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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
#1
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
#2
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
#3
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...
December 1, 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
#4
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
#5
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...
November 19, 2016: 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
#6
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
#7
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
#8
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
https://www.readbyqxmd.com/read/27846236/disruption-of-higher-order-dna-structures-in-friedreich-s-ataxia-gaa-n-repeats-by-pna-or-lna-targeting
#9
Helen Bergquist, Cristina S J Rocha, Rubén Álvarez-Asencio, Chi-Hung Nguyen, Mark W Rutland, C I Edvard Smith, Liam Good, Peter E Nielsen, Rula Zain
Expansion of (GAA)n repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich's ataxia. (GAA)n expansions form non-canonical structures, including intramolecular triplex (H-DNA), and R-loops and are associated with epigenetic modifications. With the aim of interfering with higher order H-DNA (like) DNA structures within pathological (GAA)n expansions, we examined sequence-specific interaction of peptide nucleic acid (PNA) with (GAA)n repeats of different lengths (short: n=9, medium: n=75 or long: n=115) by chemical probing of triple helical and single stranded regions...
2016: PloS One
https://www.readbyqxmd.com/read/27836755/discovery-of-the-first-dual-g-triplex-g-quadruplex-stabilizing-compound-a-new-opportunity-in-the-targeting-of-g-rich-dna-structures
#10
Jussara Amato, Alessia Pagano, Sandro Cosconati, Giorgio Amendola, Iolanda Fotticchia, Nunzia Iaccarino, Jessica Marinello, Alessio De Magis, Giovanni Capranico, Ettore Novellino, Bruno Pagano, Antonio Randazzo
BACKGROUND: Guanine-rich DNA motifs can form non-canonical structures known as G-quadruplexes, whose role in tumorigenic processes makes them attractive drug-target candidates for cancer therapy. Recent studies revealed that the folding and unfolding pathways of G-quadruplexes proceed through a quite stable intermediate named G-triplex. METHODS: Virtual screening was employed to identify a small set of putative G-triplex ligands. The G-triplex stabilizing properties of these compounds were analyzed by CD melting assay...
November 9, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27833775/assessment-for-melting-temperature-measurement-of-nucleic-acid-by-hrm
#11
Jing Wang, Xiaoming Pan, Xingguo Liang
High resolution melting (HRM), with a high sensitivity to distinguish the nucleic acid species with small variations, has been widely applied in the mutation scanning, methylation analysis, and genotyping. For the aim of extending HRM for the evaluation of thermal stability of nucleic acid secondary structures on sequence dependence, we investigated effects of the dye of EvaGreen, metal ions, and impurities (such as dNTPs) on melting temperature (Tm ) measurement by HRM. The accuracy of HRM was assessed as compared with UV melting method, and little difference between the two methods was found when the DNA Tm was higher than 40°C...
2016: Journal of Analytical Methods in Chemistry
https://www.readbyqxmd.com/read/27816585/a-rapid-and-visual-aptasensor-for-lipopolysaccharides-detection-based-on-the-bulb-like-triplex-turn-on-switch-coupled-with-hcr-hrp-nanostructures
#12
Wentao Xu, Jingjing Tian, Xiangli Shao, Longjiao Zhu, Kunlun Huang, Yunbo Luo
For previously reported aptasensor, the sensitivity and selectivity of aptamers to targets were often suppressed due to the reporter label of single-stranded molecular beacon or hindrance of the duplex DNA strand displacement. To solve the affinity declining of aptamers showed in traditional way and realize on-site rapid detection of Lipopolysaccharides (LPS), we developed an ingenious structure-switching aptasensor based on the bulb-like triplex turn-on switch (BTTS) as the effective molecular recognition and signal transduction element and streptavidin-horseradish peroxidase modified hybridization chain reaction (HCR-HRP) nanocomposites as the signal amplifier and signal report element...
October 5, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27809385/in-vitro-selection-of-ph-activated-dna-nanostructures
#13
Faye Yi Fong, Seung Soo Oh, Craig J Hawker, H Tom Soh
We report the first in vitro selection of DNA nanostructures that switch their conformation when triggered by change in pH. Previously, most pH-active nanostructures were designed using known pH-active motifs, such as the i-motif or the triplex structure. In contrast, we performed de novo selections starting from a random library and generated nanostructures that can sequester and release Mipomersen, a clinically approved antisense DNA drug, in response to pH change. We demonstrate extraordinary pH-selectivity, releasing up to 714-fold more Mipomersen at pH 5...
November 3, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27801432/label-free-dna-based-biosensors-using-structure-selective-light-up-dyes
#14
Yahui Guo, Lijun Xu, Shanni Hong, Qingqing Sun, Weirong Yao, Renjun Pei
Label-free biosensors (LFBs) have demonstrated a great potential in cost-effective applications, and most of the DNA-based LFBs are based on the principle of binding-induced structural transformation. This review is a collection of the latest reported studies, which have employed structure-selective nucleic acid dyes for the development of DNA-based LFBs. The collections in this review have been structured based on the selective binding of dyes towards specific DNA conformations, including single-stranded DNA, double-stranded DNA, triplex DNA, i-motifs and G-quadruplexes...
