of traditional analytical techniques is limited because they are generally time-consuming and require high consumption of reagents, complicated sample preparation and expensive equipment. Therefore, it is of great interest to achieve sensitive, rapid and simple detection methods. It is believed that nucleic acids assays, especially aptamers, are very important in modern life sciences for target detection and biological analysis. Aptamers and DNA-based sensors have been widely used for the design of various sensors owing to their unique features...
April 3, 2018: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29626318/thermal-stability-and-conformation-of-dna-and-proteins-under-the-confined-condition-in-the-matrix-of-hydrogels
#2
Shu-Ichi Nakano, Daisuke Yamaguchi, Naoki Sugimoto
Spatially confined environments are seen in biological systems and in the fields of biotechnology and nanotechnology. The confinement restricts the conformational space of polymeric molecules and increasing the degree of molecular crowding. Here, we developed preparation methods for agarose and polyacrylamide gels applicable to UV spectroscopy that can evaluate the confinement effects on DNA and protein structures. Measurements of UV absorbance and CD spectra showed no significant effect of the confinement in the porous media of agarose gels on the base-pair stability of DNA polynucleotides [poly(dA)/poly(dT)] and oligonucleotides (hairpin, duplex, and triplex structures)...
April 6, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29622628/structure-of-the-herpes-simplex-virus-1-capsid-with-associated-tegument-protein-complexes
#3
Xinghong Dai, Z Hong Zhou
Herpes simplex viruses (HSVs) rely on capsid-associated tegument complex (CATC) for long-range axonal transport of their genome-containing capsids between sites of infection and neuronal cell bodies. Here we report cryo-electron microscopy structures of the HSV-1 capsid with CATC up to 3.5-angstrom resolution and atomic models of multiple conformers of capsid proteins VP5, VP19c, VP23, and VP26 and tegument proteins pUL17, pUL25, and pUL36. Crowning every capsid vertex are five copies of heteropentameric CATC, each containing a pUL17 monomer supporting the coiled-coil helix bundle of a pUL25 dimer and a pUL36 dimer, thus positioning their flexible domains for potential involvement in nuclear capsid egress and axonal capsid transport...
April 6, 2018: Science
https://www.readbyqxmd.com/read/29622627/cryo-em-structure-of-a-herpesvirus-capsid-at-3-1-%C3%A3
#4
Shuai Yuan, Jialing Wang, Dongjie Zhu, Nan Wang, Qiang Gao, Wenyuan Chen, Hao Tang, Junzhi Wang, Xinzheng Zhang, Hongrong Liu, Zihe Rao, Xiangxi Wang
Structurally and genetically, human herpesviruses are among the largest and most complex of viruses. Using cryo-electron microscopy (cryo-EM) with an optimized image reconstruction strategy, we report the herpes simplex virus type 2 (HSV-2) capsid structure at 3.1 angstroms, which is built up of about 3000 proteins organized into three types of hexons (central, peripentonal, and edge), pentons, and triplexes. Both hexons and pentons contain the major capsid protein, VP5; hexons also contain a small capsid protein, VP26; and triplexes comprise VP23 and VP19C...
April 6, 2018: Science
https://www.readbyqxmd.com/read/29621581/a-multiplex-real-time-pcr-assay-based-on-inva-and-pagc-genes-for-the-detection-and-quantification-of-salmonella-enterica-from-cattle-lymph-nodes
#5
Jianfa Bai, Valentina Trinetta, Xiaorong Shi, Lance W Noll, Gabriela Magossi, Wanglong Zheng, Elizabeth P Porter, Natalia Cernicchiaro, David G Renter, T G Nagaraja
Cattle lymph nodes can harbor Salmonella and potentially contaminate beef products. We have developed and validated a new real-time PCR (qPCR) assay for the detection and quantification of Salmonella enterica in cattle lymph nodes. The assay targets both the invA and pagC genes, the most conserved molecular targets in Salmonella enterica. An 18S rRNA gene assay that amplifies from cattle and other animal species was also included as an internal control. Available DNA sequences for invA, pagC and 18S rRNA genes were used for primer and probe selections...
