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Hai-Bo Wang, Li-Hong Ma, Bi-Yun Fang, Yuan-Di Zhao, Xue-Bin Hu
This study has reported that a GR-5 DNAzyme based lead ion strip biosensor could exhibit an enhanced specificity with the assistance of graphene oxide (GO). This enhancement results from the specific π-stacking interaction between the ribose rings of the nucleobases and the carbon hexagons in GO which can reduce the false positive interference by removing unhybridized ssDNA during the annealing of GR-5 DNAzyme. Meanwhile, conjugate pad was sprayed with two kinds of AuNP-DNA probes, and nitrocellulose membrane test zone and control zone were immobilized with two kinds of biotin-DNA probes, respectively...
May 21, 2018: Colloids and Surfaces. B, Biointerfaces
Ayyanu Ravikumar, Perumal Panneerselvam, Norhashimah Morad
In this paper, we propose a metal-polydopamine framework (MPDA) with specific molecular probe which appears to be the most promising approach to a strong fluorescence quencher. The MPDA framework quenching ability towards various organic fluorophore such as aminoethylcomarin acetate (AMCA), 6-carboxyfluorescein (FAM), carboxyteramethylrhodamine (TAMRA) and Cy5 are used to establish a fluorescent biosensor that can selectively recognize Hg2+ and Ag+ ion. The fluorescent quenching efficiency was sufficient to achieve more than 96%...
May 24, 2018: ACS Applied Materials & Interfaces
Yuanling Sun, Chaofan Ding, Yanna Lin, Weiyan Sun, Hao Liu, Xiaodong Zhu, Yuxue Dai, Chuannan Luo
In this work, a highly selective and sensitive chemiluminescence (CL) biosensor was prepared for adenosine (AD) detection based on carbon quantum dots (CQDs) catalyzing the CL system of luminol-H2 O2 under alkaline environment and CQDs was released from the surface of AD aptamers functionalized graphene @ magnetic β-cyclodextrin polymers (GO@Fe3 O4 @β-CD@A-Apt). Firstly, GO@Fe3 O4 @β-CD and CQDs were prepared and characterized by transmission electron microscopy (TEM), scanning electron microscope (SEM), UV-Vis absorption spectra (UV), fluorescence spectra (FL), fourier transform infrared (FTIR) and X-ray powder diffraction (XRD)...
August 15, 2018: Talanta
Dinko Novosel, Daniel Cadar, Tamás Tuboly, Andreja Jungic, Tomasz Stadejek, Tahar Ait-Ali, Attila Cságola
BACKGROUND: Porcine parvovirus 2 (PPV2) was detected in swine serum without showing any relationship with disease. The emergence of the virus seemed to be a unique event until other genetically highly similar parvoviruses were identified in China and, later in 2012, the presence of the virus was also described in Europe. PPV2 is widely distributed in pig populations where it is suspected to be involved in respiratory conditions, based on its frequent detection in lung samples. In order to investigate the potential pathogenic involvement of PPV2, 60 dead pigs were examined from two farms...
May 21, 2018: BMC Veterinary Research
Katarína Nemčeková, Ján Labuda, Viktor Milata, Jana Blaškovičová, Jozef Sochr
The understanding of DNA-drug interaction mechanism is among the important aspects of biological studies for drug design, discovery and pharmaceutical development processes. Published rather detailed FTIR and UV-visible spectroscopic studies on the interactions of theophylline, theobromine and caffeine with calf thymus DNA have shown effective binding of these methylxanthine derivatives to DNA and RNA involving H-bonds. However, to our knowledge, there is no such investigation using electrochemical approach...
May 3, 2018: Bioelectrochemistry
Ganggang Huang, Zhenwei Zhong, Shane Miersch, Sachdev S Sidhu, Shin-Chen Hou, Donghui Wu
Demand for monoclonal antibodies (mAbs) in basic research and medicine is increasing yearly. Hybridoma technology has been the dominant method for mAb development since its first report in 1975. As an alternative technology, phage display methods for mAb development are increasingly attractive since Humira, the first phage-derived antibody and one of the best-selling mAbs, was approved for clinical treatment of rheumatoid arthritis in 2002. As a non-animal based mAb development technology, phage display bypasses antigen immunogenicity, humanization, and animal maintenance that are required from traditional hybridoma technology based antibody development...
