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Dna aptamer

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https://www.readbyqxmd.com/read/29156407/ultrasensitive-detection-of-prostate-specific-antigen-by-electrochemical-aptasensor-using-enzyme-free-recycling-amplification-via-target-induced-catalytic-hairpin-assembly
#1
Juncai Zhao, Zhanfang Ma
Based on the target-induced catalytic hairpin assembly and bimetallic catalyst, the enzyme-free recycling amplification strategy for sensitive detection of prostate specific antigen (PSA) has been designed. The aptamer and its complementary DNA (C-apt) are modified on the magnetic particles. The aptamer-PSA binding event can release the C-apt that triggers the catalytic assembly between hairpin capture DNA and hairpin help DNA. Then the catalytic hairpin assembly leads to cyclic reuse the C-apt and the generation of many opened hairpin capture DNA, which can associate with the prepared Au/Pt-polymethylene blue (PMB) probes to yield electrochemical signal...
November 15, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29148722/acoustic-wave-driven-functionalized-particles-for-aptamer-based-target-biomolecule-separation
#2
Raheel Ahmad, Ghulam Destgeer, Muhammad Afzal, Jinsoo Park, Husnain Ahmed, Jin Ho Jung, Kwangseok Park, Tae-Sung Yoon, Hyung Jin Sung
We developed a hybrid microfluidic device that utilized acoustic waves to drive functionalized microparticles inside a continuous flow microchannel and to separate particle-conjugated target proteins from a complex fluid. The acoustofluidic device comprised of an interdigitated transducer (IDT) that produced high-frequency surface acoustic waves (SAW) in a polydimethylsiloxane (PDMS) microfluidic channel. The SAW interacted with the sample fluid flow inside the microchannel and deflected particles from their original streamlines to achieve separation...
November 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29147108/muc1-aptamer-targeted-sers-nanoprobes
#3
Suchetan Pal, Stefan Harmsen, Anton Oseledchyk, Hsiao-Ting Hsu, Moritz F Kircher
Recently, surface-enhanced Raman scattering (SERS) nanoprobes (NPs) have shown promise in the field of cancer imaging due to their unparalleled signal specificity and high sensitivity. Here we report the development of a DNA aptamer targeted SERS NP. Recently, aptamers are being investigated as a viable alternative to more traditional antibody targeting due to their low immunogenicity and low cost of production. We developed a strategy to functionalize SERS NPs with DNA aptamers, which target Mucin1 (MUC1) in human breast cancer (BC)...
August 25, 2017: Advanced Functional Materials
https://www.readbyqxmd.com/read/29146902/single-molecule-multiplexed-nanopore-protein-screening-in-human-serum-using-aptamer-modified-dna-carriers
#4
Jasmine Y Y Sze, Aleksandar P Ivanov, Anthony E G Cass, Joshua B Edel
The capability to screen a range of proteins at the single-molecule level with enhanced selectivity in biological fluids has been in part a driving force in developing future diagnostic and therapeutic strategies. The combination of nanopore sensing and nucleic acid aptamer recognition comes close to this ideal due to the ease of multiplexing, without the need for expensive labelling methods or extensive sample pre-treatment. Here, we demonstrate a fully flexible, scalable and low-cost detection platform to sense multiple protein targets simultaneously by grafting specific sequences along the backbone of a double-stranded DNA carrier...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29144411/nucleic-acid-aptamers-emerging-applications-in-medical-imaging-nanotechnology-neurosciences-and-drug-delivery
#5
REVIEW
Pascal Röthlisberger, Cécile Gasse, Marcel Hollenstein
Recent progresses in organic chemistry and molecular biology have allowed the emergence of numerous new applications of nucleic acids that markedly deviate from their natural functions. Particularly, DNA and RNA molecules-coined aptamers-can be brought to bind to specific targets with high affinity and selectivity. While aptamers are mainly applied as biosensors, diagnostic agents, tools in proteomics and biotechnology, and as targeted therapeutics, these chemical antibodies slowly begin to be used in other fields...