April 2, 2018: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/29594738/a-gold-nanoparticle-based-fluorescent-probe-for-simultaneous-recognition-of-single-stranded-dna-and-double-stranded-dna
#6
Haiyan Ma, Zongbing Li, Ning Xue, Zhiyuan Cheng, Xiangmin Miao
A fluorescent method is described for simultaneous recognition of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). It is based on the quenching of the fluorescence of fluorophore labeled DNA probes by gold nanoparticles (AuNPs). To demonstrate feasibility, two DNA probes labeled with spectrally different fluorophores were designed. The first DNA probe (P1 ) was modified with 6-carboxyfluorescein (FAM; with green fluorescence, peaking at 518 nm), while the second (P2 ) was modified with carboxy-X-rhodamine (ROX; with yellow fluorescence, 610 nm)...
January 10, 2018: Mikrochimica Acta
https://www.readbyqxmd.com/read/29575511/triplex-formation-by-oligonucleotides-bearing-organomercurated-base-moieties
#7
Dattatraya Uttam Ukale, Tuomas Lönnberg
Homothymine oligonucleotides bearing a single 5-mercuricytosine or 5-mercuriuracil residue at their termini have been synthesized and their capacity to form triplexes has been examined with an extensive array of double-helical targets. UV and CD melting experiments revealed formation and thermal denaturation of pyrimidine*purine*pyrimidine -type triple helices with all oligonucleotide combinations studied. Nearly all triplexes were destabilized on mercuration of the 3´-terminal residue of the triplex forming oligonucleotide (TFO), in all likelihood due to competing intramolecular Hg(II)-mediated base pairing...
March 25, 2018: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29570443/single-step-production-of-cas9-mrna-for-zygote-injection
#8
Bethany K Redel, Benjamin P Beaton, Lee D Spate, Joshua A Benne, Stephanie L Murphy, Chad W O'Gorman, Anna M Spate, Randall S Prather, Kevin D Wells
Production of Cas9 mRNA in vitro typically requires the addition of a 5´ cap and 3´ polyadenylation. A plasmid was constructed that harbored the T7 promoter followed by the EMCV IRES and a Cas9 coding region. We hypothesized that the use of the metastasis associated lung adenocarcinoma transcript 1 (Malat1) triplex structure downstream of an IRES/Cas9 expression cassette would make polyadenylation of in vitro produced mRNA unnecessary. A sequence from the mMalat1 gene was cloned downstream of the IRES/Cas9 cassette described above...
March 1, 2018: BioTechniques
https://www.readbyqxmd.com/read/29564423/ph-responsive-spherical-nucleic-acid-for-intracellular-lysosome-imaging-and-an-effective-drug-delivery-system
#9
Hui Li, Xiang Zhou, Dongbao Yao, Haojun Liang
Herein, a class of pH-responsive spherical nucleic acid (SNA) nanostructures prepared by functionalizing gold nanoparticles with DNA nanodevices is presented, which can perform duplex-to-triplex transition upon pH change via pH-sensitive parallel Hoogsteen interactions. The SNA nanostructures exhibit tunable pH sensitivity and a highly rapid and reversible allosteric effect. Furthermore, they can exactly image lysosomes in living cells. We next engineered pH-triggered doxorubicin(Dox)-SNA conjugates that could deliver Dox molecules into cancer cells and achieve pH-dependent drug release...
March 22, 2018: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29537270/modeling-pk-shift-in-dna-triplexes-containing-locked-nucleic-acids
#10
Yossa Dwi Hartono, You Xu, Andrey Karshikoff, Lennart Nilsson, Alessandra Villa
The protonation states for nucleic acid bases are difficult to assess experimentally. In the context of triplex DNA, the protonation state of cytidine in the third strand is particularly important, because it needs to be protonated in order to form Hoogsteen hydrogen bonds. A sugar modification, locked nucleic acid (LNA), is widely used in triplex forming oligonucleotides to target sites in the human genome. In this study, the parameters for LNA are developed in line with the CHARMM nucleic acid force field and validated towards the available structural experimental data...
