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Dna aptamer

Hongmei Yang, Yan Zhang, Lina Zhang, Kang Cui, Shenguang Ge, Jiadong Huang, Jinghua Yu
Highly conductive, robust, and multifunctional integrated paper-supported electrodes are requisite to fulfill the promise of paper-based analytical application. Herein, an all-in-one Au electrode comprising of detection zone, waterproof electronic bridge, and signal output contactor was engineered via combining the double-sided growth method with the secondary wax-printing. Benefiting from the strongly omnidirectional conductivity and desirably mechanical robustness of the as-prepared electrode, a stackable lab-on-paper cyto-device integrated with high-efficiency photoelectrochemical strategy was developed for the MCF-7 cells assay...
May 21, 2018: Analytical Chemistry
Svetlana V Harbaugh, Jennifer Martin, Jenna Weinstein, Grant Ingram, Nancy Kelley-Loughnane
Synthetic riboswitches are engineered to regulate gene expression in response to a variety of non-endogenous small molecules, and a challenge to select this engineered response requires robust screening tools. A new synthetic riboswitch can be created by linking an in vitro-selected aptamer library with a randomized expression platform followed by in vivo selection and screening. In order to determine response to analyte, we developed a dual-color reporter comprising elements of the E. coli fimbriae phase variation system: recombinase FimE controlled by a synthetic riboswitch and an invertible DNA segment (fimS) containing a constitutively active promoter placed between two fluorescent protein genes...
May 17, 2018: Methods: a Companion to Methods in Enzymology
Mohammad Hasanzadeh, Amir Zargami, Hossein Navay Baghban, Ahad Mokhtarzadeh, Nasrin Shadjou, Soltanali Mahboob
The genetic disorder phenylketonuria (PKU) is the inability to metabolize phenylalanine because of a lack of the enzyme phenylalanine hydroxylase. Phenylalanine is used to biochemically form proteins, coded for by DNA. The development of an apta-assay for detection of l-Phenylalanine is presented in this work. A highly specific DNA-aptamer, selected to l-Phenylalanine was immobilized onto a gold nanostructure and electrochemical measurements were performed in a solution containing the phosphate buffer solution with physiological pH...
May 16, 2018: International Journal of Biological Macromolecules
Zhanmin Liu, Chenhui Yao, Cuiyun Yang, Yanming Wang, Sibao Wan, Junyi Huang
Listeria monocytogenes is an important food-borne pathogen, and it can cause severe diseases. Rapid detection of L. monocytogenes is crucial to control this pathogen. A simple and robust strategy based on the cascade of PCR and G-quadruplex DNAzyme catalyzed reaction was used to detect L. monocytogenes. In the presence of hemin and the aptamer formed during PCR, the catalytic horseradish peroxidase-mimicking G-quadruplex DNAzymes allow the colorimetric responses of target DNA from L. monocytogenes. This assay can detect genomic DNA of L...
May 16, 2018: Analytical Biochemistry
Shuzhen Lv, Kangyao Zhang, Yongyi Zeng, Dianping Tang
A new double photosystems-based 'Z-scheme' photoelectrochemical (PEC) sensing platform is designed for ultrasensitive detection of prostate-specific antigen (PSA) by coupling with three-dimensional (3D) DNA walker. Two photosystems consist of CdS quantum dots (photosystem I; PS I) and BiVO4 photoactive materials (photosystem II; PS II), whereas gold nanoparticles (AuNPs) photodeposited on high-active {010} facets of BiVO4 are used as the electron mediators to promote electron transfer from conduction band (CB) of PS II to valence band (VB) of PS I...
May 18, 2018: Analytical Chemistry
Lingying Zhou, Ning Gan, Yongxiang Wu, Futao Hu, Jianyuan Lin, Yuting Cao, Dazhen Wu
Recently, it has been crucial to be able to detect and quantify small molecular targets simultaneously in biological samples. Herein, a simple and conventional double-T type microchip electrophoresis (MCE) based platform for the multiplex detection of quality indicator molecule targets in urine, using ampicillin (AMPI), adenosine triphosphate (ATP) and estradiol (E2) as models, was developed. Several programmable hairpin probes (PHPs) were designed for detecting different targets and triggering isothermal polymerase-catalyzed target recycling (IPCTR) for signal amplification...
