2,044 results match your criteria cdnas probes

Characterizing Fluorescence Emissions of Hairpin DNA-Templated Silver Nanoclusters by cDNA Hybridization.

J Nanosci Nanotechnol 2021 Aug;21(8):4134-4138

Department of Chemistry, Gachon University, Sungnam, Kyunggido, 461-701, Korea.

Stem-loop hairpin DNA probes have high hybridization specificity and unique selectivity to target molecules such as DNA and small molecules. DNA-templated silver nanoclusters (DNA-AgNCs) has been widely used to detect biomolecules of interest due to the photostable, bright, and efficient methods. In this study, we measured fluorescence emission of hairpin DNA upon hybridization with cDNA and mutant cDNA (cDNA-1) or mutant cDNA containing mismatched bases in the stem region (cDNA-2). Read More

View Article and Full-Text PDF

Ultrasensitive multiplexed detection of miRNA targets of interest based on encoding probe extension in improved cDNA library.

Anal Chim Acta 2021 Apr 4;1152:338281. Epub 2021 Feb 4.

Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China. Electronic address:

MicroRNAs (miRNAs) are a class of regulatory small RNA molecules that play critical roles in a wide variety of biological processes. Abnormally expressed miRNAs have been increasingly utilized as biomarkers for cancer diagnosis. Generally, a specific cancer is associated with expression alterations of several species of miRNAs and different types of cancers are related to different miRNA species. Read More

View Article and Full-Text PDF

Radiolabeling of Subtracted cDNA Probes by Random Oligonucleotide Extension.

Cold Spring Harb Protoc 2021 02 1;2021(2). Epub 2021 Feb 1.

In this procedure, synthesis of cDNA is performed in the presence of saturating concentrations of all four dNTPs and trace amounts of a single radiolabeled dNTP. After subtraction hybridization, the enriched single-stranded cDNA is radiolabeled to high specific activity in a second synthetic reaction by extension of random oligonucleotide primers using the Klenow fragment of DNA Pol I. Because the concentrations of dNTP in the first reaction are nonlimiting, both the amounts and size of cDNA generated are greater than those achieved in standard labeling protocols. Read More

View Article and Full-Text PDF
February 2021

Reference gene selection for miRNA and mRNA normalization in potato in response to potato virus Y.

Mol Cell Probes 2021 02 25;55:101691. Epub 2020 Dec 25.

Plant Breeding and Acclimatization Institute, National Research Institute, Młochów Research Center, Platanowa 19, Młochów, PL-05-831, Poland.

This was the first report on evaluating candidate reference genes for quantifying the expression profiles of both coding (e.g., mRNA) and non-coding (e. Read More

View Article and Full-Text PDF
February 2021

Highly sensitive detection of multiple antibiotics based on DNA tetrahedron nanostructure-functionalized magnetic beads.

Anal Chim Acta 2020 Jul 30;1120:50-58. Epub 2020 Apr 30.

College of Food and Biological Engineering, Jimei University, Xiamen, 361021, China; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, 361021, China. Electronic address:

Functional DNAs-functionalized magnetic beads (MBs) offer great potential in bioanalysis field because of their target recognition and magnetic separation functions. However, the recognition capability and hybridization affinity of DNA probes often suffer from limited available space, poor probe conformation and non-selective adsorption. To overcome these limitations, we herein used aptamer-pendant DNA tetrahedron nanostructure-functionalized MBs (TETapt-tet MBs) to develop a target-response fluorescence method with tetracycline (TET) as a model. Read More

View Article and Full-Text PDF

Expression of the syncytin-1 and syncytin-2 genes in the trophoblastic tissue of the early pregnancy losses with normal and abnormal karyotypes.

Gene 2020 May 4;741:144533. Epub 2020 Mar 4.

Gazi University, Faculty of Medicine, Department of Obstetrics and Gynaecology, Ankara, Turkey.