May 1, 2018: Journal of Visualized Experiments: JoVE
Penyu Zhou, Zhengyuan Zhai, Xiong Yao, Peihua Ma, Yanling Hao
A novel cryptic plasmid from Enterococcus durans 1-8, designated as pMK8, was sequenced and analyzed in this study. It consists of 3337 bp with a G + C content of 33.11%. Sequence analysis of pMK8 revealed three putative open reading frames (ORFs). Based on homology, two of them were identified as genes encoding replication initiation (RepC) and mobilization (Mob) protein, respectively. Sequence analysis revealed a pT181 family double-strand origin (dso) and a putative single-strand origin (sso) located upstream of the repC gene...
May 17, 2018: Current Microbiology
Andrzej Kaźmierczak, Kamila Soboska
In animals during apoptosis, the best examined type of programmed cell death (PCD), three main phases are distinguished: (i) specification (signaling), (ii) killing and (iii) execution one. It has bean postulated that plant PCD also involves three subsequent phases: (i) transmission of death signals to cells (signaling), (ii) initiation of killing processes and (iii) destruction of cells. One of the most important hallmarks of animal and plant PCD are those regarding nucleus, not thoroughly studied in plants so far...
April 30, 2018: Micron: the International Research and Review Journal for Microscopy
Thomas Stefan Bronder, Max Philipp Jessing, Arshak Poghossian, Michael Keusgen, Michael J Schöning
Field-effect-based electrolyte-insulator-semiconductor (EIS) sensors were modified with a bilayer of positively charged weak polyelectrolyte (poly(allylamine hydrochloride) (PAH)) and probe single-stranded deoxyribonucleic acid (ssDNA) and are used for the detection of target complementary deoxyribonucleic acid (cDNA) in different test solutions. The sensing mechanism is based on the detection of the intrinsic molecular charge of target cDNA molecules after the hybridization event between cDNA and immobilized probe ssDNA...
May 17, 2018: Analytical Chemistry
Yang Chen, Jine Wang, Yajie Zhang, Lijun Xu, Tian Gao, Bing Wang, Renjun Pei
Aptamers are short single-stranded DNA or RNA, which can be selected in vitro by systematic evolution of ligands by exponential enrichment (SELEX). In order to develop novel light-up probes to substitute G-quadruplex (G4), we selected a DNA aptamer for crystal violet (CV), a triphenylmethane light-up dye, by a modified affinity chromatography-based SELEX. The ssDNA pool was first coupled on streptavidin-coated agarose beads through a biotin labeled complementary oligonucleotide, and then the aptamer sequences would be released from agarose beads by CV affinity...
May 17, 2018: Photochemical & Photobiological Sciences
Tania V Silvas, Shurong Hou, Wazo Myint, Ellen Nalivaika, Mohan Somasundaran, Brian A Kelch, Hiroshi Matsuo, Nese Kurt Yilmaz, Celia A Schiffer
The APOBEC3 (A3) family of human cytidine deaminases is renowned for providing a first line of defense against many exogenous and endogenous retroviruses. However, the ability of these proteins to deaminate deoxycytidines in ssDNA makes A3s a double-edged sword. When overexpressed, A3s can mutate endogenous genomic DNA resulting in a variety of cancers. Although the sequence context for mutating DNA varies among A3s, the mechanism for substrate sequence specificity is not well understood. To characterize substrate specificity of A3A, a systematic approach was used to quantify the affinity for substrate as a function of sequence context, length, secondary structure, and solution pH...
May 14, 2018: Scientific Reports
Chengpeng Huang, Xiaoya Fan, Qiaomei Yuan, Xinfeng Zhang, Xiandeng Hou, Peng Wu
Various DNA-modulated photosensitization schemes have been reported for various applications, but DNAzyme has not yet been included. Here, we found the DNAzyme with metal ion as cofactor could also be efficient in modulation of photosensitization process. The UO2 2+ -specific DNAzyme can switch between double strand DNA (dsDNA) and single strand DNA (ssDNA) upon UO2 2+ cleavage, which can regulate the photosensitization process of SYBR Green I. Coupling with photosensitization-induced chromogenic reaction (TMB oxidation), a simple colorimetric sensor for UO2 2+ was developed accordingly...
August 1, 2018: Talanta
Dongmin Shi, Feifan Sheng, Xiaojun Zhang, Guangfeng Wang
This paper reported a novel colorimetric assay strategy for avidin and biotin interactions based on terminal protection of the biotinylated single-stranded DNA and the surface plasmon resonance adsorption of gold nanoparticles (AuNPs). In this assay, it was firstly found that biotin-ssDNA specifically bound to the target protein avidin with strong affinity could be protected from hydrolysis by exonuclease I (Exo I). Furthermore, a colorimetric strategy was designed for the detection of avidin and biotin interactions...
