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https://www.readbyqxmd.com/read/28092851/plasmid-dna-affinity-partitioning-using-polyethylene-glycol-sodium-sulfate-aqueous-two-phase-systems
#1
Behzad Nazer, Mohammad Reza Dehghani, Bahram Goliaei
Extraction of plasmid DNA (pDNA) from an alkaline bacterial cell lysate has been investigated using partitioning and affinity partitioning in aqueous two-phase systems (ATPSs) containing 12% (w/w) polyethylene glycol and 12% (w/w) sodium sulfate. In this work, a modified 20bp pyrimidine oligonucleotide acting as a triplex-forming oligonucleotide (TFO) was employed as an affinity ligand to improve the partition behavior. The pUC118 plasmid was chosen to be extracted because of its specific oligonucleotide recognition sequence...
January 3, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28081498/enhancing-analysis-throughput-sensitivity-and-specificity-in-lc-esi-ms-ms-assay-of-plasma-25-hydroxyvitamin-d3-by-derivatization-with-triplex-4-4-dimethylaminophenyl-1-2-4-triazoline-3-5-dione-daptad-isotopologues
#2
Shoujiro Ogawa, Hiroki Kittaka, Akiho Nakata, Kenji Komatsu, Takahiro Sugiura, Mamoru Satoh, Fumio Nomura, Tatsuya Higashi
The plasma/serum concentration of 25-hydroxyvitamin D3 [25(OH)D3] is a diagnostic index for vitamin D deficiency/insufficiency, which is associated with a wide range of diseases, such as rickets, cancer and diabetes. We have reported that the derivatization with 4-(4-dimethylaminophenyl)-1,2,4-triazoline-3,5-dione (DAPTAD) works well in the liquid chromatography/electrospray ionization-tandem mass spectrometry (LC/ESI-MS/MS) assay of the serum/plasma 25(OH)D3 for enhancing the sensitivity and the separation from a potent interfering metabolite, 3-epi-25-hydroxyvitamin D3 [3-epi-25(OH)D3]...
November 17, 2016: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28076350/emergence-of-rare-species-of-nontuberculous-mycobacteria-as-potential-pathogens-in-saudi-arabian-clinical-setting
#3
Bright Varghese, Mushira Enani, Mohammed Shoukri, Sahar AlThawadi, Sameera AlJohani, Sahal Al-Hajoj
BACKGROUND: Clinical relevance of nontuberculous mycobacteria (NTM) is increasing worldwide including in Saudi Arabia. A high species diversity of NTM's has been noticed in a recent study. However, the identification in diagnostic laboratories is mostly limited to common species. The impact of NTM species diversity on clinical outcome is so far neglected in most of the clinical settings. METHODOLOGY/PRINCIPAL FINDINGS: During April 2014 to September 2015, a nationwide collection of suspected NTM clinical isolates with clinical and demographical data were carried out...
January 11, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28074208/optomagnetic-detection-of-dna-triplex-nanoswitches
#4
Gabriel Antonio S Minero, Jeppe Fock, John S McCaskill, Mikkel F Hansen
We report on optomagnetic dose-dependent detection of DNA triplex-mediated and pH-switchable clusters of functionalised magnetic nanoparticles.
January 11, 2017: Analyst
https://www.readbyqxmd.com/read/28067256/polypurine-reverse-hoogsteen-pprh-oligonucleotides-can-form-triplexes-with-their-target-sequences-even-under-conditions-where-they-fold-into-g-quadruplexes
#5
Anna Solé, Emmanuelle Delagoutte, Carlos J Ciudad, Véronique Noé, Patrizia Alberti
Polypurine reverse-Hoogsteen (PPRH) oligonucleotides are non-modified DNA molecules composed of two mirror-symmetrical polypurine stretches linked by a five-thymidine loop. They can fold into reverse-Hoogsteen hairpins and bind to their polypyrimidine target sequence by Watson-Crick bonds forming a three-stranded structure. They have been successfully used to knockdown gene expression and to repair single-point mutations in cells. In this work, we provide an in vitro characterization (UV and fluorescence spectroscopy, gel electrophoresis and nuclease assays) of the structure and stability of two repair-PPRH oligonucleotides and of the complexes they form with their single-stranded targets...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28029775/combining-a-ru-ii-building-block-and-rapid-screening-approach-to-identify-dna-structure-selective-light-switch-compounds
#6
Erin Wachter, Diego Moyá, Edith C Glazer
A chemically reactive Ru(II) "building block", able to undergo condensation reactions with substituted diamines, was utilized to create a small library of luminescent "light switch" dipyrido-[3,2-a:2',3'-c] phenazine (dppz) complexes. The impact of substituent identity, position, and the number of substituents on the light switch effect was investigated. An unbiased, parallel screening approach was used to evaluate the selectivity of the compounds for a variety of different biomolecules, including protein, nucleosides, single stranded DNA, duplex DNA, triplex DNA, and G-quadruplex DNA...