Background: Syncytin-1 and syncytin-2 which are endogenous retroviral genes products play a great role in syncytialization during trophoblast differentiation in normal placental tissues. In aneuploidic placentas due to the low level of pregnancy-induced hormones an alteration was occurred in the syncytialization process, while in the presence of cytogenetically abnormal karyotype the effect of syncytin gene expression levels on syncytialization process and in occured to spontaneous abortions is not clear. To reveal this, we investigated in syncytin-1 and syncytin-2 genes expression levels of chromosomally abnormal and normal trophophoblastic tissues and we also discussed the effect of the syncytin gene expression levels to the occurense of the spontaneous abortion. Read More

View Article and Full-Text PDF

Detection and Molecular Characterization of Novel dsRNA Viruses Related to the Family in .

Front Cell Infect Microbiol 2019 11;9:249. Epub 2019 Jul 11.

Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary.

is an oleaginous fungus belonging to the Mucoromycotina subphylum. Our group had previously detected four double-stranded RNA (dsRNA) bands in the NRRL 1296 strain by gel electrophoresis. Here we describe the molecular characterization of its dsRNA elements as well as the discovery of four novel dsRNA viruses: Umbelopsis ramanniana virus 1 (UrV1), Umbelopsis ramanniana virus 2 (UrV2), Umbelopsis ramanniana virus 3 (UrV3), and Umbelopsis ramanniana virus 4 (UrV4). Read More

View Article and Full-Text PDF

TaqMan real-time PCR for detecting bovine viral diarrhea virus.

Pol J Vet Sci 2019 Jun;22(2):405-413

Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China.

The present study was aimed to establish a novel TaqMan real-time PCR (RTm-PCR) for detecting and typing bovine viral diarrhea virus (BVDV), and also to develop a diagnostic protocol which simplifies sample collection and processing. Universal primers and TaqMan-MGB probes were designed from the known sequences of conserved 5' - and 3'-untranslated regions (5'UTR, 3'UTR) of the NADL strain of BVDV. Prior to optimizing the assay, cDNAs were transcribed in vitro to make standard curves. Read More

View Article and Full-Text PDF

mCerulean3-Based Cameleon Sensor to Explore Mitochondrial Ca Dynamics In Vivo.

iScience 2019 Jun 27;16:340-355. Epub 2019 May 27.

Neuroscience Institute, National Research Council (CNR), 35131 Padua, Italy; Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; Venetian Institute of Molecular Medicine (VIMM), 35131 Padua, Italy. Electronic address:

Genetically Encoded Ca Indicators (GECIs) are extensively used to study organelle Ca homeostasis, although some available probes are still plagued by a number of problems, e.g., low fluorescence intensity, partial mistargeting, and pH sensitivity. Read More

View Article and Full-Text PDF

Upconversion fluorescent aptasensor for bisphenol A and 17β-estradiol based on a nanohybrid composed of black phosphorus and gold, and making use of signal amplification via DNA tetrahedrons.

Mikrochim Acta 2019 02 2;186(3):151. Epub 2019 Feb 2.

Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China.

This study describes an upconversion fluorescent aptasensor based on black phosphorus nanohybrids and self-assembled DNA tetrahedrons dual-amplification strategy for rapid detection of the environmental estrogens bisphenol A (BPA) and 17β-estradiol (E2). Tetrahedron complementary DNAs (T-cDNAs) were self-assembled in an oriented fashion on a 2D nanohybrid composed of black phosphorus (BP) and gold to give a materials of architecture BP-Au@T-cDNAs. In parallel, core-shell upconversion nanoparticles were modified with aptamers (UCNPs@apts) and used as capture probes. Read More

View Article and Full-Text PDF
February 2019

Identification of Homologous Recombination Events in Mouse Embryonic Stem Cells Using Southern Blotting and Polymerase Chain Reaction.

J Vis Exp 2018 11 20(141). Epub 2018 Nov 20.

Lab of Animal Models and Functional Genomics (LAMFG), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU);

Relative to the issues of off-target effects and the difficulty of inserting a long DNA fragment in the application of designer nucleases for genome editing, embryonic stem (ES) cell-based gene-targeting technology does not have these shortcomings and is widely used to modify animal/mouse genome ranging from large deletions/insertions to single nucleotide substitutions. Notably, identifying the relatively few homologous recombination (HR) events necessary to obtain desired ES clones is a key step, which demands accurate and reliable methods. Southern blotting and/or conventional PCR are often utilized for this purpose. Read More

View Article and Full-Text PDF
November 2018

DNA microarray analysis using a smartphone to detect the BRCA-1 gene.

