This paper develops a high-throughput platform to rapidly adapt DNA aptamers against evolving SARS-CoV-2 variants, identifying mutants with improved binding affinity and specificity.

ACS Nano · Aug 14, 2026Peer-reviewedBioengineering

Fluorogenic Aptamer Optimizations on a Massively Parallel Sequencing Platform

Yu-An Kuo, Y.-I. Chen, Naseem Siraj, Yujie He, Zhenglin Yang, Yanxing Wang, Emile J. Batchelder-Schwab, Zeynep Korkmaz, Siem Yonas, Trung D. Nguyen, Soonwoo Hong, Anh-Thu Nguyen, S H Kim, Saeed Seifi, Po‐Hsun Fan, , Hsin‐Chih Yeh

This paper optimizes a DNA-based fluorogenic aptamer (D-FAP) using a screening-and-simulation pipeline on a repurposed sequencing platform, achieving improved fluorescence properties.

ACS Sensors · May 11, 2026Peer-reviewedBiophysics

Lifetime-based multiplexed detection of viral RNA using fluorogenic aptamers

Y R Chen, Yu-An Kuo, Yujie He, Naseem Siraj, Emile J. Batchelder-Schwab, Yin-Jui Chang, Siem Yonas, Yuting Wu, Zhenglin Yang, Anh-Thu Nguyen, S H Kim, Yi Lu, Chengde Mao, Pengyu Y. Ren, Hsin‐Chih Yeh

This paper introduces a fluorescence-lifetime-based multiplexed detection strategy using fluorogenic aptamers to distinguish viral RNA targets with minimal cross-reactivity and spectral overlap.

bioRxiv · Apr 15, 2026 · PreprintBioengineering

Mechanistic insights into the color transformation of a non-FRET substrate for RNase activity detection

Sohyun Kim, Soonwoo Hong, Jada N. Walker, Yujie He, Anh-Thu Nguyen, Wei-Ru Chen, Saeed Seifi, Yuan-I Chen, Yu-An Kuo, Jennifer S. Brodbelt, Hsin‐Chih Yeh

This paper identifies the mechanism of color change in DNA/AgNC substrates upon nucleolytic cleavage and demonstrates their application in sensitive virus detection.

bioRxiv · Mar 13, 2026 · PreprintBioengineering