November 1, 2016: Analyst
https://www.readbyqxmd.com/read/27801366/evaluation-of-paiusp-subtyping-to-characterize-uropathogenic-e-coli-isolates
#15
Yun Mei Lai, Myo Thura Zaw, Shamsul Bahari Shamsudin, Zaw Lin
INTRODUCTION: Uropathogenic virulence factors have been identified by comparing the prevalence of these among urinary tract isolates and environmental strains. The uropathogenic-specific protein (USP) gene is present on the pathogenicity island (PAI) of uropathogenic Escherichia coli (UPEC) and, depending on its two diverse gene types and the sequential patterns of three open reading frame units (orfUs) following it, there is a method to characterize UPEC epidemiologically called PAIusp subtyping...
October 31, 2016: Journal of Infection in Developing Countries
https://www.readbyqxmd.com/read/27790656/correction-triplex-forming-peptide-nucleic-acid-modified-with-2-aminopyridine-as-a-new-tool-for-detection-of-a-to-i-editing
#16
Chiara Annoni, Tamaki Endoh, Dziyana Hnedzko, Eriks Rozners, Naoki Sugimoto
Correction for 'Triplex-forming peptide nucleic acid modified with 2-aminopyridine as a new tool for detection of A-to-I editing' by Chiara Annoni et al., Chem. Commun., 2016, 52, 7935-7938.
October 28, 2016: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/27782131/in-vivo-correction-of-anaemia-in-%C3%AE-thalassemic-mice-by-%C3%AE-pna-mediated-gene-editing-with-nanoparticle-delivery
#17
Raman Bahal, Nicole Ali McNeer, Elias Quijano, Yanfeng Liu, Parker Sulkowski, Audrey Turchick, Yi-Chien Lu, Dinesh C Bhunia, Arunava Manna, Dale L Greiner, Michael A Brehm, Christopher J Cheng, Francesc López-Giráldez, Adele Ricciardi, Jagadish Beloor, Diane S Krause, Priti Kumar, Patrick G Gallagher, Demetrios T Braddock, W Mark Saltzman, Danith H Ly, Peter M Glazer
The blood disorder, β-thalassaemia, is considered an attractive target for gene correction. Site-specific triplex formation has been shown to induce DNA repair and thereby catalyse genome editing. Here we report that triplex-forming peptide nucleic acids (PNAs) substituted at the γ position plus stimulation of the stem cell factor (SCF)/c-Kit pathway yielded high levels of gene editing in haematopoietic stem cells (HSCs) in a mouse model of human β-thalassaemia. Injection of thalassemic mice with SCF plus nanoparticles containing γPNAs and donor DNAs ameliorated the disease phenotype, with sustained elevation of blood haemoglobin levels into the normal range, reduced reticulocytosis, reversal of splenomegaly and up to 7% β-globin gene correction in HSCs, with extremely low off-target effects...
October 26, 2016: Nature Communications
https://www.readbyqxmd.com/read/27780087/surface-modification-of-nanostructure-lipid-carrier-nlc-by-oleoyl-quaternized-chitosan-as-a-mucoadhesive-nanocarrier
#18
Jakarwan Yostawonkul, Suvimol Surassmo, Tawin Iempridee, Wittaya Pimtong, Kunat Suktham, Warayuth Sajomsang, Pattarapond Gonil, Uracha Rungsardthong Ruktanonchai
A nanostructure lipid carrier (NLC) composed of solid, and liquid lipid as a core has been developed as a delivery system for hydrophobic drug molecules. The aim of this research was to fabricate an oleoyl-quaternized-chitosan (CS)-coated NLC, where the mucoadhesive property of nanoparticles is enhanced for more efficient drug delivery. NLC loaded with alpha-mangostin (AP), a model hydrophobic drug, were fabricated using a high pressure homogenization process and subsequently coated with CS. The fabricated nanoparticles showed particle sizes in the range of 200-400nm, with low polydispersity, high physical stability and excellent encapsulation efficiency (EE>90%)...
September 29, 2016: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/27773629/rna-dna-triplex-formation-by-long-noncoding-rnas
#19
REVIEW
Yue Li, Junetha Syed, Hiroshi Sugiyama
Long noncoding RNAs (lncRNAs) play a pivotal role in the regulation of biological processes through various mechanisms that are not fully understood. Proposed mechanisms include regulation based on RNA-protein interactions, as well as RNA-RNA interactions and RNA-DNA interactions. Here, we focus on one possible mechanism that lncRNA might be using to impact biological function, the RNA-DNA triplex formation. We summarize currently available examples of lncRNA triplex formation and discuss the details surrounding orientation of triplex formation as one of the key properties guiding this process...
November 17, 2016: Cell Chemical Biology
https://www.readbyqxmd.com/read/27769486/a-microchip-for-integrated-single-cell-genotoxicity-assay
#20
Hui Dong, Hao Sun, Jianping Zheng
With the development of large-scale biologic databases, precision medicine is becoming a frontier in biomedical research. As a main focus of precision medicine study, cancer has been widely accepted as a disease born out of inherited genetic variations or accumulating genomic damage. At the single-cell level, microfluidics or lab-on-a-chip technology for cancer study is an emerging tool for improving risk assessment, diagnostic categories and therapeutic strategies. This work presents a multi-layer microchip for single-cell gene expression profiling...
December 1, 2016: Talanta
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