May 18, 2018: Analyst
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
Yi-Bin Zhang, Yan-Peng Wang, Jing Liu
Aptamers are single-stranded DNA or RNA which are isolated from synthesized random oligonucleotide library in vitro via systematic evolution of ligands by exponential enrichment (SELEX) and can bind to metal ions, small molecules, carbohydrates, lipids, proteins, and others targets with high affinity and specificity. Aptamers have the advantages of simple preparation, good thermal stability, and low immunogenicity and have great potential in the medical fields such as molecular imaging, biosensing, early diagnosis of diseases, and targeted therapy...
May 2018: Zhongguo Dang Dai Er Ke za Zhi, Chinese Journal of Contemporary Pediatrics
Yan Wu, Tingting Jiang, Zhaoyang Wu, Ruqin Yu
A ratiometric surface-enhanced Raman scattering (SERS) aptasensor based on internal standard (IS) methods was proposed for the ultrasensitive and reproducible quantitative detection of silver ion (Ag+ ) with Au@Ag core-shell nanoparticle (Au@Ag NP) substrate. In principle, the thiolated 5'-Rox C-containing labeled aptamer probe (Rox-aptamer) is firstly immobilized on the SERS substrate surface and then hybridizes with the complementary DNA (cDNA) to form a rigid double-stranded DNA (dsDNA), in which the Rox Raman labels is used to produce the Raman signal...
August 1, 2018: Talanta
Shuhuai Li, Jianping Li, Jinhui Luo, Zhi Xu, Xionghui Ma
An electrochemical microfluidic chip is described for the determination of the insecticide carbofuran. It is making use of a molecularly imprinted film (MIP) and a DNA aptamer as dual recognition units. The analyte (carbofuran) is transported to the MIP and captured at the identification site in the channel. Then, carbofuran is eluted with carbinol-acetic acid and transported to the DNA aptamer on the testing position of the chip. It is captured again, this time by the aptamer, and detected by differential pulse voltammetry (DPV)...
May 11, 2018: Mikrochimica Acta
Elisa Scatena, Sara Pascale, Cristina Cairone, Filippo Fabbri, Costantino Del Gaudio
Aptamers, synthetic single-stranded DNA or RNA molecules, can be regarded as a valuable improvement to develop novel ad hoc sensors to diagnose several clinical pathologies. Their intrinsic potential is related to the high specificity and sensitivity to the selected target biomarkers, being capable of detecting very low concentrations and thus allowing an early diagnosis of a possible disease. This kind of probe can be usefully integrated into a number of different devices in order to provide a reliable acquisition of the analyte and properly elaborate the related signal...
2018: BioMed Research International
Elisa Biondi, Steven A Benner
Directed evolution was first applied to diverse libraries of DNA and RNA molecules a quarter century ago in the hope of gaining technology that would allow the creation of receptors, ligands, and catalysts on demand. Despite isolated successes, the outputs of this technology have been somewhat disappointing, perhaps because the four building blocks of standard DNA and RNA have too little functionality to have versatile binding properties, and offer too little information density to fold unambiguously. This review covers the recent literature that seeks to create an improved platform to support laboratory Darwinism, one based on an artificially expanded genetic information system (AEGIS) that adds independently replicating nucleotide “letters” to the evolving “alphabet”...
May 9, 2018: Biomedicines
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
Abigail J Van Riesen, Kaila L Fadock, Prashant S Deore, Ahmed Desoky, Richard A Manderville, Shahin Sowlati-Hashjin, Stacey D Wetmore
Chemically modified aptamers have the opportunity to increase aptamer target binding affinity and provide structure-activity relationships to enhance our understanding of molecular target recognition by the aptamer fold. In the current study, 8-aryl-2'-deoxyguanosine nucleobases have been inserted into the G-tetrad and central TGT loop of the thrombin binding aptamer (TBA) to determine their impact on antiparallel G-quadruplex (GQ) folding and thrombin binding affinity. The aryl groups attached to the dG nucleobase vary greatly in aryl ring size and impact on GQ stability (∼20 °C change in GQ thermal melting (Tm) values) and thrombin binding affinity (17-fold variation in dissociation constant (Kd))...
