Homogeneous assay for evaluation of aptamer–protein interaction

Lautner, Gergely; Balogh, Zsófia; Gyurkovics, Anna; Gyurcsányi, Róbert E.; Mészáros, Tamás

doi:10.1039/c2an35419e

Cited by 16 publications

(7 citation statements)

References 21 publications

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“…Previously, we demonstrated the application of simple mix-and-measure Amplified Luminescent Proximity Homogenous Assay (ALPHA) for assessing the K D of protein–aptamer complexes 15 . The approach relies on the use of donor and acceptor beads, which are coated with the binding partners.…”

Section: Resultsmentioning

confidence: 99%

Aptamers for respiratory syncytial virus detection

Percze

Szakács

Scholz

et al. 2017

Sci Rep

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The identification of the infectious agents is pivotal for appropriate care of patients with viral diseases. Current viral diagnostics rely on selective detection of viral nucleic acid or protein components. In general, detection of proteins rather than nucleic acids is technically more suitable for rapid tests. However, protein-based virus identification methods depend on antibodies limiting the practical applicability of these approaches. Aptamers rival antibodies in target selectivity and binding affinity, and excel in terms of robustness and cost of synthesis. Although aptamers have been generated for virus identification in laboratory settings, their introduction into routine virus diagnostics has not been realized, yet. Here, we demonstrate that the rationally designed SELEX protocol can be applied on whole virus to select aptamers, which can potentially be applied for viral diagnostics. This approach does not require purified virus protein or complicated virus purification. The presented data also illustrate that corroborating the functionality of aptamers with various approaches is essential to pinpoint the most appropriate aptamer amongst the panel of candidates obtained by the selection. Our protocol yielded aptamers capable of detecting respiratory syncytial virus (RSV), an important pathogen causing severe disease especially in young infants, at clinically relevant concentrations in complex matrices.

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Section: Resultsmentioning

confidence: 99%

Aptamers for respiratory syncytial virus detection

Percze

Szakács

Scholz

et al. 2017

Sci Rep

Self Cite

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“…For example, emerging technologies are enabling fluorescence-based detection to achieve high sensitivity and selectivity [1,2], and advanced luminescence assay can be specifically designed to fit different applications [3]. However, such performance requirements may not be necessary for most point-of-care (PoC) [4] and fast diagnostic applications where low cost and ease of operation are key design considerations.…”

Section: Introductionmentioning

confidence: 99%

Heterogeneously integrated impedance measuring system with disposable thin-film electrodes

Cheng

et al. 2015

Sensors and Actuators B: Chemical

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a b s t r a c tWe propose a novel integrated impedance measurement system with disposable thin-film electrodes. Most modern CMOS-based biosensors use on-chip electrodes to interface between the electronics and biosamples, which forces disposal of the CMOS chip after a few measurements, since most biological reactions are non-reversible. The sensor performance is also limited by the design of on-chip electrodes due to the physical dimensions and the CMOS design rules restrictions. In this work, we extract the electrodes from the silicon chip for relocation onto a low-cost, disposable substrate. This enables reusability of the high-performance CMOS chip, at the same time providing a low-cost route for manufacture of the active thin-film electrodes using large-area processing. The use of disposable thin-film chip also enables customised designed electrodes for different applications, such as extra high sensitivity concentration sensors. In this work, DNA concentration measurements are performed, and it shows a doubling of sensitivity over the previously reported system.

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“…Previous studies have focused on aptamer-protein interactions [ 6 ]. With the development of biochemistry and molecular biology, compounds have been shown to play an increasingly significant role in several biological processes; therefore, it is necessary to focus on aptamer-compound interactions.…”

Section: Introductionmentioning

confidence: 99%

Analysis and Identification of Aptamer-Compound Interactions with a Maximum Relevance Minimum Redundancy and Nearest Neighbor Algorithm

Wang

Zhang

Lü

et al. 2016

BioMed Research International

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The development of biochemistry and molecular biology has revealed an increasingly important role of compounds in several biological processes. Like the aptamer-protein interaction, aptamer-compound interaction attracts increasing attention. However, it is time-consuming to select proper aptamers against compounds using traditional methods, such as exponential enrichment. Thus, there is an urgent need to design effective computational methods for searching effective aptamers against compounds. This study attempted to extract important features for aptamer-compound interactions using feature selection methods, such as Maximum Relevance Minimum Redundancy, as well as incremental feature selection. Each aptamer-compound pair was represented by properties derived from the aptamer and compound, including frequencies of single nucleotides and dinucleotides for the aptamer, as well as the constitutional, electrostatic, quantum-chemical, and space conformational descriptors of the compounds. As a result, some important features were obtained. To confirm the importance of the obtained features, we further discussed the associations between them and aptamer-compound interactions. Simultaneously, an optimal prediction model based on the nearest neighbor algorithm was built to identify aptamer-compound interactions, which has the potential to be a useful tool for the identification of novel aptamer-compound interactions. The program is available upon the request.

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Homogeneous assay for evaluation of aptamer–protein interaction

Cited by 16 publications

References 21 publications

Aptamers for respiratory syncytial virus detection

Aptamers for respiratory syncytial virus detection

Heterogeneously integrated impedance measuring system with disposable thin-film electrodes

Analysis and Identification of Aptamer-Compound Interactions with a Maximum Relevance Minimum Redundancy and Nearest Neighbor Algorithm

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