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Aptamers

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https://www.readbyqxmd.com/read/28431362/rna-aptamer-based-electrochemical-aptasensor-for-c-reactive-protein-detection-using-functionalized-silica-microspheres-as-immunoprobes
#1
Junchun Wang, Jinjin Guo, Junjun Zhang, Wenjuan Zhang, Yuzhong Zhang
C-reactive protein (CRP) is a widely accepted biomarker of cardiovascular disease and inflammation. In this study, a RNA aptamer-based electrochemical sandwich type aptasensor for CRP detection was described using the functionalized silica microspheres as immunoprobes. Silica microspheres (Si MSs), which have good monodispersity and uniform shape, were firstly synthesized. The silica microspheres functionlized with gold nanoparticles (Au NPs) provided large surface area for immobilizing signal molecules (Zinc ions, Zn(2+)) and antibodies (Ab)...
April 13, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28431169/spa-ln-a-scoring-function-of-ligand-nucleic-acid-interactions-via-optimizing-both-specificity-and-affinity
#2
Zhiqiang Yan, Jin Wang
Nucleic acids have been widely recognized as potential targets in drug discovery and aptamer selection. Quantifying the interactions between small molecules and nucleic acids is critical to discover lead compounds and design novel aptamers. Scoring function is normally employed to quantify the interactions in structure-based virtual screening. However, the predictive power of nucleic acid-ligand scoring functions is still a challenge compared to other types of biomolecular recognition. With the rapid growth of experimentally determined nucleic acid-ligand complex structures, in this work, we develop a knowledge-based scoring function of nucleic acid-ligand interactions, namely SPA-LN...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28430279/microcontact-printing-with-aminosilanes-creating-biomolecule-micro-and-nanoarrays-for-multiplexed-microfluidic-bioassays
#3
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/28429183/label-free-okadaic-acid-detection-using-growth-of-gold-nanoparticles-in-sensor-gaps-as-a-conductive-tag
#4
Yuxiang Pan, Zijian Wan, Longjie Zhong, Xueqin Li, Qi Wu, Jun Wang, Ping Wang
Okadaic acid (OA) is a marine toxin ingested by shellfish. In this work, a simple, sensitive and label-free gap-based electrical competitive bioassay has been developed for this biotoxin detection. The gap-electrical biosensor is constructed by modifying interdigitated microelectrodes with gold nanoparticles (AuNPs) and using the self-catalytic growth of AuNPs as conductive bridges. In this development, the AuNPs growth is realized in the solution of glucose and chloroauric acid, with glucose oxidation used as the catalysis for growth of the AuNPs...
June 2017: Biomedical Microdevices
https://www.readbyqxmd.com/read/28429063/direct-fluorescence-anisotropy-assay-for-cocaine-using-tetramethylrhodamine-labeled-aptamer
#5
Yingxiong Liu, Qiang Zhao
Development of simple, sensitive, and rapid method for cocaine detection is important in medicine and drug abuse monitoring. Taking advantage of fluorescence anisotropy and aptamer, this study reports a direct fluorescence anisotropy (FA) assay for cocaine by employing an aptamer probe with tetramethylrhodamine (TMR) labeled on a specific position. The binding of cocaine and the aptamer causes a structure change of the TMR-labeled aptamer, leading to changes of the interaction between labeled TMR and adjacent G bases in aptamer sequence, so FA of TMR varies with increasing of cocaine...
April 20, 2017: Analytical and Bioanalytical Chemistry
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
#6
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
#7
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/28425453/aptamer-mediated-impairment-of-egfr-integrin-%C3%AE-v%C3%AE-3-complex-inhibits-vasculogenic-mimicry-and-growth-of-triple-negative-breast-cancers
#8
Simona Camorani, Elvira Crescenzi, Matteo Gramanzini, Monica Fedele, Antonella Zannetti, Laura Cerchia
Current treatment options for triple-negative breast cancers (TNBCs) is limited by the absence of well-defined biomarkers, excluding a targeted therapy. Notably, epidermal growth factor receptor (EGFR) is overexpressed in a great proportion of TNBCs and is a negative prognostic factor. In clinical trials, however, existing EGFR inhibitors showed disappointing outcome. Oligonucleotide aptamers are a valid alternative to antibodies for diagnostic and therapeutic uses. Here, we prove that, when applied to aggressive TNBC cell lines with unique stem-like plasticity, the anti-EGFR CL4 aptamer, but not erlotinib or cetuximab, prevents the vasculogenic mimicry (VM) capability of the cells and destroys previously formed channels in three-dimensional culture...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28422250/a-novel-nanomissile-targeting-two-biomarkers-and-accurately-bombing-ctcs-with-doxorubicin
#9
Yu Gao, Xiaodong Xie, Fengqiao Li, Yusheng Lu, Tao Li, Shu Lian, Yingying Zhang, Huijuan Zhang, Hao Mei, Lee Jia
Rare circulating tumor cells (CTCs) cause >50% of primary colorectal cancer survivors to develop deadly metastasis at 3-5 years after surgery; the current chemotherapies can do nothing about these cells. Herein, we synthesized a novel doxorubicin (DOX)-entrapped mesoporous silica nanoparticle (MSN), covalently-conjugated with two aptamers, for simultaneously targeting EpCAM and CD44, the typical surface biomarkers of colorectal CTCs. The nanomissile can specifically capture the metastasis-prone CTCs spiked in healthy human blood in a competitive-binding manner...
