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Aptamers

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https://www.readbyqxmd.com/read/28100695/mapping-the-affinity-landscape-of-thrombin-binding-aptamers-on-2-f-ana-dna-chimeric-g-quadruplex-microarrays
#1
Jory Lietard, Hala Abou Assi, Irene Gómez-Pinto, Carlos González, Mark M Somoza, Masad J Damha
In situ fabricated nucleic acids microarrays are versatile and very high-throughput platforms for aptamer optimization and discovery, but the chemical space that can be probed against a given target has largely been confined to DNA, while RNA and non-natural nucleic acid microarrays are still an essentially uncharted territory. 2'-Fluoroarabinonucleic acid (2'F-ANA) is a prime candidate for such use in microarrays. Indeed, 2'F-ANA chemistry is readily amenable to photolithographic microarray synthesis and its potential in high affinity aptamers has been recently discovered...
January 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28094326/remission-of-lymphoblastic-leukaemia-in-an-intravascular-fluidic-environment-by-pliable-drug-carrier-with-a-sliding-target-ligand
#2
Donghyun Jang, Yeong Mi Lee, Jaehyun Lee, Junsang Doh, Won Jong Kim
A polyrotaxane-based nanoconstruct with pliable structure carrying a chemotherapeutic drug was developed for targeting circulating lymphoblastic leukaemia cells in a fluidic environment of blood vessels in vivo. By introducing lymphoblast targeting aptamer DNA through cyclodextrin, threaded in poly(ethylene glycol) as polyrotaxane, target aptamer slides along the long polymeric chain and actively search for target ligand, leading to active targeting in dynamic fluidic system which is enhanced by up to 6-fold compared with that of control carriers with non-sliding targeting ligands...
January 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28094182/dna-duplex-linker-for-afm-selex-of-dna-aptamer-against-human-serum-albumin
#3
Musashi Takenaka, Yuzo Okumura, Tomokazu Amino, Yusuke Miyachi, Chiaki Ogino, Akihiko Kondo
DNA-duplex interactions in thymines and adenins are used as a linker for the novel methodology of Atomic Force Microscope-Systematic Evolution of Ligands by EXpotential enrichment (AFM-SELEX). This study used the hydrogen bonds in 10 mer of both thymines (T10) and adenines (A10). Initially, the interactive force in T10-A10 was measured by AFM, which returned an average interactive force of approximately 350pN. Based on this result, DNA aptamers against human serum albumin could be selected in the 4th round, and 15 different clones could be sequenced...
January 7, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28092358/recurrent-rna-motifs-as-scaffolds-for-genetically-encodable-small-molecule-biosensors
#4
Ely B Porter, Jacob T Polaski, Makenna M Morck, Robert T Batey
Allosteric RNA devices are increasingly being viewed as important tools capable of monitoring enzyme evolution, optimizing engineered metabolic pathways, facilitating gene discovery and regulators of nucleic acid-based therapeutics. A key bottleneck in the development of these platforms is the availability of small-molecule-binding RNA aptamers that robustly function in the cellular environment. Although aptamers can be raised against nearly any desired target through in vitro selection, many cannot easily be integrated into devices or do not reliably function in a cellular context...
January 16, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28090219/integrated-microfluidic-aptasensor-for-mass-spectrometric-detection-of-vasopressin-in-human-plasma-ultrafiltrate
#5
J Yang, J Zhu, R Pei, J A Oliver, D W Landry, M N Stojanovic, Q Lin
We present a microfluidic aptamer-based biosensor for detection of low-molecular-weight biomarkers in patient samples. Using a microfluidic device that integrates aptamer-based specific analyte extraction, isocratic elution, and detection by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, we demonstrate rapid, sensitive and label-free detection of arginine vasopressin (AVP) in human plasma ultrafiltrate. AVP molecules in complex matrices are specifically captured by an aptamer that is immobilized on microbeads via affinity binding in a microchamber...