December 28, 2016: ACS Combinatorial Science
https://www.readbyqxmd.com/read/28029772/oxidation-of-iron-under-physiologically-relevant-conditions-in-biological-fluids-from-healthy-and-alzheimer-s-disease-subjects
#7
Linh Q Lam, Bruce X Wong, Tony Frugier, Qiao-Xin Li, Steven J Collins, Ashley I Bush, Peter J Crack, James A Duce
Ferroxidase activity has been reported to be altered in various biological fluids in neurodegenerative disease, but the sources contributing to the altered activity are uncertain. Here we assay fractions of serum and cerebrospinal fluid with a newly validated triplex ferroxidase assay. Our data indicate that while ceruloplasmin, a multicopper ferroxidase, is the predominant source of serum activity, activity in CSF predominantly derives from a <10 kDa component, specifically from polyanions such as citrate and phosphate...
January 3, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28027304/decoding-single-molecule-time-traces-with-dynamic-disorder
#8
Wonseok Hwang, Il-Buem Lee, Seok-Cheol Hong, Changbong Hyeon
Single molecule time trajectories of biomolecules provide glimpses into complex folding landscapes that are difficult to visualize using conventional ensemble measurements. Recent experiments and theoretical analyses have highlighted dynamic disorder in certain classes of biomolecules, whose dynamic pattern of conformational transitions is affected by slower transition dynamics of internal state hidden in a low dimensional projection. A systematic means to analyze such data is, however, currently not well developed...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/28018569/effect-of-surface-treatment-methods-on-the-shear-bond-strength-of-auto-polymerized-resin-to-thermoplastic-denture-base-polymer
#9
Roodabeh Koodaryan, Ali Hafezeqoran
PURPOSE: Polyamide polymers do not provide sufficient bond strength to auto-polymerized resins for repairing fractured denture or replacing dislodged denture teeth. Limited treatment methods have been developed to improve the bond strength between auto-polymerized reline resins and polyamide denture base materials. The objective of the present study was to evaluate the effect of surface modification by acetic acid on surface characteristics and bond strength of reline resin to polyamide denture base...
December 2016: Journal of Advanced Prosthodontics
https://www.readbyqxmd.com/read/28011414/an-electrochemical-dna-sensor-without-electrode-pre-modification
#10
Nian Hong, Lin Cheng, BingGuo Wei, ChaDan Chen, Ling Ling He, DeRong Kong, JinXiang Ceng, Han-Feng Cui, Hao Fan
We present a non-modification electrochemical DNA sensing strategy, which used Potential-Assisted Au-S Deposition and a clamp-like DNA probe. The dual-hairpin probe DNA was tagged with a methylene blue (MB) at the 3' terminal and a thiol at the 5' terminal., Without being hybridized with target DNA, the loop of probe prevented the thiol from reaching the bare gold electrode surface with an applied potential., After hybridization with the target DNA, the probe' s loop-stem structure opened through two distinct and sequential events, which led to the formation of a triplex DNA structure...
October 5, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27979677/folding-of-guanine-quadruplex-molecules-funnel-like-mechanism-or-kinetic-partitioning-an-overview-from-md-simulation-studies
#11
Jiří Šponer, Giovanni Bussi, Petr Stadlbauer, Petra Kührová, Pavel Banáš, Barira Islam, Shozeb Haider, Stephen Neidle, Michal Otyepka
BACKGROUND: Guanine quadruplexes (GQs) play vital roles in many cellular processes and are of much interest as drug targets. In contrast to the availability of many structural studies, there is still limited knowledge on GQ folding. SCOPE OF REVIEW: We review recent molecular dynamics (MD) simulation studies of the folding of GQs, with an emphasis paid to the human telomeric DNA GQ. We explain the basic principles and limitations of all types of MD methods used to study unfolding and folding in a way accessible to non-specialists...