May 10, 2018: Organic & Biomolecular Chemistry
Shan Zhang, Shuai Zhao, Sai Wang, Jiahui Liu, Yiyang Dong
Lateral flow immunochromatographic strips based on colorants of aptamer-functionalized nanogold particles weredeveloped for the detection of micropollutants aflatoxin B1 (AFB1) and chloramphenicol (CAP). The lateral flow immunochromatographic strip was based on a competitive reaction of thiolated-aptamer between micropollutants and bio-DNA probe-streptavidin as capture material immobilized at the test line. General crucial parameters that might influence the sensitivity have been systematically investigated...
May 9, 2018: Journal of AOAC International
Zhixin Zhou, Guo-Feng Luo, Verena Wulf, Itamar Willner
The study introduces an analytical platform for the detection of genes or aptamer-ligand complexes by nucleic acid barcode patterns generated by DNA machineries. The DNA machineries consist of nucleic acid scaffolds that include specific recognition sites for the different genes or aptamer-ligands analytes. The binding of the analytes to the scaffolds initiate, in the presence of the nucleotide mixture, cyclic polymerization/nicking machinery that yields displaced strands of variable lengths. The electrophoretic separation of the resulting strands provides barcode patterns for the specific detection of the different analytes...
May 8, 2018: Analytical Chemistry
Gang Peng, Xiaoyan Li, Feng Cui, Qianying Qiu, Xiaojun Chen, He Huang
In the food safety evaluation, aflatoxin B1 (AFB1) is an important indicator. In this work, we developed an AFB1 electrochemical aptasensor based on tetrahedral DNA nanostructures (TDNs) immobilized three dimensionally ordered macroporous MoS2-AuNPs hybrid (3DOM MoS2-AuNPs) recognition interface and horseradish peroxidase (HRP) functionalized magnetic signal amplifier. To greatly enhance the recognition efficiency, sensitivity and stability of the aptasensor, the AFB1 aptamer-incorporated TDNs were ingeniously combined with the 3DOM MoS2-AuNPs film for the construction of the sensing interface...
May 7, 2018: ACS Applied Materials & Interfaces
Louis Chonco, Gerónimo Fernández, Rahul Kalhapure, María J Hernáiz, Cecilia García-Oliva, Victor M Gonzalez, M Elena Martín, Thirumala Govender, Raveen Parboosing
The chemokine (C-C motif) ligand 21 (CCL21) is a cytokine that attracts CCR7-positive cells to the T cell (paracortical) zone of lymph nodes by directional migration of these cells along the CCL21 gradient. In this article, we sought to mimic this chemotactic mechanism, by identifying a novel aptamer that binds CCL21 with high affinity. In vitro selection of DNA aptamers was performed by the Systematic Evolution of Ligands by Exponential Enrichment. Quantitative polymerase chain reaction (qPCR) and enzyme-linked oligonucleotide assay were used to screen for high-affinity aptamers against human and mouse CCL21 protein, respectively...
May 7, 2018: Nucleic Acid Therapeutics
Moira L Flanagan, A Emilia Arguello, Drew E Colman, Jiyeon Kim, Jesse N Krejci, Shimu Liu, Yueyu Yao, Yu Zhang, David J Gorin
The challenge of site-selectivity must be overcome in many chemical research contexts, including selective functionalization in complex natural products and labeling of one biomolecule in a living system. Synthetic catalysts incorporating molecular recognition domains can mimic naturally-occurring enzymes to direct a chemical reaction to a particular instance of a functional group. We propose that DNA-conjugated small molecule catalysts (DCats), prepared by tethering a small molecule catalyst to a DNA aptamer, are a promising class of reagents for site-selective transformations...
February 28, 2018: Chemical Science
Liping Du, Jian Wang, Wei Chen, Luhang Zhao, Chunsheng Wu, Ping Wang
This paper presents a dual functional extracellular recording biosensor based on a light-addressable potentiometric sensor (LAPS). The design and fabrication of this biosensor make it possible to record both extracellular membrane potential changes and ATP release from a single taste bud cell for the first time. For detecting ATP release, LAPS chip was functionalized with ATP-sensitive DNA aptamer by covalent immobilization. Taste bud cells isolated from rat were cultured on LAPS surface. When the desired single taste bud cell was illuminated by modulated light, ATP release from single taste bud cells can be measured by recording the shifts of bias voltage-photocurrent curves (I-V curves) when the LAPS chip is working in discrete mode...
August 31, 2018: Analytica Chimica Acta
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