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Dna aptamer

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https://www.readbyqxmd.com/read/28430279/microcontact-printing-with-aminosilanes-creating-biomolecule-micro-and-nanoarrays-for-multiplexed-microfluidic-bioassays
#1
Shivani Sathish, Sébastien G Ricoult, Kazumi Toda-Peters, Amy Q Shen
Microfluidic systems integrated with protein and DNA micro- and nanoarrays have been the most sought-after technologies to satisfy the growing demand for high-throughput disease diagnostics. As the sensitivity of these systems relies on the bio-functionalities of the patterned recognition biomolecules, the primary concern has been to develop simple technologies that enable biomolecule immobilization within microfluidic devices whilst preserving bio-functionalities. To address this concern, we introduce a two-step patterning approach to create micro- and nanoarrays of biomolecules within microfluidic devices...
April 21, 2017: Analyst
https://www.readbyqxmd.com/read/28426093/biophysical-properties-thermal-stability-and-functional-impact-of-8-oxo-7-8-dihydroguanine-on-oligonucleotides-of-rna-a-study-of-duplex-hairpins-and-the-aptamer-for-preq1-as-models
#2
Yu J Choi, Krzysztof S Gibala, Tewoderos Ayele, Katherine V Deventer, Marino J E Resendiz
A better understanding of the effects that oxidative lesions have on RNA is of importance to understand their role in the development/progression of disease. 8-oxo-7,8-dihydroguanine was incorporated into RNA to understand its structural and functional impact on RNA:RNA and RNA:DNA duplexes, hairpins and pseudoknots. One to three modifications were incorporated into dodecamers of RNA [AAGA GGG AUGAC] resulting in thermal destabilization (Δ T m - 10°C per lesion). Hairpins with tetraloops c-UUCG*-g* ( ), a-ACCG-g* ( ), c-UUG*G*-g* ( ) and c-ACG*G*-g* ( ) were modified and used to determine thermal stabilities, concluding that: (i) modifying the stem leads to destabilization unless adenosine is the opposing basepair of 8-oxoGua; (ii) modification at the loop is position- and sequence-dependent and varies from slight stabilization to large destabilization, in some cases leading to formation of other secondary structures (hairpin→duplex)...
February 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28425510/a-universal-split-spinach-aptamer-ussa-for-nucleic-acid-analysis-and-dna-computation
#3
Nanami Kikuchi, Dmitry M Kolpashchikov
We demonstrate how a single universal spinach aptamer (USSA) probe can be used to detect multiple (potentially any) nucleic acid sequences. USSA can be used for cost-efficient and highly selective analysis of even folded DNA and RNA analytes, as well as for the readout of outputs of DNA logic circuits.
April 20, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28418048/dna-spheres-decorated-with-magnetic-nanocomposites-based-on-terminal-transfer-reactions-for-versatile-target-detection-and-cellular-targeted-drug-delivery
#4
Yingshu Guo, Yujie Wang, Shuang Li, Li Niu, Di Wei, Shusheng Zhang
We present an elegant approach to make a magnetic nanoparticle (MNP) conjugated DNA-sphere (MNP/DNA-SP) which is integrated with disulfide (MNP/DS-SP) or an aptamer (MNP/sgc8-SP) for GSH detection, selective cancer cell recognition, effective drug delivery, and bioimaging.
April 18, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28414217/selection-of-group-specific-pae-binding-dna-aptamers-via-rational-designed-target-immobilization-and-applications-for-ultrasensitive-and-highly-selective-detection-of-paes
#5
Yu Han, Donglin Diao, Zhangwei Lu, Xiaoning Li, Qian Guo, Yumeng Huo, Qing Xu, Youshan Li, Sheng-Li Cao, Jianchun Wang, Yuan Wang, Jiaxing Zhao, Zhongfeng Li, Miao He, Zhaofeng Luo, Xinhui Lou
Phthalic acid esters(PAEs) are ubiquitous in the environment and some of them are recognized as endocrine disruptors that cause concerns on ecosystem functioning and public health. Due to the diversity of PAEs in the environment, there is a vital need to detect the total concentration of PAEs in a timely and low-cost way. To fulfill this requirement, it is highly desired to obtain group-specific PAE binders that are specific to the basic PAE skeleton. In this study, for the first time we have identified the group-specific PAE-binding aptamers via rational designed target immobilization...