July 14, 2016: Analytical Methods: Advancing Methods and Applications
https://www.readbyqxmd.com/read/28089700/new-synthetic-route-to-ethynyl-dutp-a-means-to-avoid-formation-of-acetyl-and-chloro-vinyl-base-modified-triphosphates-that-could-poison-selex-experiments
#6
Pascal Röthlisberger, Fabienne Levi-Acobas, Marcel Hollenstein
5-Ethynyl-2'-deoxyuridine is a common base-modified nucleoside analogue that has served in various applications including selection experiments for potent aptamers and in biosensing. The synthesis of the corresponding triphosphates involves a mild acidic deprotection step. Herein, we show that this deprotection leads to the formation of other nucleoside analogs which are easily converted to triphosphates. The modified nucleoside triphosphates are excellent substrates for numerous DNA polymerases under both primer extension and PCR conditions and could thus poison selection experiments by blocking sites that need to be further modified...
January 6, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28089349/development-of-new-ptk7-targeting-aptamer-fluorescent-and-radiolabelled-probes-for-evaluation-as-molecular-imaging-agents-lymphoma-and-melanoma-in-vivo-proof-of-concept
#7
Victoria Calzada, María Moreno, Jessica Newton, Joel González, Marcelo Fernández, Juan Pablo Gambini, Manuel Ibarra, Alejandro Chabalgoity, Susan Deutscher, Thomas Quinn, Pablo Cabral, Hugo Cerecetto
Aptamers are single-stranded oligonucleotides that recognize molecular targets with high affinity and specificity. Aptamer that selectively bind to the protein tyrosine kinase-7 (PTK7) receptor, overexpressed on many cancers, has been labelled as probes for molecular imaging of cancer. Two new PTK7-targeting aptamer probes were developed by coupling frameworks from the fluorescent dye AlexaFluor647 or the 6-hydrazinonicotinamide (HYNIC) chelator-labelled to (99m)Tc. The derivatizations via a 5'-aminohexyl terminal linker were done at room temperature and under mild buffer conditions...
December 24, 2016: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28088878/what-potential-do-aptamers-hold-in-therapeutic-delivery
#8
Sarah Shigdar
No abstract text is available yet for this article.
February 2017: Therapeutic Delivery
https://www.readbyqxmd.com/read/28088092/aptamer-based-environmental-biosensors-for-small-molecule-contaminants
#9
REVIEW
Van-Thuan Nguyen, Young Seop Kwon, Man Bock Gu
Aptasensors are promising biosensors, which take advantage of using aptamers as a recognition element. The combination of the excellent characteristics of aptamers and the leading detection platform techniques, such as optical, electrochemical with nanomaterial-integrated, or mass-sensitive techniques with high sensitivity and specificity draws a promising view for the application of the aptasensors for the detection of harmful small toxic chemicals and real-time monitoring in the environments. In spite of attraction of aptasensors, application of them is limited to the complex environment due to the facts that how the immobilization of aptamers onto the surface affects the functions of aptamers and their structures for the detection of environmental contaminants are not clearly known...
January 11, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28087261/dna-aptamer-probes-for-detection-of-estrogen-receptor-%C3%AE-positive-carcinomas
#10
Arghya Sett, Bibhuti Bhusan Borthakur, Jagannath Dev Sharma, Amal Chandra Kataki, Utpal Bora
Estrogen receptor alpha (ERα) which is a ligand-activated transcription factor also known as NR3A1 (nuclear receptor subfamily 3, group A, member 1). It is an important biomarker for breast cancer metastasis. In the present study, we report a novel DNA aptamer candidate against estrogen receptor (ER) alpha structure. The enriched aptamer candidate was obtained after 14 iterative cycles of in vitro protein-SELEX process. Isothermal calorimetry study suggests the nanomolar sensitivity of the candidate ER_Apt1 to its target protein...
