Relevant bibliographies by topics / Aptameri

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Academic literature on the topic 'Aptameri'

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Published: 10 March 2023

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Journal articles on the topic "Aptameri"

1

Levy, Irit Carmi, Erez Lavi, Neta Zilony Hanin, Zohar Pode, Karin Mizrahi, Ronit Farhi, Anastasia Paz, et al. "788 A novel T- lymphocyte binding aptamer assembled into a bispecifc compound for the treatment of solid tumors." Journal for ImmunoTherapy of Cancer 9, Suppl 2 (November 2021): A823. http://dx.doi.org/10.1136/jitc-2021-sitc2021.788.

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BackgroundT-cell engagers are bispecific molecules directed against the CD3 complex on one end and a tumor specific antigen on the other end, allowing a physical link of T cell to a tumor cell, resulting in tumor killing and immune activation. Bispecific molecules harnessing and redirecting T-cells towards tumor cells are a promising therapeutic agents. Aptamers are single stranded oligonucleotides with binding and recognition propensities similar to those of antibodies. Aptamers have a number of advantages over bispecific antibodies including shorter generation time and low immunogenicity. Thus, aptamers capable of targeting T cells would have great potential for use as anti-cancer therapeuticsMethodsSystematic evolution of ligands by exponential enrichment (SELEX) methodology was employed in order to identify a novel CD3e binding aptamer. CD3 binding aptamer was subsequently linked into a bispecific T cell engager structure with a tumor-targeting aptameric arm. The tumor-targeting aptamer is developed by Aummune's proprietary tailored therapeutic platform.1 based on identifying functional aptamer sequences capable of specifically killing targeted tumor cells and sparing healthy tissue .Exemplary bispecific aptamers were tested for T cell stimulation by flow cytometry. In vivo antitumor activity was investigated in syngeneic and in xenograft tumor models.ResultsWe have successfully identified a novel CD3e –targeting aptamer with a Kd of 31nM. A bispecific T cell engager comprised of this aptamer and a tumor-targeting aptamer induced a potent stimulation of T cells in vitro, resulting in CD69 upregulation and IFNg secretion.Next, the CD3e targeting aptamer was hybridized to tumoricidal aptamers identified by Aummune's platform (VS12) to target either the human colon carcinoma HCT116 cells or (VS32) the murine triple negative breast cancer 4T1 cells. Both bispecific entities (CS6-VS12 and CS6-VS32) effectively lead to inhibition of tumor growth in vivo and increased survival in the corresponding models.ConclusionsOur data above provide a proof-of-concept for Aummune's Bispecific Aptamer efficacy and provide a framework for the clinical development of this novel tailored immune therapeutic agents. Indeed, we are currently in the process of developing a first-in-human clinical study in subjects with solid tumors.ReferenceMamet N, et al, Commun Biol 2020.
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Norris, Vic, Sergey N. Krylov, Pratul K. Agarwal, and Glenn J. White. "Synthetic, Switchable Enzymes." Journal of Molecular Microbiology and Biotechnology 27, no. 2 (2017): 117–27. http://dx.doi.org/10.1159/000464443.

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The construction of switchable, radiation-controlled, aptameric enzymes - “<i>swenzymes” -</i> is, in principle, feasible. We propose a strategy to make such catalysts from 2 (or more) aptamers each selected to bind specifically to one of the substrates in, for example, a 2-substrate reaction. Construction of a combinatorial library of candidate swenzymes entails selecting a set of a million aptamers that bind one substrate and a second set of a million aptamers that bind the second substrate; the aptamers in these sets are then linked pairwise by a linker, thus bringing together the substrates. In the presence of the substrates, some linked aptamer pairs catalyze the reaction when exposed to external energy in the form of a specific frequency of low-intensity, nonionizing electromagnetic or acoustic radiation. Such swenzymes are detected via a separate<i> product-capturing</i> aptamer that changes conformation on capturing the product; this altered conformation allows it (1) to bind to every potential swenzyme in its vicinity (thereby giving a higher probability of capture to the swenzymes that generate the product) and (2) to bind to a sequence on a magnetic bead (thereby permitting purification of the swenzyme plus product-capturing aptamer by precipitation). Attempts to implement the swenzyme strategy may help elucidate fundamental problems in enzyme catalysis.
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Hosseini, Seyed Mohammad Hasan, Mohammad Reza Bassami, Alireza Haghparast, Mojtaba Sankian, and Gholamreza Hashemi Tabar. "Identification of Aptamers that Specifically Bind to A1 Antigen by Performing Cell-on Human Erythrocytes." Galen Medical Journal 9 (June 27, 2020): 1657. http://dx.doi.org/10.31661/gmj.v9i0.1657.

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Background: The apply of aptamers as a new generation’s way to probe diagnostic for the detection of target molecules has gained ground. Aptamers can be used as alternatives to diagnostic antibodies for detection of blood groups due to their unique features. This study was aimed to produce DNA diagnostic aptamer detecting the antigen of A1 blood group using the Cell-Selex method. Materials and Methods: DNA aptamer was isolated against A1 RBC antigen after ten stages of Cell-Selex and amplification by an asymmetric polymerase chain reaction. The progress of the stages of selection was evaluated using flow cytometry analysis, which the DNA aptamer isolated from the tenth cycle with an affinity of 70% fluorescent intensity, was selected from four positive colonies followed by determination of the sequences and secondary structures. Results: The aptameric sequence obtained from C4 cloning was calculated with the highest binding affinity to A1 antigen having an apparent dissociation constant (Kd value) of at least 29.5 ± 4.3 Pmol, which was introduced as the selected aptamer-based on ΔG obtained from a colony of C4 equal to –13.13. Conclusion: The aptamer obtained from using Cell-Selex method could be used as an example for the development of diagnostic tools such as biosensors for detecting A1 blood group antigens. [GMJ.2020;9:e1657]
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Lin, Jun Sheng, and Kenneth P. McNatty. "Aptamer-Based Regionally Protected PCR for Protein Detection." Clinical Chemistry 55, no. 9 (September 1, 2009): 1686–93. http://dx.doi.org/10.1373/clinchem.2009.127266.

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Abstract Background: DNA aptamers are single-stranded nucleotide sequences that bind specifically to target molecules. By combining the advantages of PCR for amplifying specific DNA sequences and aptamer technology, we have developed a new strategy to detect target molecules such as proteins. Methods: Ovine follicle-stimulating hormone α subunit (oFSHα) was used as the model protein to generate a specific DNA aptamer via an in vitro evolutionary process. A targeted regional-mapping approach and a target-capturing assay were used to identify the binding region on the aptamer molecule. In the detection assay, referred to as “aptamer-based regionally protected PCR” (ARP-PCR), the aptamer was allowed to bind to the target protein in solution before digestion with DNase I. The region of the aptamer bound to the target was protected from DNase I cleavage. The target-binding region of the aptamer protected from the enzymatic treatment was then amplified by the PCR. Results: Aptamers against oFSHα were generated. Six sequences of 20 selected aptamer clones were identical. This aptamer sequence was divided into 4 regions according to the aptamer’s secondary structure. From examination of the target-binding ability of each region, we determined the specific binding region, for which primers were designed. With the aptamer and primers to detect oFSHα by means of the ARP-PCR method, we were able to detect the target protein at concentrations as low as 10−14 mol/L. Conclusions: Combining the use of a DNA aptamer with the PCR is a potentially useful analytic tool for detection of proteins at low concentrations. .
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Ponzo, Irene, Friederike M. Möller, Herwin Daub, and Nena Matscheko. "A DNA-Based Biosensor Assay for the Kinetic Characterization of Ion-Dependent Aptamer Folding and Protein Binding." Molecules 24, no. 16 (August 8, 2019): 2877. http://dx.doi.org/10.3390/molecules24162877.