April 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28414074/a-novel-chemotherapy-drug-free-delivery-system-composed-of-three-therapeutic-aptamers-for-the-treatment-of-prostate-and-breast-cancers-in-vitro-and-in-vivo
#6
Khalil Abnous, Noor Mohammad Danesh, Mohammad Ramezani, Rezvan Yazdian-Robati, Mona Alibolandi, Seyed Mohammad Taghdisi
In this study, a novel chemotherapy drug-free DNA nanocomplex composed of three therapeutic aptamers (IDA, AS1411 and apMNK2F) was designed for treatment of cancer cells. For MTT assay, PC-3 and 4T1 cells (target cells) and CHO cells (nontarget cells) were treated with apMNK2F-AS1411-IDA complex (DNA nanocomplex), as well as AS1411, IDA and apMNK2F alone. Internalization of apMNK2F-AS1411-IDA complex was analyzed by fluorescence imaging and flow cytometry analysis. In the last step, the presented DNA nanocomplex was applied for prohibition of tumor growth in vivo...
April 13, 2017: Nanomedicine: Nanotechnology, Biology, and Medicine
https://www.readbyqxmd.com/read/28412238/chitosan-modified-plga-nanoparticles-tagged-with-5tr1-aptamer-for-in-vivo-tumor-targeted-drug-delivery
#7
Sahar Taghavi, Mohammad Ramezani, Mona Alibolandi, Khalil Abnous, Seyed Mohammad Taghdisi
In this study, we reported epirubicin (Epi) encapsulated nanoparticles (NPs) formulated with biocompatible and biodegradable poly (lactic-co-glycolic acid) (PLGA) modified with chitosan (CS) through a physical adsorption method. Using chitosan, the solubility and surface charge of PLGA was modified to make efficient drug carriers for cancer cells. To improve the anti-tumor efficacy, we developed targeted therapy of tumor cells using a 5TR1 DNA aptamer (Apt) against the MUC1 receptor. To prove the MUC1 receptor-mediated uptake of Epi-PLGA-CS-Apt NPs in the cells, competition experiments were carried out...
April 12, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28411826/a-novel-fluorescent-biosensor-for-adenosine-triphosphate-detection-based-on-the-polydopamine-nanospheres-integrating-with-enzymatic-recycling-amplification
#8
Xiaoting Ji, Bingqing Yi, Yujuan Xu, Yanan Zhao, Hua Zhong, Caifeng Ding
Based on the protective performance of polydopamine nanospheres (PDANSs) for DNA against nuclease digestion and the specific recognition characteristic of aptamer, we have developed an enzymatic recycling signal amplification method for highly sensitive and selective detection of adenosine triphosphate (ATP). Fluorescence measurements were carried out to verify the DNA polymerase and exonuclease III (Exo III) assisted target recycling process and fluorescence signal amplification. In the absence of the ATP, initially, the signal DNA-PDANSs complex was in the "off" state due to the efficient fluorescence quenching of 6-carboxyfluorescein (FAM) adjacent to the surface of PDANSs...
July 1, 2017: Talanta
https://www.readbyqxmd.com/read/28400564/a-novel-4-arm-dna-rna-nanoconstruct-triggering-rapid-apoptosis-of-triple-negative-breast-cancer-cells-within-24%C3%A2-hours
#9
Joline Tung, Lih Shin Tew, Yuan-Man Hsu, Yit Lung Khung
Measuring at ~30 nm, a fully customizable holliday junction DNA nanoconstruct, was designed to simultaneously carry three unmodified SiRNA strands for apoptosis gene knockout in cancer cells without any assistance from commercial transfection kits. In brief, a holliday junction structure was intelligently designed to present one arm with a cell targeting aptamer (AS1411) while the remaining three arms to carry different SiRNA strands by means of DNA/RNA duplex for inducing apoptosis in cancer cells. By carrying the three SiRNA strands (AKT, MDM2 and Survivin) into triple negative breast MDA-MB-231 cancer cells, cell number had reduced by up to ~82% within 24 hours solely from one single administration of 32 picomoles...
April 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28395772/an-electrochemical-aptasensor-for-multiplex-antibiotics-detection-using-y-shaped-dna-based-metal-ions-encoded-probes-with-nmof-substrate-and-csrp-target-triggered-amplification-strategy
#10
Meng Chen, Ning Gan, Tianhua Li, Ye Wang, Qing Xu, Yinji Chen
An effective electrochemical aptasensor has been developed for the detection of multiplex antibiotics using Y-shaped DNA probes. These probes-based metal ions encoded the nanoscale metal-organic frameworks (NMOF) as a substrate, and circular strand-replacement DNA polymerization (CSRP) target triggered the amplification strategy. The Y-DNA probes (Y-DNA) were assembled using an assisted DNA probe (assisted DNA labeled with magnetic gold nanoparticles) which can hybridize to the captured DNA probe (consisting of aptamer and primer recognition region), and signal tags (NMOF encapsulating signal DNAs and different metal ions such as Pb(2+) or Cd(2+))...