December 13, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27915983/recognition-mechanisms-and-applications-of-peptide-nucleic-acids-targeting-double-stranded-dna
#12
Wenjia Li, Huanhuan Shi, Bo Dong, Kaixuan Nie, Zhengchun Liu, Nongyue He
Targeting double-stranded DNA (dsDNA) with high affinity and specificity has become a hot topic in biochemistry and molecular biology research. Gene diagnosis and therapy, DNA manipulation, and gene expression regulation could be achieved based on certain recognition principles through specific interactions between dsDNA and natural nucleotides or synthesized ligands. Some ligands (e.g., peptide nucleic acids (PNAs), triple helix-forming oligonucleotides (TFOs), oligopolyamides, and zinc-finger peptides) show sufficient affinity and specificity for targeting dsDNA sequences...
October 28, 2016: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/27911399/tools-to-study-the-role-of-architectural-protein-hmgb1-in-the-processing-of-helix-distorting-site-specific-dna-interstrand-crosslinks
#13
Anirban Mukherjee, Karen M Vasquez
High mobility group box 1 (HMGB1) protein is a non-histone architectural protein that is involved in regulating many important functions in the genome, such as transcription, DNA replication, and DNA repair. HMGB1 binds to structurally distorted DNA with higher affinity than to canonical B-DNA. For example, we found that HMGB1 binds to DNA interstrand crosslinks (ICLs), which covalently link the two strands of the DNA, cause distortion of the helix, and if left unrepaired can cause cell death. Due to their cytotoxic potential, several ICL-inducing agents are currently used as chemotherapeutic agents in the clinic...
November 10, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27907175/p53-specifically-binds-triplex-dna-in-vitro-and-in-cells
#14
Marie Brázdová, Vlastimil Tichý, Robert Helma, Pavla Bažantová, Alena Polášková, Aneta Krejčí, Marek Petr, Lucie Navrátilová, Olga Tichá, Karel Nejedlý, Martin L Bennink, Vinod Subramaniam, Zuzana Bábková, Tomáš Martínek, Matej Lexa, Matej Adámik
Triplex DNA is implicated in a wide range of biological activities, including regulation of gene expression and genomic instability leading to cancer. The tumor suppressor p53 is a central regulator of cell fate in response to different type of insults. Sequence and structure specific modes of DNA recognition are core attributes of the p53 protein. The focus of this work is the structure-specific binding of p53 to DNA containing triplex-forming sequences in vitro and in cells and the effect on p53-driven transcription...
2016: PloS One
https://www.readbyqxmd.com/read/27902982/limitation-of-simultaneous-analysis-of-t-cell-receptor-and-%C3%AE%C2%BA-deleting-recombination-excision-circles-based-on-multiplex-real-time-polymerase-chain-reaction-in-common-variable-immunodeficiency-patients
#15
Faranaz Atschekzei, Fareed Ahmad, Torsten Witte, Roland Jacobs, Reinhold E Schmidt
AIM OF STUDY: We used a triplex real-time polymerase chain reaction (PCR) to classify our common variable immunodeficiency (CVID) patients into distinct groups according to the amount of their T-cell receptor excision circles (TRECs) and κ-deleting recombination excision circles (KRECs). MATERIALS AND METHODS: TREC and KREC analysis was performed using a multiplex real-time PCR assay. The T- and B-lymphocyte subsets were measured by flow cytometry. RESULTS: The copy number of TRECs and KRECs was significantly reduced in CVID patients compared to healthy controls...