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Therapeutic and diagnostic nucleic acid aptamers are designed to bind tightly and specifically to their target. The combination of structural and kinetic analyses of aptamer interactions has gained increasing importance. Here, we present a fluorescence-based switchSENSE aptasensor for the detailed kinetic characterization of aptamer–analyte interaction and aptamer folding, employing the thrombin-binding aptamer (TBA) as a model system. Thrombin-binding aptamer folding into a G-quadruplex and its binding to thrombin strongly depend on the type and concentration of ions present in solution. We observed conformational changes induced by cations in real-time and determined the folding and unfolding kinetics of the aptamer. The aptamer’s affinity for K+ was found to be more than one order of magnitude higher than for other cations (K+ > NH4+ >> Na+ > Li+). The aptamer’s affinity to its protein target thrombin in the presence of different cations followed the same trend but differed by more than three orders of magnitude (KD = 0.15 nM to 250 nM). While the stability (kOFF) of the thrombin–TBA complex was similar in all conditions, the cation type strongly influenced the association rate (kON). These results demonstrated that protein–aptamer binding is intrinsically related to the correct aptamer fold and, hence, to the presence of stabilizing ions. Because fast binding kinetics with on-rates exceeding 108 M−1s−1 can be quantified, and folding-related phenomena can be directly resolved, switchSENSE is a useful analytical tool for in-depth characterization of aptamer–ion and aptamer–protein interactions.
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Schilling-Loeffler, Katja, Rachel Rodriguez, and Jacquelina Williams-Woods. "Target Affinity and Structural Analysis for a Selection of Norovirus Aptamers." International Journal of Molecular Sciences 22, no. 16 (August 18, 2021): 8868. http://dx.doi.org/10.3390/ijms22168868.

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Aptamers, single-stranded oligonucleotides that specifically bind a molecule with high affinity, are used as ligands in analytical and therapeutic applications. For the foodborne pathogen norovirus, multiple aptamers exist but have not been thoroughly characterized. Consequently, there is little research on aptamer-mediated assay development. This study characterized seven previously described norovirus aptamers for target affinity, structure, and potential use in extraction and detection assays. Norovirus-aptamer affinities were determined by filter retention assays using norovirus genotype (G) I.1, GI.7, GII.3, GII.4 New Orleans and GII.4 Sydney virus-like particles. Of the seven aptamers characterized, equilibrium dissociation constants for GI.7, GII.3, GII.4 New Orleans and GII.4 Sydney ranged from 71 ± 38 to 1777 ± 1021 nM. Four aptamers exhibited affinity to norovirus GII.4 strains; three aptamers additionally exhibited affinity toward GII.3 and GI.7. Aptamer affinity towards GI.1 was not observed. Aptamer structure analysis by circular dichroism (CD) spectroscopy showed that six aptamers exhibit B-DNA structure, and one aptamer displays parallel/antiparallel G-quadruplex hybrid structure. CD studies also showed that biotinylated aptamer structures were unchanged from non-biotinylated aptamers. Finally, norovirus aptamer assay feasibility was demonstrated in dot-blot and pull-down assays. This characterization of existing aptamers provides a knowledge base for future aptamer-based norovirus detection and extraction assay development and aptamer modification.
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Samokhvalov, A. V., A. V. Zherdev, and B. B. Dzantiev. "Electrophoretic study of G-quadruplex aptamer interactions with different short single-strand complementary oligonucleotides." Journal of Physics: Conference Series 2212, no. 1 (February 1, 2022): 012001. http://dx.doi.org/10.1088/1742-6596/2212/1/012001.

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Abstract Aptamers are single-stranded nucleic acids, typically 20-80 nucleobases (nb) in length, which can bind different compounds with high affinity and selectively. Their ligand-binding properties can be attenuated by adding short complementary strands. These interactions open new opportunities for aptamer-based assays. Strong dependence between the length and electrophoretic mobility of short nucleic acids makes polyacrylamide gel electrophoresis a powerful tool for studying their complexes. The interactions between the 36 nb DNA G-quadruplex aptamer (5’-GAT-CGG-GTG-TGG-GTG-GCG-TAA-AGG-GAG-CAT-CGG-ACA-3’) specific to ochratoxin A and 9 complementary single-stranded DNA (ssDNA) were studied. The length of ssDNA varied from 5 to 9 nb. To maintain ligand-binding conformation of the aptamer, a high ionic strength buffer was used. The best resolution between the aptamer and its complex was provided for the gel with 15% monomer and a monomer/cross-linker ratio of 15:1. Bands of free aptamer and ssDNA were observed for all studied variants. If the ssDNA length was less than 9 nb, the position of the aptamer’s band remained unchanged, independent of the aptamer/ssDNA ratios, and additional bands did not appear. The longest ssDNA (5’-CGC-CAC-CCA-3’) did not lead to the appearance of a new band, but it slowed the aptamer’s migration depending on the ssDNA concentration. Under a 27-fold excess of the given ssDNA, the relative mobility of the aptamer band changed from 0.566 to 0.468. Thus, electrophoresis visualizes aptamer-ssDNA interactions and can be used in the development of aptamer-based analytical systems.
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Amero, Paola, Soumen Khatua, Cristian Rodriguez-Aguayo, and Gabriel Lopez-Berestein. "Aptamers: Novel Therapeutics and Potential Role in Neuro-Oncology." Cancers 12, no. 10 (October 9, 2020): 2889. http://dx.doi.org/10.3390/cancers12102889.

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A relatively new paradigm in cancer therapeutics is the use of cancer cell–specific aptamers, both as therapeutic agents and for targeted delivery of anticancer drugs. After the first therapeutic aptamer was described nearly 25 years ago, and the subsequent first aptamer drug approved, many efforts have been made to translate preclinical research into clinical oncology settings. Studies of aptamer-based technology have unveiled the vast potential of aptamers in therapeutic and diagnostic applications. Among pediatric solid cancers, brain tumors are the leading cause of death. Although a few aptamer-related translational studies have been performed in adult glioblastoma, the use of aptamers in pediatric neuro-oncology remains unexplored. This review will discuss the biology of aptamers, including mechanisms of targeting cell surface proteins, various modifications of aptamer structure to enhance therapeutic efficacy, the current state and challenges of aptamer use in neuro-oncology, and the potential therapeutic role of aptamers in pediatric brain tumors.
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Nakatsuka, Nako, Kyung-Ae Yang, John M. Abendroth, Kevin M. Cheung, Xiaobin Xu, Hongyan Yang, Chuanzhen Zhao, et al. "Aptamer–field-effect transistors overcome Debye length limitations for small-molecule sensing." Science 362, no. 6412 (September 6, 2018): 319–24. http://dx.doi.org/10.1126/science.aao6750.

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Detection of analytes by means of field-effect transistors bearing ligand-specific receptors is fundamentally limited by the shielding created by the electrical double layer (the “Debye length” limitation). We detected small molecules under physiological high–ionic strength conditions by modifying printed ultrathin metal-oxide field-effect transistor arrays with deoxyribonucleotide aptamers selected to bind their targets adaptively. Target-induced conformational changes of negatively charged aptamer phosphodiester backbones in close proximity to semiconductor channels gated conductance in physiological buffers, resulting in highly sensitive detection. Sensing of charged and electroneutral targets (serotonin, dopamine, glucose, and sphingosine-1-phosphate) was enabled by specifically isolated aptameric stem-loop receptors.
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Wang, Zhong, Xiuying Yang, Nicholas Zhou Lee, and Xudong Cao. "Multivalent Aptamer Approach: Designs, Strategies, and Applications." Micromachines 13, no. 3 (March 12, 2022): 436. http://dx.doi.org/10.3390/mi13030436.

