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Dna aptamer

Cécile Gasse, Marwa Zaarour, Sam Noppen, Mikhail Abramov, Philippe Marlière, Sandra Liekens, Bart De Strooper, Piet Herdewijn
A modified DNA aptamer was developed that binds BACE1, a therapeutic target involved in Alzheimer's disease. This ssXNA not only tightly binds to BACE1 but also inhibits its protease activity in vitro in the same range as a previously described unmodified aptamer. We report the in vitro selection of functional oligonucleotides using two nucleobase modifications: 5-chlorouracil and 7-deazaadenine. The nucleoside analog 5-chloro-2'-deoxyuridine has already been explored to replace thymidine in a chemically modified genome of a bacterium...
January 11, 2018: Chembiochem: a European Journal of Chemical Biology
Sarah Jessica Reinholt, Harold G Craighead
We present a microfluidic device for specifically capturing cancer cells and isolating their genomic DNA (gDNA) for specific amplification and sequence analysis. To capture cancer cells within the device, nucleic acid aptamers that specifically bind to cancer cells were immobilized within a channel containing micropillars designed to increase capture efficiency. The cap-tured cells were lysed in situ and their gDNA was isolated by physical entanglement within a second smaller-dimensioned micropillar array. This type of isolation allowed the gDNA to be retained and purified within the channel, and enables ampli-fication and analysis to be performed on the gDNA without the loss of the original template...
January 11, 2018: Analytical Chemistry
Fahimeh Charbgoo, Mona Alibolandi, Seyed Mohammad Taghdisi, Khalil Abnous, Fatemeh Soltani, Mohammad Ramezani
Targeted delivery of DNA nanoparticles is a promising approach in cancer therapy. Using aptamers, target specific delivery of DNA nanoparticles can be achieved. Further, aptamers can indirectly improve drug encapsulation efficiency of DNA nanoparticles for drugs intercalated within nucleic acid base pairs. Using DNA blocks, a micellar hybrid nanoparticle was prepared for the targeted co-delivery of doxorubicin and a pro-apoptotic peptide, KLA to tumor cells. Results demonstrated that anti-MUC1 aptamer could specifically deliver the synthesized DNA micelle into MCF-7 cells by improving its cellular uptake...
January 6, 2018: Nanomedicine: Nanotechnology, Biology, and Medicine
Yueyue Yao, Xiuzhong Wang, Wenna Duan, Feng Li
A label-free, versatile and low-background chemiluminescence (CL) sensing strategy based on gold nanocluster catalysis combined with the separation of magnetic beads (MBs) was developed. Kanamycin was selected as the target analyte to exhibit the analytical performance of this platform. Two single-stranded DNA (named DNA1 and DNA2) are ingeniously designed. DNA1, containing an aptamer sequence of the targets, was firstly immobilized on the MBs which were modified with many amino groups by amidation reaction...
January 9, 2018: Analyst
Pingping Liang, Juan Canoura, Haixiang Yu, Obtin Alkhamis, Yi Xiao
DNA-modified gold nanoparticles (AuNPs) are useful signal-reporters for the detection of a variety of molecules via different hybridization- and enzyme-based assays. However, their performance is heavily dependent on the surface coverage of the immobilized probe DNA, which can influence both target binding and enzymatic processing of the bound probes. Current methods used to adjust DNA surface coverage on AuNPs require the production of multiple batches of AuNPs under different conditions, which is costly and laborious...
January 9, 2018: ACS Applied Materials & Interfaces
Li-Ping Jia, Li-Juan Wang, Rong-Na Ma, Lei Shang, Wei Zhang, Qing-Wang Xue, Huai-Sheng Wang
In the present work a highly sensitive and selective aptasensor was developed for the determination of 8-hydroxy-2'-deoxyguanosine (8-OH-dG) based on the hybridization chain reaction (HCR) signal amplification. It was observed that the aptamer of 8-OH-dG could hybridize with the capture DNA immobilized on the gold electrode with a sticky tail left, which initiated the HCR and led to the formation of extended dsDNA structure on the electrode surface. Then the electroactive species ([Ru(NH3)6]3+, RuHex) intercalated into the dsDNA grooves to generate the amplified signal...
March 1, 2018: Talanta
Xiaoting Liu, Lina Wu, Lei Wang, Wei Jiang
To enhance efficacy of chemotherapy and achieve real-time imaging of cancer cells, it is crucial to develop nanocarriers with targeted drug delivery capacity and fluorescence property for cancer theranostics. Herein, a dual-targeting DNA tetrahedron nanocarrier (MUC1-Td-AS1411) was constructed for breast cancer cell imaging and targeted drug delivery. This nanocarrier consisted of three components: (i) DNA tetrahedron core for multivalent conjugation of function ligands and loading doxorubicin (Dox); (ii) activatable MUC1 aptamer probe (MUC1-probe), formed by the hybridization of MUC1 aptamer sequence with fluorophore extended from one vertex and complementary sequence with quencher, for targeting and imaging MUC1 protein on cytomembrane; (iii) AS1411 aptamer, which was hybridized to the overhang on three vertexes via prolonged sequence, for binding to nucleolin...