Analyst 2018 Dec;144(1):197-205

Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, USA.

DNA microarrays are used to examine changes in gene expression of a large number of genes simultaneously by fluorescent labeling of complementary DNAs (cDNAs). The major bottleneck in implementing microarray technology in resource-limited settings lies in the detection instrument used for generating images of spotted oligonucleotides post-hybridization. While various methods such as a lateral flow assay have been presented to accomplish point-of-care disease detection, there is no simple and effective instrument available to gather spot images maintaining the standard microarray procedures. Read More

View Article and Full-Text PDF
December 2018

The Agropyron cristatum karyotype, chromosome structure and cross-genome homoeology as revealed by fluorescence in situ hybridization with tandem repeats and wheat single-gene probes.

Theor Appl Genet 2018 Oct 1;131(10):2213-2227. Epub 2018 Aug 1.

Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic.

Key Message: Fluorescence in situ hybridization with probes for 45 cDNAs and five tandem repeats revealed homoeologous relationships of Agropyron cristatum with wheat. The results will contribute to alien gene introgression in wheat improvement. Crested wheatgrass (Agropyron cristatum L. Read More

View Article and Full-Text PDF
October 2018

Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis.

Gene 2018 Jul 12;663:165-177. Epub 2018 Apr 12.

Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA; Department of Plant & Soil Sciences, Mississippi State University, Mississippi State, MS 39762, USA. Electronic address:

Loblolly pine (LP; Pinus taeda L.) is an economically and ecologically important tree in the southeastern U.S. Read More

View Article and Full-Text PDF

Molecular cloning and expression analysis of the tyramine
receptor genes in Apis cerana cerana.

Yi Chuan 2018 Feb;40(2):155-161

Honeybee Research Institute, Jiangxi Agricultural University, Nanchang 330045, China.

Tyramine is a biological polyamine, which serves important functions as neurotransmitters, neuromodulators and neurohormone of the central nervous system. It participates in the regulation of various behavior and physiological processes in insects. For example, tyramine and its receptor genes are involved in the regulation of learning and memory in the animals. Read More

View Article and Full-Text PDF
February 2018

Actin genes and their expression in pacific white shrimp, Litopenaeus vannamei.

Mol Genet Genomics 2018 Apr 30;293(2):479-493. Epub 2017 Nov 30.

Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.

Actin is a multi-functional gene family that can be divided into muscle-type actins and non-muscle-type actins. In this study, 37 unigenes encoding actins were identified from RNA-Seq data of Pacific white shrimp, Litopenaeus vannamei. According to phylogenetic analysis, four and three cDNAs belong to cytoplasmic- and heart-type actins and were named LvActinCT and LvActinHT, respectively. Read More

View Article and Full-Text PDF

Tetrahedral DNA probe coupling with hybridization chain reaction for competitive thrombin aptasensor.

Biosens Bioelectron 2018 Feb 15;100:274-281. Epub 2017 Sep 15.

College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, China; Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang 464000, China.

A novel competitive aptasensor for thrombin detection is developed by using a tetrahedral DNA (T-DNA) probe and hybridization chain reaction (HCR) signal amplification. Sulfur and nitrogen co-doped reduced graphene oxide (SN-rGO) is firstly prepared by a simple reflux method and used for supporting substrate of biosensor. Then, T-DNA probe is modified on the electrode by Au-S bond and a competition is happened between target thrombin and the complementary DNA (cDNA) of aptamer. Read More

View Article and Full-Text PDF
February 2018

Design of a Sensitive and Selective Electrochemical Aptasensor for the Determination of the Complementary cDNA of miRNA-145 Based on the Intercalation and Electrochemical Reduction of Doxorubicin.

J AOAC Int 2017 Nov 19;100(6):1754-1760. Epub 2017 Apr 19.

Graduate University of Advanced Technology, Institute of Science and High Technology and Environmental Sciences, Department of Biotechnology, Kerman, Iran.

