Aptamers: Versatile Tools for Reagentless Aptasensing

Baldrich, Eva

doi:10.1007/978-1-4419-0919-0_17

Cited by 6 publications

(5 citation statements)

References 231 publications

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“…To show that all three components that participate in the sandwich were actively interacting with each other, i.e., to show their bioactivity in the liquid phase, we performed gel electrophoresis in native polyacrylamide gels with subsequent protein staining employing different combinations of both aptamer TBA1 and TBA2 and thrombin, see details in the Supporting Information, Figure S1, and refs and .…”

Section: Experimental Sectionmentioning

confidence: 99%

“…One of the remaining challenges in the field of biological detection is related to improving the selectivity of the assay and reducing the background noise caused by unspecific adsorption. , High specificity of the whole biochemical scheme determines the detection limit of the technique. In parallel to already well-studied antibodies, , the use of engineered receptor molecules, which are more stable and can be developed at low cost, i.e., aptamers, still need to be optimized for their wider implementation into biochemical assays. − Because of its distinct sequence, each aptamer forms a tertiary structure (e.g., hairpin or quadruplex , ), which interacts with a certain recognition site of the analyte such as proteins or organic molecules . Easy labeling protocols or the attachment of functional end groups to the nucleotides, the higher stability under varying conditions such as temperature or ionic strength compared to antibodies as well as the wide variety of possible targets make aptamers a promising candidate for diverse biosensor applications in the future. ,,, …”

Section: Introductionmentioning

confidence: 99%

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Patterned Biochemical Functionalization Improves Aptamer-Based Detection of Unlabeled Thrombin in a Sandwich Assay

Römhildt

Pahlke²,

Zörgiebel³

et al. 2013

ACS Appl. Mater. Interfaces

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Here we propose a platform for the detection of unlabeled human α-thrombin down to the picomolar range in a fluorescence-based aptamer assay. In this concept, thrombin is captured between two different thrombin binding aptamers, TBA1 (15mer) and TBA2 (29mer), each labeled with a specific fluorescent dye. One aptamer is attached to the surface, the second one is in solution and recognizes surface-captured thrombin. To improve the limit of detection and the comparability of measurements, we employed and compared two approaches to pattern the chip substrate−microcontact printing of organosilanes onto bare glass slides, and controlled printing of the capture aptamer TBA1 in arrays onto functionalized glass substrates using a nanoplotter device. The parallel presence of functionalized and control areas acts as an internal reference. We demonstrate that both techniques enable the detection of thrombin concentrations in a wide range from 0.02 to 200 nM with a detection limit at 20 pM. Finally, the developed method could be transferred to any substrate to probe different targets that have two distinct possible receptors without the need for direct target labeling.

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Section: Experimental Sectionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Patterned Biochemical Functionalization Improves Aptamer-Based Detection of Unlabeled Thrombin in a Sandwich Assay

Römhildt

Pahlke²,

Zörgiebel³

et al. 2013

ACS Appl. Mater. Interfaces

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show abstract

“…The structures of the known aptamers are quite different and include G-quadruplexes, hairpins, tetraloops, and pseudoknots (Baldrich and Zourob, 2010). In our case, a double helix was selected due to the U-like conformation of the trinucleotides in the binding site.…”

Section: Discussionmentioning

confidence: 99%

Computer-aided design of aptamers for cytochrome p450

Shcherbinin

Gnedenko

Khmeleva

et al. 2015

Journal of Structural Biology

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“…A structural difference is observed in the known aptamer, which includes pseudoknots, hairpins, G-quadruplexes, and tetraloops. 39 Here, a double helix was preferred because the hexanucleotide formed a U-like conformation in the binding site of the protein. The hairpin structure was formed after the fusion of the structural and recognition parts of the aptamer.…”

Section: Discussionmentioning

confidence: 99%

Doxorubicin-Conjugated Innovative 16-mer DNA Aptamer-Based Annexin A1 Targeted Anti-Cancer Drug Delivery

Bavi

Hang

Banerjee

et al. 2020

Molecular Therapy - Nucleic Acids

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Aptamers are small, functional single-stranded DNA or RNA oligonucleotides that bind to their targets with high affinity and specificity. Experimentally, aptamers are selected by the systematic evolution of ligands by exponential enrichment (SELEX) method. Here, we have used rational drug designing and bioinformatics methods to design the aptamers, which involves three different steps. First, finding a probable aptamer-binding site, and second, designing the recognition and structural parts of the aptamers by generating a virtual library of sequences, selection of specific sequence via molecular docking, molecular dynamics (MD) simulation, binding energy calculations, and finally evaluating the experimental affinity. Following this strategy, a 16-mer DNA aptamer was designed for Annexin A1 (ANXA1). In a direct binding assay, DNA1 aptamer bound to the ANXA1 with dissociation constants value of 83 nM. Flow cytometry and fluorescence microscopy results also showed that DNA1 aptamer binds specifically to A549, HepG2, U-87 MG cancer cells that overexpress ANXA1 protein, but not to MCF7 and L-02, which are ANXA1 negative cells. We further developed a novel system by conjugating DNA1 aptamer with doxorubicin and its efficacy was studied by cellular uptake and cell viability assay. Also, anti-tumor analysis showed that conjugation of doxorubicin with aptamer significantly enhances targeted therapy against tumors while minimizing overall adverse effects on mice health.

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Aptamers: Versatile Tools for Reagentless Aptasensing

Cited by 6 publications

References 231 publications

Patterned Biochemical Functionalization Improves Aptamer-Based Detection of Unlabeled Thrombin in a Sandwich Assay

Patterned Biochemical Functionalization Improves Aptamer-Based Detection of Unlabeled Thrombin in a Sandwich Assay

Computer-aided design of aptamers for cytochrome p450

Doxorubicin-Conjugated Innovative 16-mer DNA Aptamer-Based Annexin A1 Targeted Anti-Cancer Drug Delivery

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