May 22, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28395255/universal-ratiometric-electrochemical-biosensing-platform-based-on-mesoporous-platinum-nanocomposite-and-nicking-endonuclease-assisted-dna-walking-strategy
#11
Qinli Pu, Junlong Li, Juhui Qiu, Xuanhua Yang, Yi Li, Dan Yin, Xinyuan Zhang, Yiyi Tao, Shangchun Sheng, Guoming Xie
The occurrence and development of many complex diseases are associated with various molecules, whose contents are rarely in the early stage of the disease. Thus a universal platform for the ultrasensitive detection of multilevel biomarkers should be developed. In this study, we introduced an electrochemical biosensing system based on nicking endonuclease (Nt.BbvCI) assisted DNA walking strategy. We successfully constructed a universal signal-off-on ratiometric electrochemical biosensor for various biomolecules, including small molecules, nucleic acids, and proteins, by progressively optimizing the schematics (schemes 1, 2, and 3)...
April 1, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28393521/highly-sensitive-detection-of-bisphenol-a-by-nanoaptamer-assay-with-truncated-aptamer
#12
Eun-Hee Lee, Hyun Jeong Lim, Sang-Don Lee, Ahjeong Son
For the sensitive quantification of bisphenol A (BPA), we have developed NanoAptamer assay, which employs aptamer and complementary signaling DNA, a set of quantum dots (QD), and magnetic beads (MBs). Signaling DNA-QD655 was tethered to MB-QD565 via the aptamer. The affinity of the aptamer to BPA resulted in the release of the signaling DNA-QD655 from the complex and hence the corresponding decrease in the QD655 fluorescence measurement signal. Three new aptamers (23, 58, and 24-mer) were designed via truncation of the reference aptamer (73-mer)...
April 20, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28393515/aptamer-protein-proximity-binding-triggered-molecular-machine-for-amplified-electrochemical-sensing-of-thrombin
#13
Jianmei Yang, Baoting Dou, Ruo Yuan, Yun Xiang
The development of convenient and sensitive methods without involving any enzymes or complex nanomaterials for the monitoring of proteins is of great significance in disease diagnostics. In this work, we describe the validation of a new aptamer/protein proximity binding-triggered molecular machinery amplification strategy for sensitive electrochemical assay of thrombin in complex serum samples. The sensing interface is prepared by self-assembly of three-stranded DNA complexes on the gold electrode. The association of two distinct functional aptamers with different sites of thrombin triggers proximity binding-induced displacement of one of the short single-stranded DNAs (ssDNAs) from the surface-immobilized three-stranded DNA complexes, exposing a prelocked toehold domain to hybridize with a methylene blue (MB)-tagged fuel ssDNA strand (MB-DNA)...
April 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28391845/selection-and-characterization-of-dimethylindole-red-dna-aptamers-for-the-development-of-light-up-fluorescent-probes
#14
Hongyan Wang, Jine Wang, Qinglin Wang, Xing Chen, Min Liu, Hongxia Chen, Renjun Pei
To develop novel label-free light-up probes with improved performance characteristics and low background, we selected DNA aptamers for dimethylindole red (DIR) by a modified affinity chromatography based SELEX method. DIR is an anionic propylsulfonate substituted red-emitting dye derivative of thiazole orange and exhibited weak fluorescence in fluid solution and in the presence of dsDNA. After 14 rounds of selection, a shortened 42-mer DNA aptamer with sub-micromolar dissociation constant (Kd=0.65±0.17μM) was selected...
June 1, 2017: Talanta
https://www.readbyqxmd.com/read/28385802/rage-aptamer-blocks-the-development-and-progression-of-experimental-diabetic-nephropathy
#15
Takanori Matsui, Yuichiro Higashimoto, Yuri Nishino, Nobutaka Nakamura, Kei Fukami, Sho-Ichi Yamagishi
Interaction of advanced glycation end products (AGEs) and their receptor (RAGE) plays a central role in diabetic nephropathy. We screened DNA aptamers directed against RAGE (RAGE-aptamers) in vitro, and examined the effects on development and progression of diabetic nephropathy in streptozotocin-induced diabetic rats. RAGE-aptamer bound to RAGE with a dissociation constant of 5.68 nM and resultantly blocked the binding of AGEs to RAGE. When diabetic rats received continuous intraperitoneal injection of RAGE-aptamer from week 7 to 11 of diabetes, the increases in renal NADPH oxidase activity, oxidative stress generation, AGE, RAGE, inflammatory and fibrotic gene and protein levels, macrophage and extracellular matrix accumulation, and albuminuria were significantly suppressed, which were associated with improvement of podocyte damage...