November 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29137923/the-pdgf-pdgfr-pathway-as-a-drug-target
#6
REVIEW
Natalia Papadopoulos, Johan Lennartsson
Platelet-derived growth factors (PDGF) promotes cell proliferation, survival and migration, primarily of cells of mesenchymal origin. Dysfunction of PDGF signaling has been observed in a wide array of pathological conditions, such as cancer, fibrosis, neurological conditions and atherosclerosis. Reported abnormalities of the PDGF pathway include overexpression or amplification of PDGF receptors (PDGFRs), gain of function point mutations or activating chromosomal translocations. Current development of therapeutic drugs often aims at producing compounds that specifically target interaction between PDGFs and their receptors by specific DNA aptamers and ligand traps, or downregulate PDGFRs with blocking antibodies, or inhibit tyrosine kinase activity of PDGFRs with small molecules...
November 11, 2017: Molecular Aspects of Medicine
https://www.readbyqxmd.com/read/29136911/one-step-detection-for-two-serological-biomarker-species-to-improve-the-diagnostic-accuracy-of-hepatocellular-carcinoma
#7
Tao Gao, Jun Zhi, Chaoli Mu, Shiyu Gu, Jing Xiao, Jie Yang, Zhaoxia Wang, Yang Xiang
At present, the accuracy of clinical hepatocellular carcinoma (HCC) diagnosis needs to be further improved. In this work, two kinds of serological biomarker species, microRNA and protein biomarker, have been detected simultaneously to identify HCC. Herein, a dual-aptamer hairpin DNA oligonucleotide is designed as the electrochemical sensing probe (ESP) to achieve this goal. The hairpin-structured DNA probe consists microRNA-16 (miR-16) complementary sequence and alpha fetoprotein (AFP) aptamer sequence, so it can both capture miR-16 and AFP...
February 1, 2018: Talanta
https://www.readbyqxmd.com/read/29136862/stimulus-response-click-chemistry-based-aptamer-functionalized-mesoporous-silica-nanoparticles-for-fluorescence-detection-of-thrombin
#8
Zhonghui Chen, Mi Sun, Fang Luo, Kefeng Xu, Zhenyu Lin, Lan Zhang
In most aptamer based stimulus response mesoporous silica nanoparticles (MSN) systems, the aptamer is modified on the MSN via electrostatic interaction, however leakage might exist after a certain time in the system and hence the stability is not good. In this study, the pores of MSN were capped by aptamer through click chemistry reaction for the first time and the system was then employed to develop a fluorescence biosensor. Specifically, the aptamer of the target (thrombin in this study) was hybridized with its complementary DNA (which was initially modified with alkyne at the terminal) to form a double strand DNA (dsDNA) firstly, and then this dsDNA was modified on N3 modified MSN via Cu(I) catalyzed alkyne-azide cycloaddition reaction...
February 1, 2018: Talanta
https://www.readbyqxmd.com/read/29136823/use-of-a-small-molecule-as-an-initiator-for-interchain-staudinger-reaction-a-new-atp-sensing-platform-using-product-fluorescence
#9
Huan Yu, Jing Zheng, Sheng Yang, Abdullah M Asiri, Khalid A Alamry, Mingtai Sun, Kui Zhang, Suhua Wang, Ronghua Yang
We demonstrated that a small molecule induced interchain Staudinger reaction can be employed for highly selective detection of adenosine triphosphate (ATP), an important energy-storage biomolecule. A designed ATP split aptamer (A1) was first functionalized with a weakly fluorescent coumarin derivative due to an azide group (azido-coumarin). The second DNA strand (A2) was covalently linked with triphenylphosphine, which could selectively and efficiently reduce azido to amino group through the Staudinger reaction...
February 1, 2018: Talanta
https://www.readbyqxmd.com/read/29133961/triplex-quadruplex-structural-scaffold-a-new-binding-structure-of-aptamer
#10
Tao Bing, Wei Zheng, Xin Zhang, Luyao Shen, Xiangjun Liu, Fuyi Wang, Jie Cui, Zehui Cao, Dihua Shangguan
Apart from the canonical Watson-Crick duplex, nucleic acids can often form other structures, e.g. G-quadruplex and triplex. These structures give nucleic acid additional functions besides coding for genetic information. Aptamers are one type of functional nucleic acids that bind to specific targets with high selectivity and affinity by folding into special tertiary structures. Despite the fact that numerous aptamers have been reported, only a few different types of aptamer structures are identified. Here we report a novel triplex-quadruplex hybrid scaffold formed by a codeine binding aptamer (CBA)...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29132385/aptamer-selection-and-applications-for-breast-cancer-diagnostics-and-therapy
#11
REVIEW
Mei Liu, Xiaocheng Yu, Zhu Chen, Tong Yang, Dandan Yang, Qianqian Liu, Keke Du, Bo Li, Zhifei Wang, Song Li, Yan Deng, Nongyue He
Aptamers are short non-coding, single-stranded oligonucleotides (RNA or DNA) developed through Systematic Evolution of Ligands by Exponential enrichment (SELEX) in vitro. Similar to antibodies, aptamers can bind to specific targets with high affinity, and are considered promising therapeutic agents as they have several advantages over antibodies, including high specificity, stability, and non-immunogenicity. Furthermore, aptamers can be produced at a low cost and easily modified, and are, therefore, called "chemical antibodies"...
