Fluorogenic Aptamer Optimization on a Massively Parallel Sequencing Platform

chip, we identify the C14T mutant which exhibits an improved dissociation constant, increased quantum yield, extended fluorescence lifetime, and enhanced emission intensity. Co-crystal structures of the aptamer/fluorogen complexes reveal that π-π stacking interactions are critical for the stable coordination of TO1-biotin within Lettuce. When tested in a cellular environment, both the screening-identified C14T mutant and a structure-guided rationally designed variant, C14dU, exhibit 15% and 18% stronger fluorescence intensities, respectively, compared with canonical Lettuce. Our massive screening and molecular dynamics simulation pipeline enable efficient FAP optimization without prior structural knowledge, yielding not only improved probes for fluorescence sensing but also deeper insights into aptamer-fluorogen interactions.

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Publication Details

Journal
ACS Sensors
Published
2026-05-11
DOI
https://doi.org/10.1021/acssensors.5c04046
Primary Topic
Advanced biosensing and bioanalysis techniques
Type
article
Field-Weighted Citation Impact
0.00

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article

Fluorogenic Aptamer Optimization on a Massively Parallel Sequencing Platform

Saeed Seifi, Soonwoo Hong, Yu-An Kuo, S H Kim et al.
ACS Sensors
Advanced biosensing and bioanalysis techniques
article

Fluorogenic Aptamer Optimization on a Massively Parallel Sequencing Platform

Saeed Seifi, Soonwoo Hong, Yu-An Kuo, S H Kim, Po‐Hsun Fan, Y R Chen, Hung‐wen Liu, Siem Yonas, Yanxing Wang, Zeynep Korkmaz, Trung D. Nguyen, Anh-Thu Nguyen, Emile J. Batchelder-Schwab, Pengyu Ren, Yuting Wu, Yi Lu, Yujie He, Zhenglin Yang, Chengde Mao, Hsin-Chih Yeh, Naseem Siraj
article en

Abstract

chip, we identify the C14T mutant which exhibits an improved dissociation constant, increased quantum yield, extended fluorescence lifetime, and enhanced emission intensity. Co-crystal structures of the aptamer/fluorogen complexes reveal that π-π stacking interactions are critical for the stable coordination of TO1-biotin within Lettuce. When tested in a cellular environment, both the screening-identified C14T mutant and a structure-guided rationally designed variant, C14dU, exhibit 15% and 18% stronger fluorescence intensities, respectively, compared with canonical Lettuce. Our massive screening and molecular dynamics simulation pipeline enable efficient FAP optimization without prior structural knowledge, yielding not only improved probes for fluorescence sensing but also deeper insights into aptamer-fluorogen interactions.

ACS Sensors
Purdue University West Lafayette (US), The University of Texas at Austin (US)
Welch Foundation, University of Texas at Austin, National Institute on Drug Abuse, National Institute of General Medical Sciences, Division of Computing and Communication Foundations, Division of Chemical, Bioengineering, Environmental, and Transport Systems, Division of Chemistry
Openalex Percentile: Top 9%
Advanced biosensing and bioanalysis techniques
DOISourceOpenAlex
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