March 1, 2018: Talanta
Shengfeng Huang, Ning Gan, Tianhua Li, You Zhou, Yuting Cao, Youren Dong
An ultrasensitive electrochemical aptasensor for multiplex antibiotics detection based on endonuclease and exonuclease assisted dual recycling amplification strategy was proposed. Kanamycin and chloramphenicol were selected as candidates. Firstly, aptamers of the antibiotics were immobilized on bar A and then binding with their endonuclease labeled complementary DNA strands to construct enzyme-cleavage probes. Secondly, The nano zirconium-metal organic framework (NMOF) particles with 1,4-benzene-dicarboxylate (BDC) as linker was defined as UiO-66...
March 1, 2018: Talanta
Cuiying Lin, Huixia Zheng, Mi Sun, Yajuan Guo, Fang Luo, Longhua Guo, Bin Qiu, Zhenyu Lin, Guonan Chen
A simple, low-cost, and sensitive liposome-based colorimetric aptasensor has been developed to detect ochratoxin A (OTA). Specifically, a dumbbell-shaped probe was designed, including magnetic beads (MBs), double-stranded DNA (dsDNA), and enzyme-encapsulated liposome. The dsDNA formed by the hybridization between OTA aptamer and its complementary probe. And the dsDNA was used to contact the MBs and the enzyme-encapsulated liposome. In the presence of OTA, the aptamer preferred to combine with OTA to form G-quadruplex, resulting in the release of the detection probe and the enzyme-encapsulated liposome...
March 9, 2018: Analytica Chimica Acta
Nikolay Barinov, Nikita Ivanov, Alexey Kopylov, Dmitry Klinov, Elena Zavyalova
High-resolution atomic force microscopy (AFM) is a powerful technique for the direct visualization of single molecules. Here, AFM is applied to characterize the oligomeric state of hemagglutinins of the influenza virus. Hemagglutinins are known to be present in a trimeric form inside the viral envelope. However, recombinant hemagglutinins are also present as large oligomers, which impair the functional activity of the protein. Five commercial recombinant hemagglutinins from the viral strains H1, H3, H5, H7, and H9 were studied with high-resolution AFM...
January 2, 2018: Biochimie
Benmei Wei, Juntao Zhang, Xiaowen Ou, Xiaoding Lou, Fan Xia, Alexis Vallée-Bélisle
Although extensively used in all fields of chemistry, molecular recognition still suffers from a significant limitation: host-guest binding displays a fixed, hyperbolic dose-response curve, which limits its usefulness in many applications. Here we take advantage of the high programmability of DNA chemistry and propose a universal strategy to engineer bio-recognition-based sensors with dual programmable dynamic ranges. Using DNA aptamers as our model recognition element, and electrochemistry as our readout signal, we first designed a dual signaling "signal-on" and "signal-off" adenosine triphosphate (ATP) sensor composed of a ferrocene-labeled ATP aptamer in complex to a complementary, electrode-bound, methylene-blue labeled DNA...
January 4, 2018: Analytical Chemistry
Surong Zhang, Suresh Gupta, Thomas J Fitzgerald, Alexei A Bogdanov
Constitutively activated signal transducer and activator of transcription 3 (STAT3) factor is an important therapeutic target in head and neck cancer (HNC). Despite early promising results, a reliable systemic delivery system for STAT3- targeted oligonucleotide (ODN) drugs is still needed for future clinical translation of anti-STAT3 therapies. We engineered and tested a novel ODN duplex/gold nanoparticle (AuNP)-based system carrying a therapeutic STAT3 decoy (STAT3d) payload. This strategy is two-pronged because of the additive STAT3 antagonism and radiosensitizing properties of AuNP...
2018: Nanotheranostics
Haoran Liu, Junhua Mai, Jianliang Shen, Joy Wolfram, Zhaoqi Li, Guodong Zhang, Rong Xu, Yan Li, Chaofeng Mu, Youli Zu, Xin Li, Ganesh L Lokesh, Varatharasa Thiviyanathan, David E Volk, David G Gorenstein, Mauro Ferrari, Zhongbo Hu, Haifa Shen
Aptamers have the potential to be used as targeting ligands for cancer treatment as they form unique spatial structures. Methods: In this study, a DNA aptamer (T1) that accumulates in the tumor microenvironment was identified through in vivo selection and validation in breast cancer models. The use of T1 as a targeting ligand was evaluated by conjugating the aptamer to liposomal doxorubicin. Results: T1 exhibited a high affinity for both tumor cells and polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs)...