The aim of this research was the determination of a microRNA (miRNA) using a DNA electrochemical aptasensor. In this biosensor, the complementary complementary DNA (cDNA) of miRNA-145 (a sense RNA transcript) was the target strand and the cDNA of miRNA-145 was the probe strand. Both cDNAs can be the product of the reverse transcriptase-polymerase chain reaction of miRNA. Read More

View Article and Full-Text PDF
November 2017

Ca Measurements in Mammalian Cells with Aequorin-based Probes.

Bio Protoc 2017 Mar;7(5)

Department of Biomedical Sciences, University of Padua, Padua, Italy.

Aequorin is a Ca sensitive photoprotein suitable to measure intracellular Ca transients in mammalian cells. Thanks to recombinant cDNAs expression, aequorin can be specifically targeted to various subcellular compartments, thus allowing an accurate measurement of Ca uptake and release of different intracellular organelles. Here, we describe how to use this probe to measure cytosolic Ca levels and mitochondrial Ca uptake in mammalian cells. Read More

View Article and Full-Text PDF

A novel CdTe quantum dots probe amplified resonance light scattering signals to detect microRNA-122.

Talanta 2017 Apr 7;165:659-663. Epub 2017 Jan 7.

Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, Hunan 411105, China. Electronic address:

We report a rapid and facile resonance light scattering (RLS) technique that utilizes CdTe quantum dots (CdTe QDs) probe to detect microRNA-122. The RLS sensor is ingeniously designed with P1 and P2, two cDNA sequence probes with partially complementary sequences to miRNA-122. The amine-modified P1 and P2 are coupled to the surface of QDs to form functional QDs-P1 and QDs-P2 conjugates, which are collectively referred to as QDs-P. Read More

View Article and Full-Text PDF

Characterization of eleven monosomic alien addition lines added from Gossypium anomalum to Gossypium hirsutum using improved GISH and SSR markers.

BMC Plant Biol 2016 10 7;16(1):218. Epub 2016 Oct 7.

State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.

Background: Gossypium anomalum (BB genome) possesses the desirable characteristics of drought tolerance, resistance to diseases and insect pests, and the potential for high quality fibers. However, it is difficult to transfer the genes associated with these desirable traits into cultivated cotton (G. hirsutum, AADD genome). Read More

View Article and Full-Text PDF
October 2016

Metatranscriptomics of Soil Eukaryotic Communities.

Methods Mol Biol 2016 ;1399:273-87

Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université Lyon 1, Université de Lyon, 43 Boulevard du 11 Novembre 1918, 69622, Villeurbanne Cedex, France.

Functions expressed by eukaryotic organisms in soil can be specifically studied by analyzing the pool of eukaryotic-specific polyadenylated mRNA directly extracted from environmental samples. In this chapter, we describe two alternative protocols for the extraction of high-quality RNA from soil samples. Total soil RNA or mRNA can be converted to cDNA for direct high-throughput sequencing. Read More

View Article and Full-Text PDF
October 2016

High-throughput quantification of chloroplast RNA editing extent using multiplex RT-PCR mass spectrometry.

Plant J 2015 Aug 6;83(3):546-54. Epub 2015 Jul 6.

Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building, Ithaca, NY, 14853, USA.

RNA editing in plants, animals, and humans modifies genomically encoded cytidine or adenosine nucleotides to uridine or inosine, respectively, in mRNAs. We customized the MassARRAY System (Sequenom Inc., San Diego, CA, USA, www. Read More

View Article and Full-Text PDF

A non-PCR SPR platform using RNase H to detect MicroRNA 29a-3p from throat swabs of human subjects with influenza A virus H1N1 infection.

Analyst 2015 Jul;140(13):4566-75

Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Room 609, Mong Man Wai Building, Shatin, NT, Hong Kong, China.

As in all RNA viruses, influenza viruses change and mutate constantly because their RNA polymerase has no proofreading ability. This poses a serious threat to public health nowadays. In addition, traditional pathogen-based detection methods may not be able to report an infection from an unknown type or a subtype of virus if its nucleotide sequence is not known. Read More

View Article and Full-Text PDF

Diversity of A-conotoxins of three worm-hunting cone snails (Conus brunneus, Conus nux, and Conus princeps) from the Mexican Pacific coast.