April 19, 2017: Nanoscale
https://www.readbyqxmd.com/read/28420169/ultrasensitive-label-free-sensing-of-il-6-based-on-pase-functionalized-carbon-nanotube-micro-arrays-with-rna-aptamers-as-molecular-recognition-elements
#10
Farhad Khosravi, Seyed Masoud Loeian, Balaji Panchapakesan
This study demonstrates the rapid and label-free detection of Interleukin-6 (IL-6) using carbon nanotube micro-arrays with aptamer as the molecular recognition element. Single wall carbon nanotubes micro-arrays biosensors were manufactured using photo-lithography, metal deposition, and etching techniques. Nanotube biosensors were functionalized with 1-Pyrenebutanoic Acid Succinimidyl Ester (PASE) conjugated IL-6 aptamers. Real time response of the sensor conductance was monitored with increasing concentration of IL-6 (1 pg/mL to 10 ng/mL), exposure to the sensing surface in buffer solution, and clinically relevant spiked blood samples...
April 17, 2017: Biosensors
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
#11
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/28414975/fullerene-doped-polyaniline-as-new-redox-nanoprobe-and-catalyst-in-electrochemical-aptasensor-for-ultrasensitive-detection-of-mycobacterium-tuberculosis-mpt64-antigen-in-human-serum
#12
Lijuan Bai, Yuhan Chen, Yan Bai, Yongjie Chen, Jing Zhou, Ailong Huang
Tuberculosis caused by Mycobacterium tuberculosis (MTB) is still a major threat to global public health. However, the existing methods for MTB detection are usually complicated and time consuming with unsatisfactory sensitivity and specificity. In this work, a relatively simple and ultrasensitive electrochemical aptasensor based on novel signal generation and amplification was constructed for the determination of MTB antigen MPT64. The coil-like fullerene (C60)-doped polyaniline (C60-PAn) nanohybrids with large surface area, abundant active groups and excellent electric performance were synthesized and used both as new redox nanoprobe and catalyst for the generation and amplification of electrochemical signal for the first time...
April 12, 2017: Biomaterials
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
#13
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
#14
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/28413748/thiamine-assays-advances-challenges-and-caveats
#15
REVIEW
Katie A Edwards, Nicole Tu-Maung, Krystal Cheng, Binbin Wang, Antje J Baeumner, Clifford E Kraft
Thiamine (vitamin B1) is essential to the health of all living organisms and deficiency has long been associated with diseases in animals such as fish, birds, alligators, and domesticated ruminant mammals. Thiamine is also implicated in several human diseases including Alzheimer's, diabetes, dementia, depression and, most notably, Wernicke-Korsakoff syndrome and Beriberi disease. Yet, highly sensitive and specific detection of thiamine remains an analytical challenge, as pM to nm levels of thiamine need to be detected in environmental and human samples, respectively, various phosphorylated variants need to be discriminated, and rapid on-site detection would be highly desirable...
April 2017: ChemistryOpen
https://www.readbyqxmd.com/read/28412238/chitosan-modified-plga-nanoparticles-tagged-with-5tr1-aptamer-for-in-vivo-tumor-targeted-drug-delivery
#16
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
#17
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/28407965/highly-sensitive-fluorescence-sensing-of-zearalenone-using-a-novel-aptasensor-based-on-upconverting-nanoparticles
#18
Zhengzong Wu, Enbo Xu, Muhammad F J Chughtai, Zhengyu Jin, Joseph Irudayaraj
A facile strategy was successfully developed for the detection of zearalenone (ZEN). In this assay, highly fluorescent upconversion nanoparticles were synthesized and conjugated with the complementary oligonucleotide of ZEN aptamer for use as signal probes. Magnetic nanoparticles immobilized with the ZEN aptamer were assigned as capture probes. The results exhibited that the linear correlation between the decreased luminescence intensity of the signal and the concentration of ZEN was very strong (R(2)=0.9957) in the range of 0...
September 1, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28403626/direct-factor-ixa-inhibition-with-the-rna-aptamer-pegnivacogin-reduces-platelet-reactivity-in-vitro-and-residual-platelet-aggregation-in-patients-with-acute-coronary-syndromes
#19
Dawid L Staudacher, Vera Putz, Lukas Heger, Jochen Reinöhl, Marcus Hortmann, Steven L Zelenkofske, Richard C Becker, Christopher P Rusconi, Christoph Bode, Ingo Ahrens
BACKGROUND: Residual platelet reactivity is a predictor of poor prognosis in patients with acute coronary syndromes (ACSs) undergoing percutaneous coronary intervention. Thrombin is a major platelet activator and upon initiation of the coagulation cascade, it is subsequently produced downstream of factor IXa, which itself is known to be increased in ACS. Pegnivacogin is a novel RNA-aptamer based factor IXa inhibitor featuring a reversal agent, anivamersen. We hypothesized that pegnivacogin could reduce platelet reactivity...
April 1, 2017: European Heart Journal. Acute Cardiovascular Care
https://www.readbyqxmd.com/read/28402873/saxs-oriented-ensemble-refinement-of-flexible-biomolecules
#20
Peng Cheng, Junhui Peng, Zhiyong Zhang
The conformational flexibility of a biomolecule may play a crucial role in its biological function. Small-angle x-ray scattering (SAXS) is a very popular technique for characterizing biomolecule flexibility. It can be used to determine a possible structural ensemble of the biomolecule in solution with the aid of a computer simulation. In this article, we present a tool written in Python, which iteratively runs multiple independent enhanced sampling simulations such as amplified collective motions and accelerated molecular dynamics, and an ensemble optimization method to drive the biomolecule toward an ensemble that fits the SAXS data well...
April 11, 2017: Biophysical Journal
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