High-Throughput Selection and Characterisation of Aptamers on Optical Next-Generation Sequencers
Aptamers feature a number of advantages, compared to antibodies. However, their application has been limited so far, mainly because of the complex selection process. ‘High-throughput sequencing fluorescent ligand interaction profiling’ (HiTS–FLIP) significantly increases the selection efficiency and...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-08-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/17/9202 |
| _version_ | 1797521350169985024 |
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| author | Alissa Drees Markus Fischer |
| author_facet | Alissa Drees Markus Fischer |
| author_sort | Alissa Drees |
| collection | DOAJ |
| description | Aptamers feature a number of advantages, compared to antibodies. However, their application has been limited so far, mainly because of the complex selection process. ‘High-throughput sequencing fluorescent ligand interaction profiling’ (HiTS–FLIP) significantly increases the selection efficiency and is consequently a very powerful and versatile technology for the selection of high-performance aptamers. It is the first experiment to allow the direct and quantitative measurement of the affinity and specificity of millions of aptamers simultaneously by harnessing the potential of optical next-generation sequencing platforms to perform fluorescence-based binding assays on the clusters displayed on the flow cells and determining their sequence and position in regular high-throughput sequencing. Many variants of the experiment have been developed that allow automation and in situ conversion of DNA clusters into base-modified DNA, RNA, peptides, and even proteins. In addition, the information from mutational assays, performed with HiTS–FLIP, provides deep insights into the relationship between the sequence, structure, and function of aptamers. This enables a detailed understanding of the sequence-specific rules that determine affinity, and thus, supports the evolution of aptamers. Current variants of the HiTS–FLIP experiment and its application in the field of aptamer selection, characterisation, and optimisation are presented in this review. |
| first_indexed | 2024-03-10T08:11:20Z |
| format | Article |
| id | doaj.art-05a51c263b114fd7a39e173ef306cf51 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T08:11:20Z |
| publishDate | 2021-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-05a51c263b114fd7a39e173ef306cf512023-11-22T10:39:40ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-08-012217920210.3390/ijms22179202High-Throughput Selection and Characterisation of Aptamers on Optical Next-Generation SequencersAlissa Drees0Markus Fischer1Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, GermanyHamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, GermanyAptamers feature a number of advantages, compared to antibodies. However, their application has been limited so far, mainly because of the complex selection process. ‘High-throughput sequencing fluorescent ligand interaction profiling’ (HiTS–FLIP) significantly increases the selection efficiency and is consequently a very powerful and versatile technology for the selection of high-performance aptamers. It is the first experiment to allow the direct and quantitative measurement of the affinity and specificity of millions of aptamers simultaneously by harnessing the potential of optical next-generation sequencing platforms to perform fluorescence-based binding assays on the clusters displayed on the flow cells and determining their sequence and position in regular high-throughput sequencing. Many variants of the experiment have been developed that allow automation and in situ conversion of DNA clusters into base-modified DNA, RNA, peptides, and even proteins. In addition, the information from mutational assays, performed with HiTS–FLIP, provides deep insights into the relationship between the sequence, structure, and function of aptamers. This enables a detailed understanding of the sequence-specific rules that determine affinity, and thus, supports the evolution of aptamers. Current variants of the HiTS–FLIP experiment and its application in the field of aptamer selection, characterisation, and optimisation are presented in this review.https://www.mdpi.com/1422-0067/22/17/9202aptamersnext-generation sequencinghigh-throughput assaymolecular biophysicskineticsHiTS–FLIP |
| spellingShingle | Alissa Drees Markus Fischer High-Throughput Selection and Characterisation of Aptamers on Optical Next-Generation Sequencers International Journal of Molecular Sciences aptamers next-generation sequencing high-throughput assay molecular biophysics kinetics HiTS–FLIP |
| title | High-Throughput Selection and Characterisation of Aptamers on Optical Next-Generation Sequencers |
| title_full | High-Throughput Selection and Characterisation of Aptamers on Optical Next-Generation Sequencers |
| title_fullStr | High-Throughput Selection and Characterisation of Aptamers on Optical Next-Generation Sequencers |
| title_full_unstemmed | High-Throughput Selection and Characterisation of Aptamers on Optical Next-Generation Sequencers |
| title_short | High-Throughput Selection and Characterisation of Aptamers on Optical Next-Generation Sequencers |
| title_sort | high throughput selection and characterisation of aptamers on optical next generation sequencers |
| topic | aptamers next-generation sequencing high-throughput assay molecular biophysics kinetics HiTS–FLIP |
| url | https://www.mdpi.com/1422-0067/22/17/9202 |
| work_keys_str_mv | AT alissadrees highthroughputselectionandcharacterisationofaptamersonopticalnextgenerationsequencers AT markusfischer highthroughputselectionandcharacterisationofaptamersonopticalnextgenerationsequencers |