November 13, 2017: Journal of Nanobiotechnology
https://www.readbyqxmd.com/read/29131594/primary-amine-clustered-dna-aptamer-for-dna-protein-conjugation-catalyzed-by-microbial-transglutaminase
#12
Mari Takahara, Rie Wakabayashi, Kosuke Minamihata, Masahiro Goto, Noriho Kamiya
DNA-protein conjugates are promising biomolecules for use in areas ranging from therapeutics to analysis because of the dual functionalities of DNA and protein. Conjugation requires site-specific and efficient covalent bond formation without impairing the activity of both biomolecules. Herein, we have focused on the use of a microbial transglutaminase (MTG) that catalyzes the cross-linking reaction between a glutamine residue and a primary amine. In a model bioconjugation, a highly MTG-reactive Gln (Q)-donor peptide (FYPL<u>Q</u>MRG, FQ) was fused to enhanced green fluorescent protein (FQ-EGFP) and a primary amine-clustered DNA aptamer was enzymatically synthesized as a novel acyl-acceptor substrate of MTG, whose combination leads to efficient and convenient preparation of DNA-protein conjugates with high purity...
November 13, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/29130087/polyethylenimine-coated-fe3o4-nanoparticles-effectively-quench-fluorescent-dna-which-can-be-developed-as-a-novel-platform-for-protein-detection
#13
Long Ma, Nana Sun, Jinyan Zhang, Chunhao Tu, Xiuqi Cao, Demin Duan, Aipo Diao, Shuli Man
We report a novel assembly of polyethyleneimine (PEI)-coated Fe3O4 nanoparticles (NPs) with single-stranded DNA (ssDNA), and the fluorescence of the dye labeled in the DNA is remarkably quenched. In the presence of a target protein, the protein-DNA aptamer mutual interaction releases the ssDNA from this assembly and hence restores the fluorescence. This feature could be adopted to develop an aptasensor for protein detection. As a proof-of-concept, for the first time, we have used this proposed sensing strategy to detect thrombin selectively and sensitively...
November 13, 2017: Nanoscale
https://www.readbyqxmd.com/read/29127900/a-reusable-ratiometric-electrochemical-biosensor-on-the-basis-of-the-binding-of-methylene-blue-to-dna-with-alternating-at-base-sequence-for-sensitive-detection-of-adenosine
#14
Lin Cui, Mengfei Lu, Ying Li, Bo Tang, Chun-Yang Zhang
We develop a reusable ratiometric electrochemical biosensor on the basis of the binding of methylene blue (MB) to DNA with alternating AT base sequence for sensitive detection of adenosine. We design a strand 1 with MB-modified thymine (T) base in the proximal 3' termini as the capture probe for its immobilization on the gold electrode and a 3' termini ferrocene (Fc)-modified aptamer for the recognition of adenosine. The hybridization of strand 1 with the aptamer leads to the formation of a double-stranded DNA (dsDNA) and consequently the away of MB from the electrode surface and the close of Fc to the electrode surface, generating a small value of IMB/IFc (IMB and IFc are the peak currents of MB and Fc, respectively)...
November 7, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29127898/capacitive-aptasensor-based-on-interdigitated-electrode-for-breast-cancer-detection-in-undiluted-human-serum
#15
Sunil K Arya, Pavel Zhurauski, Pawan Jolly, Marina R Batistuti, Marcelo Mulato, Pedro Estrela
We report the development of a simple and powerful capacitive aptasensor for the detection and estimation of human epidermal growth factor receptor 2 (HER2), a biomarker for breast cancer, in undiluted serum. The study involves the incorporation of interdigitated gold electrodes, which were used to prepare the electrochemical platform. A thiol terminated DNA aptamer with affinity for HER2 was used to prepare the bio-recognition layer via self-assembly on interdigitated gold surfaces. Non-specific binding was prevented by blocking free spaces on surface via starting block phosphate buffer saline-tween20 blocker...