December 25, 2016: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/28071153/novel-chemical-scaffolds-for-inhibition-of-rifamycin-resistant-rna-polymerase-discovered-from-high-throughput-screening
#11
Nathan T Scharf, Vadim Molodtsov, Arrin Kontos, Katsuhiko S Murakami, George A Garcia
Rifampin has been a cornerstone of tuberculosis (TB) treatment since its introduction. The rise of multidrug-resistant and extensively drug-resistant TB makes the development of novel therapeutics effective against these strains an urgent need. Site-specific mutations in the target enzyme of rifampin, RNA polymerase (RNAP) comprises the majority (~97%) of rifamycin-resistant (Rif(R)) strains of Mycobacterium tuberculosis (MTB). To identify novel inhibitors of bacterial RNAP, an in vitro plasmid-based transcription assay that uses malachite green (MG) to detect transcribed RNA containing MG aptamers was developed...
December 1, 2016: Journal of Biomolecular Screening
https://www.readbyqxmd.com/read/28069939/real-time-measurement-of-small-molecules-directly-in-awake-ambulatory-animals
#12
Netzahualcóyotl Arroyo-Currás, Jacob Somerson, Philip A Vieira, Kyle L Ploense, Tod E Kippin, Kevin W Plaxco
The development of a technology capable of tracking the levels of drugs, metabolites, and biomarkers in the body continuously and in real time would advance our understanding of health and our ability to detect and treat disease. It would, for example, enable therapies guided by high-resolution, patient-specific pharmacokinetics (including feedback-controlled drug delivery), opening new dimensions in personalized medicine. In response, we demonstrate here the ability of electrochemical aptamer-based (E-AB) sensors to support continuous, real-time, multihour measurements when emplaced directly in the circulatory systems of living animals...
January 9, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28069377/development-of-an-aptamer-ampicillin-conjugate-for-treating-biofilms
#13
Cheng Lijuan, Yan Xing, Wu Minxi, Li Wenkai, Deng Le
Biofilm formation involves the development of extracellular matrix and initially depends on adherence and tropism by flagellar movement. With the widespread development of antibiotic resistance and tolerance of biofilms, there is a growing need for novel anti-infective strategies. No currently approved medications specifically target biofilms. Aptamers are single-stranded nucleic acid molecules that may bind to their targets with high affinity and affect the target functions. We developed a bifunctional conjugate by linking an aptamer targeting bacterial flagella with ampicillin...
January 6, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28067047/solvatochromic-and-fluorogenic-dyes-as-environment-sensitive-probes-design-and-biological-applications
#14
Andrey S Klymchenko
Fluorescent environment-sensitive probes are specially designed dyes that change their fluorescence intensity (fluorogenic dyes) or color (e.g., solvatochromic dyes) in response to change in their microenvironment polarity, viscosity, and molecular order. The studies of the past decade, including those of our group, have shown that these molecules become universal tools in fluorescence sensing and imaging. In fact, any biomolecular interaction or change in biomolecular organization results in modification of the local microenvironment, which can be directly monitored by these types of probes...
January 9, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28063413/chronopotentiometric-sensing-of-specific-interactions-between-lysozyme-and-the-dna-aptamer
#15
Veronika Ostatná, Veronika Kasalová-Vargová, László Kékedy-Nagy, Hana Černocká, Elena E Ferapontova
Specific DNA-protein interactions are vital for cellular life maintenance processes, such as transcriptional regulation, chromosome maintenance, replication and DNA repair, and their monitoring gives valuable information on molecular-level organization of those processes. Here, we propose a new method of label-free electrochemical sensing of sequence specific binding between the lysozyme protein and a single stranded DNA aptamer specific for lysozyme (DNAapta) that exploits the constant current chronopotentiometric stripping (CPS) analysis at modified mercury electrodes...