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Aptamers are short and single-stranded DNA or RNA molecules with highly programmable structures that give them the ability to interact specifically with a large variety of targets, including proteins, cells, and small molecules. Multivalent aptamers refer to molecular constructs that combine two or more identical or different types of aptamers. Multivalency increases the avidity of aptamers, a particularly advantageous feature that allows for significantly increased binding affinities in comparison with aptamer monomers. Another advantage of multivalency is increased aptamer stabilities that confer improved performances under physiological conditions for various applications in clinical settings. The current study aims to review the most recent developments in multivalent aptamer research. The review will first discuss structures of multivalent aptamers. This is followed by detailed discussions on design strategies of multivalent aptamer approaches. Finally, recent developments of the multivalent aptamer approach in biosensing and biomedical applications are highlighted.
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Dissertations / Theses on the topic "Aptameri"

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Wang, Tianjiao. "Function and dynamics of aptamers a case study on the malachite green aptamer /." [Ames, Iowa : Iowa State University], 2008.

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Savonnet, Maud. "Développement d'une méthode de détection innovante appliquée au diagnostic terrain des pathologies cardiaques." Thesis, Université Grenoble Alpes, 2020. http://www.theses.fr/2020GRALY061.

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Diagnostiquer au plus tôt les pathologies cardiaques est aujourd’hui un enjeur majeur dans le monde de la santé. En effet, la rapidité du diagnostic de l’infarctus du myocarde a un impact non seulement sur la santé du patient, mais aussi sur la gestion des services hospitaliers d’urgence. Ainsi, l’utilisation de dispositifs de diagnostic au chevet du patient est une solution pertinente pour répondre efficacement à un tel enjeu. C’est pour cette raison que l’on assiste aujourd’hui à une croissance sur le marché du nombre de systèmes Point-Of-Care dédiés au diagnostic terrain des pathologies cardiaques. Ces dispositifs disposent néanmoins d’un certain nombre d’inconvénients qu’il s’agit de surmonter.C’est dans ce contexte que s’inscrit ce travail de thèse. Aussi, un travail de recherche et de mise au point d’une méthode de détection des biomarqueurs cardiaques innovante a été mené. Cette méthode a pour objectif la détection de tout type d’analyte dans un milieu complexe avec une bonne sensibilité permise par l’amplification biomoléculaire mise en œuvre. Cette méthode générique est basée sur l’amplification LAMP d’une sonde oligonucléotidique. Elle emploie des sondes aptamères, spécifiques de la cible à détecter, et qui ont été validées par imagerie de résonance des plasmons de surface. Cette méthode a été mise en œuvre de manière pertinente sur différents modèles et appliquée à la détection d’un biomarqueur cardiaque d’intérêt, la troponine I. L’intégration de cette méthode dans un dispositif microfluidique portable a finalement été abordée dans la perspective d’une utilisation future pour le diagnostic de terrain
Today, early diagnosis of cardiac pathologies is a major issue in healthcare world. Indeed, the speed of myocardial infarction diagnosis has an impact not only on the patient's health, but also on the management of emergency hospital services. The use of diagnostic devices at the patient’s bedside is a relevant solution to overcome effectively such a challenge. Consequently, the number of Point-Of-Care systems dedicated to the diagnosis of cardiac pathologies is growing. However, these devices have some disadvantages that need to be overcome.This thesis work has been conducted in this context. Research and development of an innovative method for the detection of cardiac biomarkers has been carried out. The objective of this method is the detection of any type of analyte in a complex medium with a good sensitivity allowed by the biomolecular amplification used. This generic method is based on the LAMP amplification of an oligonucleotide probe. It uses aptamer probes, specific to the target to be detected, which have been validated by surface plasmon resonance imaging. This method has been implemented in a relevant manner on different models and applied to the detection of a cardiac biomarker of interest, troponin I. The integration of this method in a portable microfluidic device was finally addressed for future use in field diagnostics
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Dibenedetto, Silvia. "Direct activation of endogenous Calcineurin A : biological impact of selective peptide aptamers." Phd thesis, Ecole normale supérieure de lyon - ENS LYON, 2011. http://tel.archives-ouvertes.fr/tel-00757018.

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Therapeutic approaches leading to the stimulation of regeneration, and/or inhibition of degeneration processes in neuromuscular disorders are believed to offer valid therapeutic strategies that would preserve muscle tone and contribute to the quality of life while lengthening patient life span. Activation of CalcineurinA (CnA), a threonine-serine phosphatase, controls gene regulatory programs in skeletal muscle by stimulating slow muscle fiber (type I) gene expression. This phosphatase has been also identified as a key mediator in the hypertrophic response and in skeletal muscle regeneration. Activation of CnA is, therefore, considered as a potentially interesting means of stimulating muscle regeneration in myopathies. We have identified a peptide aptamer that activates CnA in vitro, in cells and in vivo. In a mouse model for denervation-induced muscle atrophy, CnA-activating peptide aptamers show significant positive impact. This is reflected in larger overall muscle cross-sectional surface area due to an increased number of fibers and larger individual fiber surface area. Insight into the biological mechanism is afforded by observation of increased levels of nuclear NFAT transcription factor in these fibers, in agreement with peptide aptamer-mediated activation of CnA. Furthermore, a significant increase in central nuclei, characteristic of the presence of new fibers, is observed in muscles treated with the peptide aptamers specifically activating CnA. Identification of the specific binding site of the peptide aptamer on CnA was achieved using several truncations of the phosphatase, offering insight into the molecular mechanism of action. Together, these studies offer the first proof that direct activation of endogenous CnA has a measureable impact on cellular responses resulting in stimulation of muscle regeneration and enhancement of pathophysiological state in selected animal models.
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Kimura, Mari, and 木村摩利. "Towards intracellular aptamers: delivery of anti-SCV helicase aptamers and development of aptamers againstSATB1." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hub.hku.hk/bib/B48079893.