August 1, 2018: Talanta
Ying Zou, Nuo Duan, Shijia Wu, Mofei Shen, Zhouping Wang
Enterohemorrhagic Escherichia coli O157:H7 (E.coli O157:H7) is known as an important food-borne pathogens related to public health. In this study, aptamers which could bind to different stages of E.coli O157:H7 (adjustment phase, log phase and stationary phase) with high affinity and specificity was obtained by Whole Cell-SELEX method through fourteen selection rounds including three counter-selection rounds. Altogether, thirty-two sequences were obtained and nine families were classified to select the optimal aptamer...
May 14, 2018: Journal of Agricultural and Food Chemistry
Yen-Hua Huang, Cheng-Yang Huang
Single-stranded DNA-binding proteins (SSBs) play crucial roles in DNA replication, repair, and recombination. Unlike E. coli , which contains only one type of SSB (EcSSB), some bacteria have two paralogous SSBs, namely, SsbA and SsbB. In this study, we found the third SSB-like protein in Staphylococcus aureus , SAAV2152, which was designated as SaSsbC. SaSsbC is a protein of 131 amino acids and shares 38%, 36%, and 33% sequence identity to SaSsbB, SaSsbA, and EcSSB, respectively. Gene map analysis showed that unlike the E...
April 17, 2018: Oncotarget
Yalda Shoja, Ahmad Kermanpur, Fathallah Karimzadeh
In this present work we made a novel, fast, selective and sensitive electrochemical genobiosensor to detection of EGFR exon 21 point mutation based on two step electropolymerization of Ni(II)-oxytetracycline conducting metallopolymer nanoparticles (Ni-OTC NPs) on the surface of pencil graphite electrode (PGE) which was modified by reduced graphene oxide/carboxyl functionalized ordered mesoporous carbon (rGO/f-OMC) nanocomposite. ssDNA capture probe with amine groups at the5' end which applied as recognition element was immobilized on the rGO/f-OMC/PGE surface via the strong amide bond...
April 14, 2018: Biosensors & Bioelectronics
Ravikumar A, Panneerselvam P
We describe a highly sensitive fluorescence biosensor incorporating polydopamine nanotubes (PDNTs) based on the mechanism of exonuclease III (Exo III) assisted signal amplification for the determination of Hg2+ in aqueous solution. Fluorescent probes of FAM labeled ssDNA (FAM-ssDNA) adsorbed on the PDNTs act as an efficient quencher. In the presence of Hg2+, the FAM-ssDNA can bind to Hg2+ to form double stranded DNA (dsDNA) via the formation of T-Hg2+-T base pairs. Then, the dsDNA was removed from the surface of the PDNTs to restore the fluorescence...
May 11, 2018: Analyst
Qin Pan, Fengling Luo, Min Liu, Xiao-Lian Zhang
The entire human population is at risk of infectious diseases worldwide. Thus far, the diagnosis and treatment of human infectious diseases at the molecular and nanoscale levels have been extremely challenging tasks because of the lack of effective probes to identify and recognize biomarkers of pathogens. Oligonucleotide aptamers are a class of small nucleic acid ligands that are composed of single-stranded DNA (ssDNA) or RNA and act as affinity probes or molecular recognition elements for a variety of targets...
May 7, 2018: Journal of Infection
Eloy Povedano, Alejandro Valverde, Víctor Ruiz-Valdepeñas Montiel, María Pedrero, Paloma Yáñez-Sedeño, Rodrigo Barderas, Pablo San Segundo-Acosta, Alberto Peláez-García, Marta Mendiola, David Hardisson, Susana Campuzano, José Manuel Pingarron
We report a rapid and sensitive electrochemical strategy for the detection of gene-specific 5-methylcytosine DNA methylation. Magnetic beads (MBs) modified with an antibody specific for 5-methylcytosines (5-mC) are employed for the selective capture of any 5-mC methylated single-stranded (ss)DNA sequence. A flanking region next to the 5-mCs of the captured methylated ssDNA is recognized by selective hybridization with a synthetic biotinylated DNA sequence, further labeled with an HRP streptavidin conjugate...
May 9, 2018: Angewandte Chemie
Nidhi Nandu, Mustafa Salih Hizir, Mehmet Veysel Yigit
We have performed a systematic study to analyze the effect of ssDNA length, nucleobase composition and the type of 2D-nps on the desorption response of 36 2D-NAs against several proteins. The studies were performed using fluorescently labeled polyA, polyC and polyT with 23, 18, 12 and 7 nucleotide-long sequences. The results suggest that the ssDNAs with polyC and longer sequences are more resistant to desorption compared to their counterparts. In addition, 2D-NAs assembled using WS2 were least susceptible to desorption by the proteins tested whereas nGO 2D-NAs were the most susceptible nanoassemblies...
May 9, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
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