December 23, 2016: Bioelectrochemistry
https://www.readbyqxmd.com/read/28061688/aptamers-as-therapeutics
#16
Shahid M Nimjee, Rebekah R White, Richard C Becker, Bruce A Sullenger
Aptamers are single-stranded nucleic acid molecules that bind to and inhibit proteins and are commonly produced by systematic evolution of ligands by exponential enrichment (SELEX). Aptamers undergo extensive pharmacological revision, which alters affinity, specificity, and therapeutic half-life, tailoring each drug for a specific clinical need. The first therapeutic aptamer was described 25 years ago. Thus far, one aptamer has been approved for clinical use, and numerous others are in preclinical or clinical development...
January 6, 2017: Annual Review of Pharmacology and Toxicology
https://www.readbyqxmd.com/read/28059418/highly-versatile-spion-encapsulated-plga-nanoparticles-as-photothermal-ablators-of-cancer-cells-and-as-multimodal-imaging-agents
#17
Balasubramanian Sivakumar, Ravindran Girija Aswathy, Rebeca Romero-Aburto, Trevor Mitcham, Keith A Mitchel, Yutaka Nagaoka, Richard R Bouchard, Pulickel M Ajayan, Toru Maekawa, Dasappan Nair Sakthikumar
We have designed versatile polymeric nanoparticles with cancer cell specific targeting capabilities via aptamer conjugation after the successful encapsulation of curcumin and superparamagnetic iron oxide nanoparticles (SPIONs) inside a PLGA nanocapsule. These targeted nanocomposites were selectively taken up by tumor cells, under in vitro conditions, demonstrating the effectiveness of the aptamer targeting mechanism. Moreover, the nanocomposite potentially functioned as efficient multiprobes for optical, magnetic resonance imaging (MRI) and photoacoustic imaging contrast agents in the field of cancer diagnostics...
January 6, 2017: Biomaterials Science
https://www.readbyqxmd.com/read/28059415/computational-design-of-cyclic-peptides-for-the-customized-oriented-immobilization-of-globular-proteins
#18
Miguel A Soler, Alex Rodriguez, Anna Russo, Abimbola Feyisara Adedeji, Cedrix J Dongmo Foumthuim, Cristina Cantarutti, Elena Ambrosetti, Loredana Casalis, Alessandra Corazza, Giacinto Scoles, Daniela Marasco, Alessandro Laio, Sara Fortuna
The oriented immobilization of proteins, key for the development of novel responsive biomaterials, relies on the availability of effective probes. These are generally provided by standard approaches based on in vivo maturation and in vitro selection of antibodies and/or aptamers. These techniques can suffer technical problems when a non-immunogenic epitope needs to be targeted. Here we propose a strategy to circumvent this issue by in silico design. In our method molecular binders, in the form of cyclic peptides, are computationally evolved by stochastically exploring their sequence and structure space to identify high-affinity peptides for a chosen epitope of a target globular protein: here a solvent-exposed site of β2-microglobulin (β2m)...
January 6, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28054983/aptamer-sensors
#19
EDITORIAL
Giovanna Marrazza
In the last years, great progress has been accomplished in the development of aptamer sensors with different transducers. In order to improve the sensitivity of these biosensors, several methodologies have been employed. In this Special Issue, the state of art and the future trends in the field of aptamer sensors have been explored.
January 4, 2017: Biosensors
https://www.readbyqxmd.com/read/28054670/ultra-sensitive-detection-of-kanamycin-for-food-safety-using-a-reduced-graphene-oxide-based-fluorescent-aptasensor
#20
Na-Reum Ha, In-Pil Jung, Im-Joung La, Ho-Sup Jung, Moon-Young Yoon
Overuse of antibiotics has caused serious problems, such as appearance of super bacteria, whose accumulation in the human body through the food chain is a concern. Kanamycin is a common antibiotic used to treat diverse infections; however, residual kanamycin can cause many side effects in humans. Thus, development of an ultra-sensitive, precise, and simple detection system for residual kanamycin in food products is urgently needed for food safety. In this study, we identified kanamycin-binding aptamers via a new screening method, and truncated variants were analyzed for optimization of the minimal sequence required for target binding...
January 5, 2017: Scientific Reports
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