March 14, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29534473/peptide-nucleic-acids-as-a-tool-for-site-specific-gene-editing
#11
REVIEW
Adele S Ricciardi, Elias Quijano, Rachael Putman, W Mark Saltzman, Peter M Glazer
Peptide nucleic acids (PNAs) can bind duplex DNA in a sequence-targeted manner, forming a triplex structure capable of inducing DNA repair and producing specific genome modifications. Since the first description of PNA-mediated gene editing in cell free extracts, PNAs have been used to successfully correct human disease-causing mutations in cell culture and in vivo in preclinical mouse models. Gene correction via PNAs has resulted in clinically-relevant functional protein restoration and disease improvement, with low off-target genome effects, indicating a strong therapeutic potential for PNAs in the treatment or cure of genetic disorders...
March 11, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29527200/whole-genome-sequence-analysis-of-ctx-m-15-producing-klebsiella-isolates-allowed-dissecting-a-polyclonal-outbreak-scenario
#12
Laura Becker, Stephan Fuchs, Yvonne Pfeifer, Torsten Semmler, Tim Eckmanns, Gerit Korr, Dagmar Sissolak, Michael Friedrichs, Edith Zill, Mei-Lin Tung, Christian Dohle, Martin Kaase, Sören Gatermann, Holger Rüssmann, Matthias Steglich, Sebastian Haller, Guido Werner
Extended-spectrum β-lactamase (ESBL) producing Klebsiella pneumoniae pose an important threat of infection with increased morbidity and mortality, especially for immunocompromised patients. Here, we use the rise of multidrug-resistant K. pneumoniae in a German neurorehabilitation center from April 2015 to April 2016 to dissect the benefit of whole genome sequencing (WGS) for outbreak analyses. In total, 53 isolates were obtained from 52 patients and examined using WGS. Two independent analysis strategies (reference-based and -free) revealed the same distinct clusters of two CTX-M-15 producing K...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29522153/nessie-a-tool-for-the-identification-of-approximate-dna-sequence-symmetries
#13
Michele Berselli, Enrico Lavezzo, Stefano Toppo
Motivation: Non-B DNA conformations play an important role in genomic rearrangements, structural three-dimensional organization and gene regulation. Many non-B DNA structures show symmetrical properties as palindromes and mirrors that can form hairpins, cruciform structures or triplexes. A comprehensive tool, capable to perform a fast genome wide search for exact and degenerate symmetrical patterns, is needed for further investigating nucleotide tracts potentially forming non-B DNA structures...
March 7, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29520687/effect-of-660-nm-visible-red-light-on-cell-proliferation-and-viability-in-diabetic-models-in-vitro-under-stressed-conditions
#14
S M Ayuk, N N Houreld, H Abrahamse
The current study evaluated the photobiomodulatory effect of visible red light on cell proliferation and viability in various fibroblast diabetic models in vitro, namely, unstressed normal (N) and stressed normal wounded (NW), diabetic wounded (DW), hypoxic wounded (HW) and diabetic hypoxic wounded (DHW). Cells were irradiated at a wavelength of 660 nm with a fluence of 5 J/cm2 (11.23 mW/cm2 ), which related to an irradiation time of 7 min and 25 s. Control cells were not irradiated (0 J/cm2 ). Cells were incubated for 48 h and cellular proliferation was determined by measuring 5-bromo-2'-deoxyuridine (BrdU) in the S-phase (flow cytometry), while viability was assessed by the Trypan blue exclusion test and Apoptox-glo triplex assay...
March 8, 2018: Lasers in Medical Science
https://www.readbyqxmd.com/read/29488675/analyte-triggered-dna-probe-release-from-a-triplex-molecular-beacon-for-nanopore-sensing
#15
Bingyuan Guo, Yingying Sheng, Ke Zhou, Quansheng Liu, Lei Liu, Hai-Chen Wu
A new nanopore sensing strategy based on triplex molecular beacon was developed for the detection of specific DNA or multivalent proteins. The sensor is composed of a triplex-forming molecular beacon and a stem-forming DNA component that is modified with a host-guest complex. Upon target DNA hybridizing with the molecular beacon loop or multivalent proteins binding to the recognition elements on the stem, the DNA probe is released and produces highly characteristic current signals when translocated through α-hemolysin...