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 Aptamers are small RNAs or DNAs that specifically bind to targets through complementary three-dimensional structure with high affinity. Aptamers are screened by an in vitro process called SELEX (systematic evolution of ligands by exponential enrichment) against a variety of targets, including small organic and inorganic molecules, cofactors, peptides, proteins and even whole cells, and aptamers hold great potential as diagnostic tools or as therapeutics. Aptamers are alternatives to antibodies with a variety of potential advantages. However, development of aptamers against intracellular targets is limited by delivery methods. To develop an intracellularly acting aptamer, we aimed to 1) establish an aptamer intracellular delivery system; 2) clone, express and purify the intracellular target SATB1 for aptamer selection; and 3) select an intracellularly acting aptamer against SATB1 by SELEX. An efficient delivery for the anti-SCV helicase aptamer was achieved using the pDNA transfection reagent Lipofectamine2000, whereby the aptamer was delivered exclusively to the nucleus. We also tested and improved methods to study aptamer-liposome complex formation. Expression of the SCV helicase in the cytoplasm could not alter the aptamer location within cell, suggesting that aptamer modification such as attachment of a redirecting signal or conjugation to a polymer would be required for cytoplasmic targeting. In this thesis we switched to a nuclear target, SATB1, to develop a nuclear intracellularly acting aptamer. SATB1 is a gene regulator found in the nucleus. Upon activation, SATB1 binds to the nuclear matrix and targets the chromosome via the MAR binding domain to regulate histone modification and nucleosome positioning over a long distance. A recent report demonstrated SATB1’s role in breast cancer metastasis, therefore development of aptamers against this protein has great diagnostic and therapeutic potential. We successfully cloned full length SATB1. The full length protein could not be expressed, however the MAR binding domain was successfully expressed with 6xHis tag and purified using a His trap column. ITC analysis with BUR sequence showed proper folding and selectivity of the MAR binding domain. DNA aptamers were selected by SELEX against the MAR binding domain of SATB1. Selection was successful and a highly conserved family of aptamers was observed. Sequence analysis and alignment revealed the presence of many conserved motifs that involve many A and T in a similar manner to the BUR sequence and dsDNA previously found to have high affinity towards the MAR binding domain. Altogether, we have taken a step closer towards the development of an intracellularly acting SATB1 aptamer. Future efforts involving affinity determination, application of the established delivery method and in vitro study of inhibitory mechanism will be further steps towards intracellular aptamers for cancer diagnosis or therapeutics.
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Biochemistry
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Master of Philosophy
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Brothier, Fabien. "Développement d'outils bioanalytiques miniaturisés : greffage de biomolécules sur monolithes en capillaire couplés à la nanochromatographie pour l'analyse d'échantillons complexes." Thesis, Paris 6, 2014. http://www.theses.fr/2014PA066299/document.

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L’analyse de traces dans des matrices complexes (environnementales, alimentaires ou biologiques) requiert très souvent une étape de purification et de préconcentration avant une analyse via des méthodes chromatographiques. Dans cette optique, des supports d’extraction basés sur des mécanismes de reconnaissance moléculaire ont été développés et appliqués à l’extraction de composés cibles rendant ainsi l’analyse plus sensible et plus fiable. Ces supports sélectifs peuvent entre autres résulter de l’immobilisation de biomolécules tels que les anticorps ou les aptamères (i.e. des oligonucléotides présentant une séquence capable de se lier spécifiquement à une molécule). Cette étape de traitement de l’échantillon est particulièrement nécessaire lorsqu’il s’agit de développer des systèmes séparatifs miniaturisés, tels que les microsystèmes séparatifs sur puce, du fait de la diminution de la résolution qui résulte de l’utilisation d’un canal de séparation de faible longueur. Dans ce contexte, ce projet de recherche a consisté à développer des systèmes bioanalytiques miniaturisés pour l’analyse de petites molécules ou protéines dans des échantillons complexes. Pour développer ces systèmes, la synthèse d’un monolithe hybride organique-inorganique in situ dans des capillaires de 100 µm d.i. a, dans un premier temps, été optimisée via une approche sol-gel puis caractérisée en termes de répétabilité. Dans une deuxième partie, deux toxines modèles de faible poids moléculaire ont été choisies : la microcystine-LR (MC-LR) et l’ochratoxine A (OTA). Des anticorps monoclonaux et des aptamères, spécifiques de l’une et l’autre des toxines ont ensuite été greffés sur des monolithes en capillaire. Les immuno- et oligoadsorbants miniaturisés obtenus (respectivement mIS et mOS) ont été couplés en ligne avec la nanoLC. La rétention spécifique des toxines cibles sur les mIS et mOS a été démontrée dans l’eau pure. La répétabilité de la synthèse et du greffage a été évaluée et la capacité de chacun des supports miniaturisés a été déterminée. Enfin, mIS et mOS ont été appliqués avec succès à l’extraction sélective de la MC-LR et de l’OTA à partir d’extraits de cultures de cyanobactéries, d’eaux environnementales ainsi que d’échantillons de bière dopés. Dans un troisième temps, de façon à transposer les outils sélectifs développés à l’analyse de protéines, des microréacteurs enzymatiques (IMER) ont été préparés par greffage de deux enzymes protéolytiques (pepsine et trypsine) sur des monolithes. Ces outils ont ensuite été couplés avec la nanoLC-MS² pour l’analyse d’une protéine modèle, le cytochrome C. Les rendements de digestion sur IMER se sont avérés présenter une bonne répétabilité. Toutefois, l’efficacité de la digestion sur les IMER à base de pepsine reste à ce jour insuffisante et nécessite de réadapter la procédure de greffage et/ou de digestion
The analysis of ultra-traces from complex matrices (environmental, foodstuff or biological) often requires a step of purification and preconcentration before their analysis by chromatographic separation methods. Therefore, extraction sorbents based on a molecular recognition mechanism can be developed and used for the selective extraction of target molecules thus rendering their quantitative analysis in complex samples more reliable and sensitive. These extraction sorbents may result, among others, from the immobilization of biomolecules such as antibodies and aptamers (i.e. oligonucleotides whose sequence is specific for a target molecule). This selective sample pretreatment step is particularly necessary when developing miniaturized devices such as separative microsystems on chip because of the decrease of the resolution that results from the use of a shorter length separation channel. In this context, the aim of our study was to develop miniaturized bioanalytical devices for the analysis of small molecules or proteins in complex samples. For the development of these devices, in-situ synthesis of a porous hybrid organic-inorganic monolith in capillaries (100 µm i.d.) by sol-gel approach was firstly optimized and characterized in terms of repeatability. Secondly, two model toxins of low molecular weight were chosen: microcystin-LR (MC-LR) and ochratoxin A (OTA). Monoclonal antibodies and aptamers specific to one and the other target molecules were then grafted on the monolithic capillaries. The resulting miniaturized immunosorbent (mIS) and oligosorbent (mOS) were then coupled on-line to nanoLC. Specific retention of MC-LR and OTA on the mIS and the mOS, respectively, was demonstrated in pure water. Synthesis repeatability and capacity of the miniaturized sorbents were evaluated. Finally, these miniaturized tools were applied to the selective extraction of MC-LR or OTA from complex samples, i.e. blue-green algae extracts, environmental waters or beer. In a third part, immobilized enzyme reactors (IMERs) were prepared by grafting two proteolytic enzymes (pepsin and trypsin) on monoliths in order to transpose the developed selective tools to the analysis of proteins. These IMERs were then coupled on-line to nanoLC-MS² for the analysis of a model protein, cytochrome C. Digestion yields on IMERs presented a good repeatability. However, digestion efficiency on the pepsin-based IMERs remains so far insufficient and grafting or digestion procedure needs to be readjusted
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Aschl, Timothy. "Biochips based on silicon for detecting the interaction between aptamers and pathogens." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLX103/document.