November 8, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29123397/highly-sensitive-protein-detection-via-covalently-linked-aptamer-to-mos2-and-exonuclease-assisted-amplification-strategy
#16
Li Gao, Qin Li, Zebin Deng, Brendan Brady, Ni Xia, Yang Zhou, Haixia Shi
Molybdenum disulfide (MoS2) has shown highly attractive superiority as a platform for sensing. However, DNA physisorption on the surface of MoS2 was susceptible to nonspecific probe displacement and false-positive signals. To solve these problems, we have developed a novel MoS2-aptamer nanosheet biosensor for detecting thrombin using a covalently linked aptamer to the MoS2 nanosheet. Ten percent Tween 80 was used to prevent thrombin from nonspecific binding and to rapidly form thiol-DNA/gold nanoparticle (AuNP) conjugates...
2017: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/29122887/a-reference-based-protein-degradation-assay-without-global-translation-inhibitors
#17
Jang-Hyun Oh, Shun-Jia Chen, Alexander Varshavsky
Although it is widely appreciated that the use of global translation inhibitors, such as cycloheximide, in protein degradation assays may result in artefacts, these inhibitors continue to be employed, owing to the absence of robust alternatives. We describe here the promoter reference technique (PRT), an assay for protein degradation with two advantageous features: a reference protein and a gene-specific inhibition of translation. In PRT assays, one measures, during a chase, the ratio of a test protein to a long-lived reference protein, a dihydrofolate reductase (DHFR)...
November 9, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29120162/y-shaped-dna-duplex-structure-triggered-gold-nanoparticle-dimers-for-ultrasensitive-colorimetric-detection-of-nucleic-acid-with-the-dark-field-microscope
#18
Jingjing Li, Qingyun Liu, Hongyan Xi, Xiangcong Wei, Zhengbo Chen
Herein, we present a novel gold nanoparticle (AuNP) enumeration-based colorimetric aptamer biosensor for ultrasensitive detection of nucleic acid. This AuNP enumeration-based colorimetric method takes advantages of the distinctive and strong localized surface plasmon resonance light scattering with the dark-field microscope. In our model system, first, cost-effective DNA1 instead of expensive 2-thioethyl ether acetic acid was capped on the surface of AuNPs to form a dense DNA1 layer. Then, two DNA strands (DNA2 and DNA3) in two different solutions were separately asymmetrically functionalized on the AuNPs capped dense DNA1 layer...
November 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29112755/in-silico-direct-folding-of-thrombin-binding-aptamer-g-quadruplex-at-all-atom-level
#19
Changwon Yang, Mandar Kulkarni, Manho Lim, Youngshang Pak
The reversible folding of the thrombin-binding DNA aptamer G-quadruplexes (GQs) (TBA-15) starting from fully unfolded states was demonstrated using a prolonged time scale (10-12 μs) parallel tempering metadynamics (PTMetaD) simulation method in conjunction with a modified version of the AMBER bsc1 force field. For unbiased descriptions of the folding free energy landscape of TBA-15, this force field was minimally modified. From this direct folding simulation using the modified bsc1 force field, reasonably converged free energy landscapes were obtained in K+-rich aqueous solution (150 mM), providing detailed atomistic pictures of GQ folding mechanisms for TBA-15...
November 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29109790/aptamer-based-therapeutic-approaches-to-target-cancer-stem-cells
#20
REVIEW
Gang Zhou, Olivier Latchoumanin, Mary Bagdesar, Lionel Hebbard, Wei Duan, Christopher Liddle, Jacob George, Liang Qiao
Cancer stem cells (CSCs) are believed to be a principal cellular source for tumour progression and therapeutic drug resistance as they are capable of self-renewal and can differentiate into cancer cells. Importantly, CSCs acquire the ability to evade the killing effects of cytotoxic agents through changes at the genetic, epigenetic and micro-environment levels. Therefore, therapeutic strategies targeting CSCs hold great potential as an avenue for cancer treatment. Aptamers or "chemical antibodies" are a group of single-stranded nucleic acid (DNA or RNA) oligonucleotides with distinctive properties such as smaller size, lower toxicity and less immunogenicity compared to conventional antibodies...
2017: Theranostics
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