Aptamers in analytics

2016-01-01
Nucleic acid aptamers are promising alternatives to antibodies in analytics. They are generally obtained through an iterative SELEX protocol that enriches a population of synthetic oligonucleotides to a subset that can recognize the chosen target molecule specifically and avidly. A wide range of targets is recognized by aptamers. Once identified and optimized for performance, aptamers can be reproducibly synthesized and offer other key features, like small size, low cost, sensitivity, specificity, rapid response, stability, and reusability. This makes them excellent options for sensory units in a variety of analytical platforms including those with electrochemical, optical, and mass sensitive transduction detection. Many novel sensing strategies have been developed by rational design to take advantage of the tendency of aptamers to undergo conformational changes upon target/analyte binding and employing the principles of base complementarity that can drive the nucleic acid structure. Despite their many advantages over antibodies, surprisingly few aptamers have yet been integrated into commercially available analytical devices. In this review, we discuss how to select and engineer aptamers for their identified application(s), some of the challenges faced in developing aptamers for analytics and many examples of their reported successful performance as sensors in a variety of analytical platforms.

Suggestions

Learning functional properties of proteins with language models
Unsal, Serbulent; Atas, Heval; ALBAYRAK, MUAMMER; TURHAN, KEMAL; Acar, Aybar Can; DOĞAN, TUNCA (2022-03-01)
Data-centric approaches have been used to develop predictive methods for elucidating uncharacterized properties of proteins; however, studies indicate that these methods should be further improved to effectively solve critical problems in biomedicine and biotechnology, which can be achieved by better representing the data at hand. Novel data representation approaches mostly take inspiration from language models that have yielded ground-breaking improvements in natural language processing. Lately, these appr...
Integer linear programming based solutions for construction of biological networks
Eren Özsoy, Öykü; Can, Tolga; Department of Health Informatics (2014)
Inference of gene regulatory or signaling networks from perturbation experiments and gene expression assays is one of the challenging problems in bioinformatics. Recently, the inference problem has been formulated as a reference network editing problem and it has been show that finding the minimum number of edit operations on a reference network in order to comply with perturbation experiments is an NP-complete problem. In this dissertation, we propose linear programming based solutions for reconstruction o...
Live-cell imaging of Pol II promoter activity to monitor gene expression with RNA IMAGEtag reporters
SHIN, Ilchung; RAY, Judhajeet; Gupta, Vinayak; İlgü, Müslüm; Beasley, Jonathan; BENDICKSON, Lee; MEHANOVIC, Samir; Kraus, George A.; Nilsen-Hamilton, Marit (Oxford University Press (OUP), 2014-01-01)
We describe a ribonucleic acid (RNA) reporter system for live-cell imaging of gene expression to detect changes in polymerase II activity on individual promoters in individual cells. The reporters use strings of RNA aptamers that constitute IMAGEtags (Intracellular MultiAptamer GEnetic tags) that can be expressed from a promoter of choice. For imaging, the cells are incubated with their ligands that are separately conjugated with one of the FRET pair, Cy3 and Cy5. The IMAGEtags were expressed in yeast from ...
Amino Acid And Peptide Based Gels
Aykent, Güzide; Özçubukçu, Salih; Department of Chemistry (2021-2-12)
Self-assembling peptides and amino acid derivatives are becoming an emerging field especially in last decades. Especially for their usage in biomedical applications, tissue engineering and drug delivery, extensive research are being done. Large variety of peptides with different physical and chemical properties were acquired by using different amino acids and their sequences. As a more easily synthesized and bio-inspired alternative materials to the compounds used nowadays for organic electronic devices, ge...
Aptamer-enabled uptake of small molecule ligands
Auwardt, Supipi Liyamali; Seo, Yeon-Jung; İlgü, Müslüm; Ray, Judhajeet; Feldges, Robert R.; Shubham, Shambhavi; Bendickson, Lee; Levine, Howard A.; Nilsen-Hamilton, Marit (Springer Science and Business Media LLC, 2018-10-24)
The relative ease of isolating aptamers with high specificity for target molecules suggests that molecular recognition may be common in the folds of natural RNAs. We show here that, when expressed in cells, aptamers can increase the intracellular concentrations of their small molecule ligands. We have named these aptamers as DRAGINs (Drug Binding Aptamers for Growing Intracellular Numbers). The DRAGIN property, assessed here by the ability to enhance the toxicity of their ligands, was found for some, but no...
Citation Formats
M. İlgü, “Aptamers in analytics,” ANALYST, pp. 1551–1568, 2016, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/36814.