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La détection rapide et sensible des agents pathogènes est d’une très grande importance pour la biosécurité. Les biopuces sont bien adaptées à cet effet, car elles permettent la détection multiplexe des cibles. Une limitation cruciale des biopuces est leur manque de fiabilité et de sensibilité. L’objectif de cette thèse est de développer une architecture reproductible de biopuces à base de couche mince de silicium amorphe carboné (a-SiC:H) déposée sur un réflecteur en aluminium pour une détection fiable et sensible des pathogènes. Nous avons choisi comme système modèle l’interaction de la toxine alimentaire ochratoxine A (OTA) avec son aptamère AntiOTA de longueur 36mer. Les aptamères (simples brins d’ADN) sont de plus en plus utilisés comme sondes en raison de leur grande spécificité et affinité vis-à-vis d’une large gamme de cibles (i.e. protéines, bactéries…). La stratégie de fabrication consiste en un greffage de monocouches organiques d’acides carboxyliques via des liaisons Si-C robustes, suivi de l’accrochage covalent des aptamères par un couplage peptidique. Les processus de greffage ont été mis au point sur silicium cristallin permettant la quantification des couches greffées par spectroscopie infrarouge en mode ATR (Attenuated total reflexion). La quantification IR des interactions OTA – AntiOTA a été montrée pour la première fois sur des surfaces par IR-ATR. La spécificité de l’aptamère a été démontrée en utilisant une molécule chimiquement similaire (warfarin), pour laquelle l’AntiOTA ne montre aucune affinité. Ces protocoles bien contrôlés ont été transférés sur l’architecture de la biopuce a-SiC:H. Les aptamères immobilisés sont hybridés avec des brins complémentaires marqués avec des fluorophores. En présence de l’OTA une déshybridation des brins complémentaires est attendue, conduisant à une diminution du signal fluorescent. Différentes longueurs de brins complémentaires ont été comparées, montrant jusqu’à 13% de diminution due à l’interaction de l’OTA
Rapid and sensitive detection of pathogenic targets play a crucial role in biosecurity. Biochips are ideal for this, as they allow easy and multiplex detection of targets. A crucial limitation in biochips is that they often suffer from low reliability and sensitivity. The goal of this thesis is to develop a stable and reproducible architecture for biochips based on an amorphous silicon carbon alloy (a-SiC:H) deposited on an aluminium back-reflector for reliable and sensitive detection of pathogens. On these biochips we introduced the interaction of the food and feed toxin ochratoxin A (OTA) with its 36mer aptamer AntiOTA as a model system. Aptamers (single strands of DNA) are ideal as probes for biochips as they display high specificity and affinity towards a wide range of targets (i.e. proteins, bacteria…). The well-controlled multi-step fabrication process consists of the reliable photochemical grafting of acid-terminated organic monolayers on silicon surfaces by robust Si C bonds, which in turn were functionalized with aptamers by stable peptide coupling. Carrying out this process on crystalline silicon allowed monitoring and quantification of every step by infrared spectroscopy (IR-ATR). The interaction OTA – AntiOTA was shown for the first time on surfaces by IR, and an IR in situ calibration allowed the quantification of OTA which was bound by the aptamers on the surface. The specificity of AntiOTA towards OTA was demonstrated by using a chemically similar molecule (warfarin), for which AntiOTA shows no affinity. The well-controlled protocols were transferred to the a-SiC:H biochip. The immobilized aptamers were hybridized with complementary and fluorescent-labeled DNA-strands. In presence of OTA, dehybridization of the complementary strands is expected, resulting in a decrease of fluorescent signal. Different lengths of complementary strands were compared, exhibiting up to 13% signal decrease due to OTA
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Daniel, Camille. "Biopuce à aptamères anti-thrombine : exploration d'une technique alternative de détection." Phd thesis, Université de Grenoble, 2013. http://tel.archives-ouvertes.fr/tel-00954086.

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Du fait de leur haute stabilité et bas coût de production, les aptamères suscitent un intérêt croissant, depuis près de 20 ans, dans le design de biocapteurs en tant qu'élément de reconnaissance idéal. Le but de ce travail de thèse est de démontrer l'intérêt et la pertinence d'un outil tel qu'une biopuce à aptamères, associant les avantages des sondes aptamères à ceux d'une détection par SPRi (Surface Plasmon Resonance imaging), permettant une détection sans marquage et en temps réel d'interactions moléculaires. Dans ce but, deux aptamères anti-thrombine (APT1 = 5′- GGT-TGG-TGT-GGT-TGG -3′ et APT2 = 5′-AGT-CCG-TGG-TAG-GGG-AGG-TTG-GGG-TGA-CT-3′) ont été choisis comme objets d'étude modèles. Ce choix a permis d'orienter différents axes de recherche : utilisés indépendamment comme sondes lors de l'élaboration de notre biopuce, ils ont tout d'abord permis de réaliser une détection cinétique optimisée de la thrombine, avec des performances remarquables pour une détection de ce type, ainsi que le calcul de constantes de dissociation en solution et à la surface des biopuces. Mais au-delà d'un simple biocapteur, la biopuce a également pu être utilisée comme véritable plateforme d'étude de la thrombine et de ses interactions, au sein de structures plus complexes telles que la structure " sandwich " entre les deux aptamères, ou d'autres interactions impliquant la thrombine en tant qu'acteur de la cascade de coagulation (inhibition de la thrombine par l'antithrombine III et le cofacteur II de l'héparine, transformation de la prothrombine au sein du complexe prothrombinase).
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Kittichan, Kanokphandharangkul. "Aptamer biosensors." Thesis, Imperial College London, 2016. http://hdl.handle.net/10044/1/39048.

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Aptamers are single stranded nucleic acids, typically composed of between twenty to eighty nucleotides in length, capable of binding selectively to non-nucleic acid ligands. Aptamers are selected through a combinatorial chemistry process called Systematic Evolution of Ligands by Exponential enrichment (SELEX), which is composed of successive cycles of selection based on target affinity, followed by amplification. This results in the Darwinian evolution of the nucleic acid library resulting in increasing library homogeneity and target affinity over time. Aptamers have been extensively investigated for potential application as sensing molecules, with roles similar to those traditionally occupied by antibodies. Aptamers and monoclonal antibodies have similar sensitivity in the pico to micro molar range. However aptamers have a number of advantages over protein antibodies, such as greater thermal stability, ease of chemical amplification, and amenability to modification, especially at the 5' and 3' prime ends. The work performed in this Thesis is divided into three categories. The first section describes the development of voltammetric Kanamycin and Tetracycline biosensors based on electrode immobilized, redox label bioconjugated nucleotide molecular beacons. These sensors relies on the target-aptamer binding induced spatial displacement of the redox label towards or away from the electrode surface as a means of signal generation. Further study was conducted to test the feasibility of this sensor design under likely field operation environments such as in soil sample analysis for microbial product discovery and in agricultural effluence for regulatory purposes. The biosensor was also enhanced by gel encapsulation for defense against nuclease degradation. Negative control was performed against structurally similar antibiotics of the same family in order to prove the specificity of the biosensor. Lastly, the sensor was moved onto an automated platform in a multichannel format in order to improve the utility of the sensor. The second section describes the development of a voltammetric biosensor based on Enzyme-Linked Oligonucleotide Assay (ELONA) technology. Two sub-types of ELONA-like biosensors were originally envisioned, based respectively on direct and indirect ELONA. Both sub-types depend on the mass of redox label rich Gold Nanoparticles (GNP) at the electrode surface as a means of signal generation. Negative controls was performed against globular proteins Bovine Serum Albumin and Lysozyme, the former since it is the most ubiquitous protein component of serum (the most likely biosensor operational environment), the latter as a worst case scenario for non-specific false positive results due to its positive charge. The last section describes an attempt to develop an automated SELEX device based on mesofluidic flow channels. It was hoped that by using flow channels of a millimeter scale it would be possible to retain both the advantages of the conventional auto sampler based SELEX protocols (large library and sequence variation), while also gaining the primary advantages of microfluidic SELEX (reduced contamination risk, low initial cost and maintenance). Essential components of the SELEX device, such as thermal cycler, liquid handling, electronics infrastructure, and software control were designed, tested and integrated. Lastly an attempt was made to perform automated SELEX against Lysozyme targets using the device, though no nucleic acid with high affinity to target had yet been successfully isolated by the end of this study.
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Bini, Alessandra. "Aptamers for biosensors." Thesis, Cranfield University, 2008. http://dspace.lib.cranfield.ac.uk/handle/1826/4004.