February 28, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29479610/the-taiji-and-eight-trigrams-chemistry-philosophy-of-chiral-iridium-iii-complexes-with-triplex-stereogenic-centers
#16
Zhi-Ping Yan, Xu-Feng Luo, Kang Liao, Zi-Xuan Lin, Zheng-Guang Wu, Yong-Hui Zhou, You-Xuan Zheng
Four novel chiral iridium(iii) complexes with triplex stereogenic centers were synthesized by introducing chiral carbon atoms into cyclometalated and ancillary ligands, and separated into eight isomers, which coincide with the old Chinese philosophy Eight Trigrams. The electron circular dichroism and circularly polarized luminescence spectra of four pairs of isomers show perfect mirror images with a dissymmetry factor (glum factor) of around 0.003.
February 26, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/29466894/a-preliminary-study-on-topical-ozonated-oil-in-the-therapeutic-management-of-atopic-dermatitis-in-murine
#17
J Lu, M Chen, L Gao, Q Cheng, Y Xiang, J Huang, K Wu, J Huang, M Li
Atopic dermatitis (AD) is an inflammatory skin disease characterized as a Th2-predominant immune response. Patients are susceptible to infection. Ozone is used for wound treatment due to its anti-infection features. However, it is unclear whether ozone can recovery AD lesions. In this study, mice were repeatedly challenged with the triplex allergens of staphylococcal enterotoxin B, ovalbumin and calcipotriol ointment on the back to develop AD lesions and were treated with ozonated oil. We found that ozonated oil significantly inhibited inflammation and healed the lesions in 7 days...
February 22, 2018: Journal of Dermatological Treatment
https://www.readbyqxmd.com/read/29464313/nuclear-chloroplast-and-mitochondrial-data-of-a-us-cannabis-dna-database
#18
Rachel Houston, Matthew Birck, Bobby LaRue, Sheree Hughes-Stamm, David Gangitano
As Cannabis sativa (marijuana) is a controlled substance in many parts of the world, the ability to track biogeographical origin of cannabis could provide law enforcement with investigative leads regarding its trade and distribution. Population substructure and inbreeding may cause cannabis plants to become more genetically related. This genetic relatedness can be helpful for intelligence purposes. Analysis of autosomal, chloroplast, and mitochondrial DNA allows for not only prediction of biogeographical origin of a plant but also discrimination between individual plants...
February 20, 2018: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/29464002/mir-205-5p-and-mir-342-3p-cooperate-in-the-repression-of-the-e2f1-transcription-factor-in-the-context-of-anticancer-chemotherapy-resistance
#19
Xin Lai, Shailendra K Gupta, Ulf Schmitz, Stephan Marquardt, Susanne Knoll, Alf Spitschak, Olaf Wolkenhauer, Brigitte M Pützer, Julio Vera
High rates of lethal outcome in tumour metastasis are associated with the acquisition of invasiveness and chemoresistance. Several clinical studies indicate that E2F1 overexpression across high-grade tumours culminates in unfavourable prognosis and chemoresistance in patients. Thus, fine-tuning the expression of E2F1 could be a promising approach for treating patients showing chemoresistance. Methods: We integrated bioinformatics, structural and kinetic modelling, and experiments to study cooperative regulation of E2F1 by microRNA (miRNA) pairs in the context of anticancer chemotherapy resistance...
2018: Theranostics
https://www.readbyqxmd.com/read/29447396/rna-dna-hybrids-promote-the-expansion-of-friedreich-s-ataxia-gaa-n-repeats-via-break-induced-replication
#20
Alexander J Neil, Miranda U Liang, Alexandra N Khristich, Kartik A Shah, Sergei M Mirkin
Expansion of simple DNA repeats is responsible for numerous hereditary diseases in humans. The role of DNA replication, repair and transcription in the expansion process has been well documented. Here we analyzed, in a yeast experimental system, the role of RNA-DNA hybrids in genetic instability of long (GAA)n repeats, which cause Friedreich's ataxia. Knocking out both yeast RNase H enzymes, which counteract the formation of RNA-DNA hybrids, increased (GAA)n repeat expansion and contraction rates when the repetitive sequence was transcribed...
February 13, 2018: Nucleic Acids Research
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