April 6, 2017: Diabetes
https://www.readbyqxmd.com/read/28383245/exploring-the-chemistry-of-genetic-information-storage-and-propagation-through-polymerase-engineering
#16
Gillian Houlihan, Sebastian Arangundy-Franklin, Philipp Holliger
Nucleic acids are a distinct form of sequence-defined biopolymer. What sets them apart from other biopolymers such as polypeptides or polysaccharides is their unique capacity to encode, store, and propagate genetic information (molecular heredity). In nature, just two closely related nucleic acids, DNA and RNA, function as repositories and carriers of genetic information. They therefore are the molecular embodiment of biological information. This naturally leads to questions regarding the degree of variation from this seemingly ideal "Goldilocks" chemistry that would still be compatible with the fundamental property of molecular heredity...
April 6, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28379065/inhibition-of-grass-carp-reovirus-infection-by-dna-aptamers-against-s10-protein
#17
Hongru Liang, Xiaozhe Fu, Lihui Liu, Qiang Lin, Huizhi Guo, Yonggang Li, JiaXu Liu, Zhibin Huang, Ningqiu Li
Grass Carp reovirus (GCRV) is one of the most pathogenic agents among aquareovirus isolates and has the ability to cause a severe epidemic outbreak of hemorrhagic disease, thus resulting in both a high mortality rate during the culture of Grass Carp Ctenopharyngodon idella and an enormous economic loss. Aptamers have been demonstrated to have strong promising applications in antiviral drug development. In the present study, a complementary DNA fragment encoding the S10 gene of GCRV was cloned. The S10 protein was expressed and purified...
June 2017: Journal of Aquatic Animal Health
https://www.readbyqxmd.com/read/28376620/bioresponsive-release-system-for-visual-fluorescence-detection-of-carcinoembryonic-antigen-from-mesoporous-silica-nanocontainers-mediated-optical-color-on-quantum-dot-enzyme-impregnated-paper
#18
Zhenli Qiu, Jian Shu, Dianping Tang
An all-in-one paper-based analytical device (PAD) was successfully developed for visual fluorescence detection of carcinoembryonic antigen (CEA) on CdTe/CdSe quantum dot (QD)-enzyme-impregnated paper by coupling with a bioresponsive controlled-release system from DNA-gated mesoporous silica nanocontainers (MSNs). The assay was carried out in a centrifuge tube by using glucose-loaded MSNs with a CEA aptamer and a QD-enzyme-paper attached on the lid. Initially, single-strand complementary DNA to a CEA aptamer was covalently conjugated to the aminated MSN, and then glucose (enzyme substrate) molecules were gated into the pore with the help of the aptamer...
April 12, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28374130/dna-nanopore-functionalized-with-aptamer-and-cell-penetrating-peptide-for-tumor-cell-recognition
#19
Xi-Lin Guo, Dan-Dan Yuan, Ting Song, Xue-Mei Li
In the present work, DNA nanopore was composed of a bundle of six DNA duplexes folded from six DNA strands and functionalized with Ramos cell aptamer and cell-penetrating peptide (CPP). Herein, we present a unique dually conjugated molecule with an aptamer and cell-penetrating peptide for targeting and recognition of Ramos cells. The aptamer sequence was specific bound to Ramos cell, at the meanwhile the nanopore assembly was taken onto the surface of cell membrane and then got into the cells with the help of CPP...
April 3, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28369541/programmable-i-motif-dna-folding-topology-for-a-ph-switched-reversible-molecular-sensing-device
#20
Lili Shi, Pai Peng, Yi Du, Tao Li
Four-stranded DNAs including G-quadruplexes and i-motifs are formed from four stretches of identical bases (G or C). A challenge remains in controlling the intermolecular folding of different G-rich or C-rich strands due to the self-association of each component. Here, we introduce a well-designed bimolecular i-motif that does not allow the dimerization of the same strand, and illustrate its usefulness in a pH-switched ATP-sensing DNA molecular device. We analyze two groups of i-motif DNAs containing two stretches of different C-residues (Cn-1TmCn and CnTmCn-1; n = 3-6, m = 1, 3) and show that their bimolecular folding patterns (L- and H-form) noticeably differs in the thermal stability...
March 23, 2017: Nucleic Acids Research
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