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Aptamers are single-stranded DNA or RNA molecules isolated in vitro by a selection and amplification method. Aptamers bind with high specificity and affinity to a wide range of target molecules, with dissociation constant comparable to antibodies. In this work aptamers were employed as a new kind of bio-recognition element in affinity biosensors for the detection of clinically relevant proteins in heterogeneous assay, using Piezoelectric Quartz Crystal Microbalance and Surface Plasmon Resonance as transducers. The work was focused on two case studies, i.e. the Thrombin-binding aptamer and the aptamer against C-Reactive Protein. From an analytical point of view, the work was devoted to the optimisation of the analytical performance of a piezoelectric and an optical aptasensor for Thrombin and C-Reactive Protein detection, respectively. Efforts towards the application of these aptasensors in complex matrices, such as human plasma and serum, were also undertaken, in order to demonstrate the wide applicability of aptamers, as an alternative to antibodies. In this work, the possibility of introducing a computationally-assisted method to study aptamer-protein interaction and aptamer selection was also evaluated. For this purpose, the Thrombin-binding aptamer was chosen as a model and a retrospective docking study was performed by comparing the affinity of mutated sequences for thrombin with that of the Thrombin-binding aptamer, on the basis of a computationally-derived binding score. Finally, the reliability of computational results was tested by experimental measurements. For this purpose, the Thrombin-binding aptamer and other mutated sequences, selected on the basis of their binding score, were employed for the development of optical biosensors and the resulting analytical performances were compared. Even if further studies should be carried out in order to validate the proposed computational approach to aptamer selection, this work can have a significant impact on future aptamers selection for sensors and diagnostics.
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Dalton, Colette. "Aptamers as biosensors." Thesis, University of Strathclyde, 2010. http://oleg.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=15484.

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Books on the topic "Aptameri"

1

Yadav, Gulab Singh, Vikas Kumar, and Neeraj K. Aggarwal, eds. Aptamers. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-8836-1.

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Mayer, Günter, and Marcus M. Menger, eds. Nucleic Acid Aptamers. New York, NY: Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-2695-5.

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Mayer, Günter, ed. Nucleic Acid Aptamers. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3197-2.

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Urmann, Katharina, and Johanna-Gabriela Walter, eds. Aptamers in Biotechnology. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-54061-6.

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Mascini, Marco, ed. Aptamers in Bioanalysis. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2009. http://dx.doi.org/10.1002/9780470380772.

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Mascini, Marco. Aptamers in bioanalysis. Hoboken, N.J: J. Wiley & Sons, 2009.

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Dong, Yiyang, ed. Aptamers for Medical Applications. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-33-4838-7.

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Dong, Yiyang, ed. Aptamers for Analytical Applications. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2018. http://dx.doi.org/10.1002/9783527806799.

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Mayer, Günter, ed. Nucleic Acid and Peptide Aptamers. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-59745-557-2.

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1972-, Mayer Günter, ed. Nucleic acid and peptide aptamers: Methods and protocols. New York, NY: Humana, 2009.

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Book chapters on the topic "Aptameri"

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Parashar, Abhishek, Munna Lal Yadav, Gulab Singh Yadav, and Ram Krishan Saini. "Aptamer: The Science of Synthetic DNA." In Aptamers, 1–18. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-8836-1_1.

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Goyal, Meenu, Ankush, Mukesh R. Jangra, Ritu Batra, and Pardeep Kumar. "Aptamer-Based Biosensors for Detection of Environmental Pollutants." In Aptamers, 155–67. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-8836-1_10.

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Yadav, Pawan K., Sunil Kumar, Sanjay Yadav, and Sandeep Kumar. "Role of Aptamers in Plant Defense Mechanism Against Viral Diseases." In Aptamers, 169–74. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-8836-1_11.

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Yadav, Gulab Singh, Abhishek Parashar, and Neeraj K. Aggarwal. "Aptamer: A Next Generation Tool for Application in Agricultural Industry for Food Safety." In Aptamers, 175–86. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-8836-1_12.

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Kumar, Vijay, and Anchal Sharma. "Recent Updates for Isolation of Aptamers for Various Biothreat Agents Using Different Strategies and Their Role in Detection Applications." In Aptamers, 19–36. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-8836-1_2.

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Mutreja, Ruchi, Pardeep Kumar, Anupama Semwal, Shubham Jain, Rajat Dhyani, Rupesh Agarwal, Umesh Chand, Shahnawaz Ahmad Baba, Naveen K. Navani, and Piyush Kumar. "Aptamer: A Futuristic Approach in Diagnosis Rivaling Antibodies." In Aptamers, 37–57. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-8836-1_3.

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Goyal, Meenu, Citu, Nidhi Singh, Varsha Singla, and Ankit Singla. "Aptamer: Apt System for Target-Specific Drug Delivery." In Aptamers, 59–71. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-8836-1_4.

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Singhal, Paavan, Anita Rani Gill, Preeti K. Sharma, Rakesh Kumar, Nabin Bhusal, Amandeep Kaur, and Pooja Sharma. "Aptamers: Novel Therapeutic and Diagnostic Molecules." In Aptamers, 73–89. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-8836-1_5.

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Parashar, Abhishek, Kush Kumar Pandey, and Munna Lal Yadav. "Different Approaches for Aptamer Conjugated Drugs Preparation." In Aptamers, 91–100. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-8836-1_6.

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Baba, Shahnawaz Ahmad, Ruchi Mutreja, Arun Beniwal, Shubham Jain, Ekta Yadav, Tamoghna Ghosh, Naveen K. Navani, and Piyush Kumar. "Nucleic Acid Guided Molecular Tool for In-Vivo Theranostic Applications." In Aptamers, 101–22. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-8836-1_7.

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Conference papers on the topic "Aptameri"

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Nguyen, Thai Huu, and Qiao Lin. "An Aptamer-Functionalized Microfluidic Platform for Biomolecular Purification and Sensing." In ASME 2009 7th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2009. http://dx.doi.org/10.1115/icnmm2009-82142.

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Aptamers are oligonucleotides (DNA or RNA) that bind to chemical and biological analyte targets via affinity interactions. Through an in vitro synthetic process, aptamers can be developed for an extremely broad spectrum of analytes, such as small molecules, proteins, cells, viruses, and bacteria. Target recognition by aptamers is highly selective, as affinity interactions result in secondary aptamer conformational structures that specifically fit the target. The aptamer-target binding is also reversible and depends strongly on external stimuli such as pH and temperature. The specificity and stimuli-responsiveness of aptamers are highly attractive to biological purification and sensing, which generally involve isolating minute quantities of targets from complex samples with non-specific molecules and impurities present at orders-of-magnitude higher concentrations. We present an aptamer-functionalized microfluidic platform that by design exploits the specificity and temperature-dependent reversibility of aptamers to enable biomolecular purification and sensing. Using the specificity of aptamers, we demonstrate highly selective capture and enrichment of biomolecules. Employing thermally induced, reversible disruption of aptamer-target binding, we accomplish isocratic elution of the captured analytes and regeneration of the aptamer surfaces, thereby eliminating the use of potentially harsh reagents. Using integrated microfluidic control, the eluted analytes are detected in a label-free fashion by mass spectrometric methods.
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Khalil Bhuiyan, Md Ebrahim, Dustin Smith, Eric J. Voss, Chin-Chuan Wei, and Mohammad Shavezipur. "Surface Functionalization of Silicon MEMS Biochemical Sensors for the Detection of Foodborne Pathogens." In ASME 2021 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2021. http://dx.doi.org/10.1115/detc2021-69708.