2016: International Archives of Allergy and Immunology
https://www.readbyqxmd.com/read/27897343/optimization-of-the-alkyl-linker-of-to-base-surrogate-in-triplex-forming-pna-for-enhanced-binding-to-double-stranded-rna
#16
Takaya Sato, Yusuke Sato, Seiichi Nishizawa
A series of triplex-forming PNA probes carrying a thiazole orange (TO) base surrogate through an alkyl linker was synthesized, and the interactions between these so-called tFIT probes and purine-rich sequences within double-stranded RNA (dsRNA) were examined. We found the TO base surrogate linker significantly affected both the binding affinity and the fluorescence response upon triplex formation with the target dsRNA. Among the probes examined, the TO base surrogate connected through the propyl linker in the tFIT probes increased the binding affinity by a factor of ten while maintaining its function as the fluorescent universal base...
November 29, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27889670/selective-recognition-of-cis-trans-isomers-of-platinum-drugs-and-the-detection-of-triplex-dna-based-on-fluorescence-reversible-model-of-quantum-dots
#17
Xiaoling Xu, Fang Gao, Xincai Xiao, Yan Hu, Chaozhen Zhu, Dan Zhao
The identification of spatial structures of drugs and the researches on their interaction mechanism with DNA are always attractive to the researchers. However, their realization is lack of simple and fast method. This paper reports the establishment of multiple-functional detection platform based on the "turn off-on" model of ZnCdSe quantum dots. In this system, ZnCdSe quantum dots work as the fluorescent probe, platinum anti-cancer drugs as the quencher and triplex DNA as the trapping agent. The seemingly similar cisplatin and transplatin exhibited different fluorescent recovery behaviors due to their difference in structure, and thus realized the selective detection of cisplatin and transplatin with the reaction time set at 10min as well as the quantitation of cisplatin over the range of 2...
February 5, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/27869270/triplex-forming-pna-modified-with-unnatural-nucleobases-the-role-of-protonation-entropy-in-rna-binding
#18
Tamaki Endoh, Chiara Annoni, Dziyana Hnedzko, Eriks Rozners, Naoki Sugimoto
Peptide nucleic acid (PNA) modified with unnatural nucleobases enables the formation of a highly stable triplex with a double-stranded RNA at physiological pH. In this communication, we evaluated kinetics and thermodynamics of PNA/RNA triplex formation as a function of both pH and temperature. Protonation entropy was found to be the major factor responsible for the destabilization of the triplex and for the progressive decrease in the association rate at more basic pHs.
November 30, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27865260/antimicrobial-resistance-and-molecular-characterization-of-virulence-genes-phylogenetic-groups-of-escherichia-coli-isolated-from-diarrheic-and-healthy-camel-calves-in-tunisia
#19
Salma Bessalah, John Morris Fairbrother, Imed Salhi, Ghyslaine Vanier, Touhami Khorchani, Mouldi Mabrouk Seddik, Mohamed Hammadi
This study was conducted to determine the prevalence of virulence genes, serogroups, antimicrobial resistance and phylogenetic groups of Escherichia coli strains isolated from diarrheic and healthy camel calves in Tunisia. From 120 fecal samples (62 healthy and 58 diarrheic camel calves aged less than 3 months), 70 E. coli isolates (53 from diarrheic herds and 17 from healthy herds) were examined by PCR for detection of the virulence genes associated with pathogenic E. coli in animals. A significantly greater frequency of the f17 gene was observed in individual camels and in herds with diarrhea, this gene being found in 44...
December 2016: Comparative Immunology, Microbiology and Infectious Diseases
https://www.readbyqxmd.com/read/27860399/toxin-a-of-the-nosocomial-pathogen-clostridium-difficile-induces-primary-effects-in-the-proteome-of-hep-2-cells
#20
Johannes Junemann, Gurbet Birgin, Jelena Erdmann, Anke Schröder, Ingo Just, Ralf Gerhard, Andreas Pich
PURPOSE: This study was carried out to investigate the impact of high concentrations of Clostridium difficile toxin A (TcdA) on the proteome of human cells. It should also be examined whether a catalytically deficient mutant (TcdANXN ) has an effect on target cells. EXPERIMENTAL DESIGN: Proteome changes were investigated after treatment of HEp-2 cells with 20 nM TcdA for 8 h using a triplex SILAC labeling method and shotgun proteomics. Proteins from differently labeled and treated cells were combined for analysis using an HPLC coupled to an Orbitrap mass spectrometer...
November 10, 2016: Proteomics. Clinical Applications
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