2018: Theranostics
Yan Zhang, Feifei Luo, Yating Zhang, Luqi Zhu, Yi Li, Shuangli Zhao, Pingang He, Qingjiang Wang
The detection of Salmonella enterica serovar Typhimurium (S. Typhimurium) is very important for the prevention of food poisoning and other infectious diseases. Here we reported a simple and sensitive strategy to test S. Typhimurium by microchip capillary electrophoresis couple with laser-induced fluorescence (MCE-LIF) based on the specific reaction between the bacterium and corresponding aptamers. Based on the differences in charge to mass ratio between bacteria-aptamer complexes and free aptamers, a separation of the complexes and free aptamers could be obtained by MCE...
December 23, 2017: Journal of Chromatography. A
Stanislav S Beloborodov, Jiayin Bao, Svetlana M Krylova, Agnesa Shala-Lawrence, Philip E Johnson, Sergey N Krylov
DNA aptamers are attractive capture probes for affinity chromatography since, in contrast to antibodies, they can be chemically synthesized and, in contrast to tag-specific capture probes (such as Nickel-NTA or Glutathione), they can be used for purification of proteins free of genetic modifications (such as His or GST tags). Despite these attractive features of aptamers as capture probes, there are only a few reports on aptamer-based protein purification and none of them includes a test of the purified protein's activity, thus, leaving discouraging doubts about method's ability to purify proteins in their active state...
December 16, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
Robert W Harkness V, Philip E Johnson, Anthony K Mittermaier
Differential scanning calorimetry (DSC) is a powerful technique for quantifying thermodynamic parameters governing biomolecular folding and binding interactions. This information is critical in the design of new pharmaceutical compounds. However, many pharmaceutically relevant ligands are chemically unstable at the high temperatures used in DSC analyses. Thus, measuring binding interactions is challenging because the concentrations of ligands and thermally-converted products are constantly changing within the calorimeter cell...
November 21, 2017: Journal of Visualized Experiments: JoVE
Peter A Mirau, Joshua E Smith, Jorge Luis Chávez, Joshua A Hagen, Nancy Kelley-Loughnane, Rajesh R Naik
DNA aptamers that bind biomolecular targets are of interest as the recognition element in colorimetric sensors based on gold nanoparticles (AuNP), where sensor functionality is related to changes in AuNP colloidal stability upon target binding. In order to understand the role of target binding on DNA-AuNP colloidal stability, we have used high-resolution NMR to characterize the interactions of the 36 nucleotide cocaine-binding aptamer (MN4) and related aptamers with AuNPs, cocaine and cocaine metabolites. Changes in the aptamer imino proton NMR spectra with low (20 nM) concentrations of AuNP show that the aptamers undergo fast-exchange adsorption on the nanoparticle surface...
December 28, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Jian Zhao, Jinhong Gao, Wenting Xue, Zhenghan Di, Hang Xing, Yi Lu, Lele Li
Designer DNA nanodevices have attracted extensive interest for detection of specific targets in living cells. However, it still re-mains a great challenge to construct DNA sensing devices that can be activated at desired time with a remotely applied stimulus. Here we report a rationally designed, synthetic DNA nanodevice that can detect ATP in living cells in a upconversion luminescence-activatable manner. The nanodevice consists of a UV light activatable aptamer probe and lanthanide-doped upconversion nanoparticles which acts as the nanotransducers to operate the device in response to NIR light...
December 27, 2017: Journal of the American Chemical Society
Ziping Zhang, Cancan Tao, Jungang Yin, Yunhui Wang, Yanshen Li
Electrochemical aptamer (EA) sensors based on aptamer-cDNA duplex probes (cDNA: complementary DNA) and target induced strand displacement (TISD) recognition are sensitive, selective and capable of detecting a wide variety of target analytes. While substantial research efforts have focused on engineering of new signaling mechanisms for the improvement of sensor sensitivity, little attention was paid to the enhancement of sensor response rate. Typically, the previous TISD based EA sensors exhibited relatively long response times larger than 30min, which mainly resulted from the suboptimal aptamer-cDNA probe structure in which most of aptamer bases were paired to the cDNA bases...
December 20, 2017: Biosensors & Bioelectronics
Mariia Andrianova, Natalia Komarova, Vitaliy Grudtsov, Evgeniy Kuznetsov, Alexander Kuznetsov
The electrochemical detection of interactions between aptamers and low-molecular-weight targets often lacks sensitivity. Signal amplification improves the detection of the aptamer-analyte complex; Bsm DNA polymerase was used to amplify the signal from the interaction of vanillin and its aptamer named Van_74 on an ion-sensitive field-effect transistor (ISFET)-based biosensor. The aptamer was immobilized on the ISFET sensitive surface. A short DNA probe was hybridized with the aptamer and dissociated from it upon vanillin addition...
December 26, 2017: Sensors
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