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Abstract This work presents the surface modification of silicon chips as a platform for silicon-based biosensors with applications aiming for the detection of foodborne bacteria in aqueous solution. The detection requires high selectivity as the solution may contain a variety of biological species, which affect the outcome of the sensing process. The silicon surface is functionalized by a self-assembled monolayer (SAM) with thiol groups followed by immobilizing a thiol-linked DNA aptamer. The DNA aptamer used in this work has reported to recognize a biological species, E. coli ATCC 25922. The presence of DNA aptamer on the sensor surface allows the capture of the specific E. coli cells on the surface, while other potential biological (and chemical) species would not attach to the sensor surface, thus improving the selectivity of the sensor. The uniform formation of the SAM on the surface is an important step toward uniformly coating the sensor surface with the desired DNA aptamer. The SAM is created on the silicon surface by surface modification with the MPTS (3-mercaptopropyl trimethoxy silane) solution. Then the aptamer DNA solution is applied as droplets on the chip followed by a cure process. The attachment of the SAM and DNA aptamers are verified by atomic force microscopy (AFM). The surface functionalization presented in this work can be used for sensors made of silicon coated with a thin layer of native oxide, and can be adopted for detection of other cells and biological agents using the proper SAM and DNA aptamer.
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Nguyen, ThaiHuu, and Qiao Lin. "Thermally Responsive Aptamer Surfaces for Microfluidic Sample Preparation." In 2008 Second International Conference on Integration and Commercialization of Micro and Nanosystems. ASMEDC, 2008. http://dx.doi.org/10.1115/micronano2008-70264.

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For many bioanalytical systems, the quality of the sample under scrutiny greatly affects the success of its analysis by the analytical instrument. Thus, sample preparatory techniques such as solid-phase extraction (SPE), purification and concentration are used to improve the quality of the sample before introduction into the equipment. This work overviews our effort in developing microdevices which exploit thermally responsive aptamers for biomolecular sample extraction, purification and concentration. We demonstrate the feasibility of this approach with a model system which consists of an adenosine monophosphate (AMP) analyte and adenosine triphosphate derived aptamer. Through systematic experimentation, we demonstrate the extraction and enrichment of AMP at physiologically relevant concentrations, release of AMP and regeneration of the aptamer through thermal stimulation, and detection of AMP by either fluorescence or mass spectrometry. In addition, completely aqueous operation of the device eliminates the use of potentially harsh reagents.
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Chen, Kok Hao, and Jong Hyun Choi. "Nanoparticle-Aptamer: An Effective Growth Inhibitor for Human Cancer Cells." In ASME 2009 International Mechanical Engineering Congress and Exposition. ASMEDC, 2009. http://dx.doi.org/10.1115/imece2009-11966.

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Semiconductor nanocrystals have unique optical properties due to quantum confinement effects, and a variety of promising approaches have been devised to interface the nanomaterials with biomolecules for bioimaging and therapeutic applications. Such bio-interface can be facilitated via a DNA template for nanoparticles as oligonucleotides can mediate the aqueous-phase nucleation and capping of semiconductor nanocrystals.[1,2] Here, we report a novel scheme of synthesizing fluorescent nanocrystal quantum dots (NQDs) using DNA aptamers and the use of this biotic/abiotic nanoparticle system for growth inhibition of MCF-7 human breast cancer cells for the first time. Particularly, we used two DNA sequences for this purpose, which have been developed as anti-cancer agents: 5-GGT GGT GGT GGT TGT GGT GGT GGT GG-3 (also called, AGRO) and 5-(GT)15-3.[3–5] This study may ultimately form the basis of unique nanoparticle-based therapeutics with the additional ability to optically report molecular recognition. Figure 1a shows the photoluminescence (PL) spectra of GT- and AGRO-passivated PbS QD that fluoresce in the near IR, centered at approximately 980 nm. A typical synthesis procedure involves rapid addition of sodium sulfide in the mixture solution of DNA and Pb acetate at a molar ratio of 2:4:1. The resulting nanocrystals are washed to remove unreacted DNA and ions by adding mixture solution of NaCl and isopropanol, followed by centrifugation. The precipitated nanocrystals are collected and re-suspended in aqueous solution by mild sonication. Optical absorption measurements reveal that approximately 90 and 77% of GT and AGRO DNA is removed after the washing process. The particle size distribution in Figure 1b suggests that the GT sequence-capped PbS particles are primarily in 3–5 nm diameter range. These nanocrystals can be easily incorporated with mammalian cells and remain highly fluorescent in sub-cellular environments. Figure 1c serially presents an optical image of a MCF-7 cell and a PL image of the AGRO-capped QD incorporated with the cell. Figure 1. (a) Normalized fluorescence spectra of PbS QD synthesized with GT and AGRO sequences, which were previously developed as anti-cancer agents. The DNA-capped QD fluoresce in the near IR centered at ∼980 nm. (b) TEM image of GT-templated nanocrystals ranging 3–5 nm in diameter. (c) Optical image of an MCF-7 human breast cancer cell after a 12-hour exposure to aptamer-capped QD. (d) PL image of AGRO-QD incorporated with the cell, indicating that these nanocrystals remain highly fluorescent in sub-cellular environments. One immediate concern for interfacing inorganic nanocrystals with cells and tissue for labeling or therapeutics is their cytotoxicity. The nanoparticle cytotoxicity is primarily determined by material composition and surface chemistry, and QD are potentially toxic by generating reactive oxygen species or by leaching heavy metal ions when decomposed.[6] We examined the toxicity of aptamer-passivated nanocrystals with NIH-3T3 mouse fibroblast cells. The cells were exposed to PbS nanocrystals for 2 days before a standard MTT assay as shown in Figure 2, where there is no apparent cytotoxicity at these doses. In contrast, Pb acetate exerts statistically significant toxicity. This observation suggests a stable surface passivation by the DNA aptamers and the absence of appreciable Pb2+ leaching. Figure 2. Viability of 3T3 mouse fibroblast cells after a 2-day exposure to DNA aptamer-capped nanocrystals. There is no apparent dose-dependent toxicity, whereas a statistically significant reduction in cell viability is observed with Pb ions. Note that Pb acetate at 133 μM is equivalent to the Pb2+ amount that was used for PbS nanocrystal synthesis at maximum concentration. Error bars are standard deviations of independent experiments. *Statistically different from control (p&lt;0.005). Finally, we examined if these cyto-compatible nanoparticle-aptamers remained therapeutically active for cancer cell growth inhibition. The MTT assay results in Figure 3a show significantly decreased growth of breast cancer cells incorporated with AGRO, GT, and the corresponding templated nanocrystals, as anticipated. In contrast, 5-(GC)15-3 and the QDs synthesized with the same sequence, which were used as negative controls along with zero-dose control cells, did not alter cell viability significantly. Here, we define the growth inhibition efficacy as (100 − cell viability) per DNA of a sample, because the DNA concentration is significantly decreased during the particle washing. The nanoparticle-aptamers demonstrate 3–4 times greater therapeutic activities compared to the corresponding aptamer drugs (Figure 3b). We speculate that when a nanoparticle-aptamer is internalized by the cancer cells, it forms an intracellular complex with nucleolin and nuclear factor-κB (NF-κB) essential modulator, thereby inhibiting NF-κB activation that would cause transcription of proliferation and anti-apoptotic genes.[7] The nanoparticle-aptamers may more effectively block the pathways for creating anti-apoptotic genes or facilitate the cellular delivery of aptamers via nanoparticle uptake. Our additional investigation indicates that the same DNA capping chemistry can be utilized to produce aptamer-mediated Fe3O4 nanocrystals, which may be potentially useful in MRI and therapeutics, considering their magnetic properties and biocompatibility. In summary, the nanoparticle-based therapeutic schemes developed here should be valuable in developing a multifunctional drug delivery and imaging agent for biological systems. Figure 3. Anti-proliferation of MCF-7 human breast cancer cells with aptamer-passivated nanocrystals. (a) Viability of MCF-7 cells exposed to AGRO and GT sequences, and AGRO-/GT-capped QD for 7 days. The DNA concentration was 10 uM, while the particles were incubated with cells at 75 nM. (b) Growth inhibition efficacy is defined as (100 − cell viability) per DNA to correct the DNA concentration after particle washing.
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Chen, Kangfu, Teodor Georgiev, and Z. Hugh Fan. "Interactions Between Circulating Tumor Cells and Aptamer-Functionalized Microposts in a Flow." In ASME 2017 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2017. http://dx.doi.org/10.1115/imece2017-70342.