Peptides 2015 Jun 19;68:25-32. Epub 2015 Feb 19.

Laboratorio de Neurofarmacología Marina, Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Campus Juriquilla, Querétaro 76230, Mexico. Electronic address:

Conus marine snails (∼500 species) are tropical predators that use venoms mainly to capture prey and defend themselves from predators. The principal components of these venoms are peptides that are known as "conotoxins" and generally comprise 7-40 amino acid residues, including 0-5 disulfide bridges and distinct posttranslational modifications. The most common molecular targets of conotoxins are voltage- and ligand-gated ion channels, G protein-coupled receptors, and neurotransmitter transporters, to which they bind, typically, with high affinity and specificity. Read More

View Article and Full-Text PDF

Dual functional graphene derivative-based electrochemical platforms for detection of the TP53 gene with single nucleotide polymorphism selectivity in biological samples.

Anal Chem 2015 Feb 30;87(4):2290-8. Epub 2015 Jan 30.

Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid , E-28040 Madrid, Spain.

Novel disposable electrochemical DNA sensors were prepared for the detection of a target DNA sequence on the p53 tumor suppressor (TP53) gene. The electrochemical platform consisted of screen-printed carbon electrodes (SPCEs) functionalized with a water-soluble reduced graphene oxide-carboxymethylcellulose (rGO-CMC) hybrid nanomaterial. Two different configurations involving hairpin specific capture probes of different length covalently immobilized through carbodiimide chemistry on the surface of rGO-CMC-modified SPCEs were implemented and compared. Read More

View Article and Full-Text PDF
February 2015

[Construction of suppression subtractive hybridization cDNA library of half-blood males of Dermacentor silvarum and analysis of differentially expressed genes].

Zhongguo Ji Sheng Chong Xue Yu Ji Sheng Chong Bing Za Zhi 2014 Aug;32(4):274-9

Objective: To construct a suppression subtractive hybridization (SSH) cDNA library of half-blood males of Dermacentor silvarum, and analyze the differentially expressed genes.

Methods: Total RNA was extracted from the half-blood males and unfed males of D. silvarum. Read More

View Article and Full-Text PDF

Detection of plant viruses in mixed infection by a macroarray-assisted method.

Methods Mol Biol 2015 ;1236:1-11

Horticultural Science, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan,

The protocol for a simple, sensitive, and specific method using a cDNA macroarray to detect multiple viruses is provided. The method can be used even at the production sites for crops, which need a reliable routine diagnosis for mixed infection of plant viruses. The method consists of three steps: RNA extraction, duplex RT-PCR, and "microtube hybridization" (MTH). Read More

View Article and Full-Text PDF

Solution hybrid selection capture for the recovery of functional full-length eukaryotic cDNAs from complex environmental samples.

DNA Res 2014 Dec 3;21(6):685-94. Epub 2014 Oct 3.

Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France

Eukaryotic microbial communities play key functional roles in soil biology and potentially represent a rich source of natural products including biocatalysts. Culture-independent molecular methods are powerful tools to isolate functional genes from uncultured microorganisms. However, none of the methods used in environmental genomics allow for a rapid isolation of numerous functional genes from eukaryotic microbial communities. Read More

View Article and Full-Text PDF
December 2014

Isolation and characterization of the papaya MADS-box E-class genes, CpMADS1 and CpMADS3, and a TM6 lineage gene CpMADS2.

Genet Mol Res 2014 Jul 24;13(3):5299-312. Epub 2014 Jul 24.

Department of Horticulture, National Taiwan University, Taipei, Taiwan.

Papaya (Carica papaya L.) plants are polygamous, with female, male, and hermaphroditic flowers. To understand the roles of MADS-box genes in flower development and sex determination, we cloned cDNAs of E-class genes CpMADS1 and CpMADS3 and a TM6 lineage of the B-class gene CpMADS2 from young flower buds of papaya. Read More

View Article and Full-Text PDF