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Circulating Tumor Cells (CTCs) have been considered as important biomarkers for cancer prognosis and treatment. However, there are only tens of CTCs in one billion of healthy blood cells. This CTC rarity challenge has been addressed by microfluidics technology that sheds light on efficient CTC detection and isolation. Using antibodies or aptamers to capture CTCs is one of the strategies for CTC isolation. A lot of work has been carried out to improve CTC capture efficiency and purity (i.e., specificity). The main consideration to optimize microfluidic device performance includes increasing surface-area-to-volume ratio and reducing shear stress, both of which are closely related to the interaction between CTCs and the microfluidic device. Here we report a detailed study on the interactions between CTCs and aptamer-functionalized microposts in a microfluidic device. We have evaluated the distribution of captured CTCs around a micropost. In addition, simulation was conducted to model CTC capture patterns around microposts. We found the simulated CTC capture pattern largely agree with the experimental results. The simulation methodology could be applicable for other affinity-based CTC isolation devices and approaches. The goal of the study is to improve the microfluidic device performance and provide a rapid and economical way to optimize the geometry design of the microfluidic devices for CTC isolation.
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Ma, Xiao, and Pranav Shrotriya. "Study on Specific Binding Interaction Between Protein and DNA Aptamer via Dynamic Force Spectroscopy." In ASME 2013 2nd Global Congress on NanoEngineering for Medicine and Biology. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/nemb2013-93119.

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Recently the need to design nanoscale, sensitive and flexible bio-sensors or biotic-abiotic interface keeps increasing. One of the essential challenges on this objective is to grasp a thorough understanding of the mechanism governing binding interaction between bio-molecules. In this study we aim to demonstrate the binding specificity and reveal force interaction between the anti-coagulation protein thrombin and the single-stranded DNA thrombin aptamer by application of Atomic Force Microscopy (AFM). The thiolated aptamer was deposited onto gold substrate, and then repeatedly brought into contact with a thrombin-coated AFM tip, and force drop-offs during the pull-off were measured to determine the unbinding force between the thrombin-aptamer pair. The results from experiment show that the thrombin-aptamer pair has specific binding and the force between the pair exhibits loading rate dependence. It was shown that the binding forces of the thrombin-aptamer interaction increases with growth of loading rates. The average binding force for a single thrombin/aptamer pair increased from 20 pN to 40 pN, with loading rate changes from 500pN/s to 13500pN/s. Distribution of the unbinding forces measured for each loading rate can be explained on the basis of single energy barrier model for molecular bond breakage.
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7

Cho, Minseon, Seung Soo Oh, Jeff Nie, Ron Stewart, Michael Eisenstein, James Chambers, Jamey D. Marth, James A. Thomson, and Tom H. Soh. "Abstract 2227: Aptamer selection for cancer markers: High-throughput, quantitative selection and characterization of nucleic acid aptamers for human angiopoietin-2." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-2227.

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8

White, Ryan J., and Kevin W. Plaxco. "Engineering new aptamer geometries for electrochemical aptamer-based sensors." In SPIE Defense, Security, and Sensing, edited by Nicholas F. Fell, Jr. and Venkataraman S. Swaminathan. SPIE, 2009. http://dx.doi.org/10.1117/12.820419.

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9

Tombelli, S., M. Minunni, and M. Mascini. "Analytical applications of aptamers." In International Congress on Optics and Optoelectronics, edited by Francesco Baldini, Jiri Homola, Robert A. Lieberman, and Miroslav Miler. SPIE, 2007. http://dx.doi.org/10.1117/12.724172.

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10

Wan, Yuan, Young-tae Kim, Li Na, Andrew D. Ellington, and Samir M. Iqbal. "Aptamer-Based Lab-on-Chip for Cancer Cell Isolation and Detection." In ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology. ASMEDC, 2010. http://dx.doi.org/10.1115/nemb2010-13195.

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Abstract:
The isolation and detection of circulating tumor cells (CTCs), when these are few in number or small in mass, can enable early cancer detection [1]. Currently, most research endeavors to isolate circulating tumor cells rely on antibodies and immunohistochemistry [2,3]. Aptamer are alternative molecules that have affinities and specificities that are comparable to those of antibodies [4,5], but these can be more readily adapted to many applications [6–9], including lab-on-a-chip devices. Here, we report use of a novel epidermal growth factor receptor (EGFR) aptamer biochip to identify and isolate cancer cells that overexpress EGFR. These results provide a solid basis for the development of diagnostic devices that can readily identify and isolate CTCs.
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Reports on the topic "Aptameri"

1

Wang, Tianjiao. Function and dynamics of aptamers: A case study on the malachite green aptamer. Office of Scientific and Technical Information (OSTI), January 2008. http://dx.doi.org/10.2172/964604.

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2

Keller, Evan. Novel Aptamers to Target Metastasis. Fort Belvoir, VA: Defense Technical Information Center, September 2010. http://dx.doi.org/10.21236/ada534850.

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3

Keller, Evan, and Greg Shelley. Novel Aptamers to Target Metastasis. Fort Belvoir, VA: Defense Technical Information Center, November 2012. http://dx.doi.org/10.21236/ada569358.

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Keller, Evan. Novel Aptamers to Target Metastasis. Fort Belvoir, VA: Defense Technical Information Center, September 2011. http://dx.doi.org/10.21236/ada555311.

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5

Niu, Li. Glutamate Receptor Aptamers and ALS. Fort Belvoir, VA: Defense Technical Information Center, January 2008. http://dx.doi.org/10.21236/ada481452.

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6

Chavez, Jorge L., Nancy Kelley-Loughnane, Morley O. Stone, and Robert I. MacCuspie. Colorimetric Detection with Aptamer-Gold Nanoparticle Conjugates: Effect of Aptamer Length on Response. Fort Belvoir, VA: Defense Technical Information Center, November 2012. http://dx.doi.org/10.21236/ada576582.

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7

Chakraborty, Srijani. The Dawn of RNA Therapeutics. Spring Library, December 2020. http://dx.doi.org/10.47496/sl.blog.19.

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8

Gmeiner, William H. Metallated DNA Aptamers for Prostate Cancer Treatment. Fort Belvoir, VA: Defense Technical Information Center, March 2013. http://dx.doi.org/10.21236/ada578778.

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Gmeiner, William. Metallated DNA Aptamers For Prostate Cancer Treatment. Fort Belvoir, VA: Defense Technical Information Center, March 2012. http://dx.doi.org/10.21236/ada559240.

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10

Kraus, G., and M. Nilsen-Hamilton. Developing Aptamers to Methaphetamine as Nucleic Acid Sensors. Office of Scientific and Technical Information (OSTI), December 2005. http://dx.doi.org/10.2172/882988.

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