Massively Parallel Selection of NanoCluster Beacons

Kuo, Y.-A.; Jung, C.; Chen, Y.-A.; Kuo, H.-C.; Zhao, O. S.; Nguyen, T. D.; Rybarski, J. R.; Hong, S.; Chen, Y.-I.; Wylie, D. C.; Hawkins, J. A.; Walker, J. N.; Shields, S. W.; Brodbelt, J. S.; Petty, J. T.; Finkelstein, I. J.; Yeh, H.-C.

doi:10.1101/2021.12.04.471212

bioRxiv · 10.1101/2021.12.04.471212

Massively Parallel Selection of NanoCluster Beacons

Kuo, Y.-A.·Jung, C.·Chen, Y.-A.·Kuo, H.-C.·Zhao, O. S.·Nguyen, T. D.·Rybarski, J. R.·Hong, S.·Chen, Y.-I.·Wylie, D. C.·Hawkins, J. A.·Walker, J. N.·Shields, S. W.·Brodbelt, J. S.·Petty, J. T.·Finkelstein, I. J.·Yeh, H.-C.

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Abstract

NanoCluster Beacons (NCBs) are multicolor silver nanocluster probes whose fluorescence can be activated or tuned by a proximal DNA strand called the activator. While a single-nucleotide difference in a pair of activators can lead to drastically different activation outcomes, termed the polar opposite twins (POTs), it is difficult to discover new POT-NCBs using the conventional low-throughput characterization approaches. Here we report a high-throughput selection method that takes advantage of repurposed next-generation-sequencing (NGS) chips to screen the activation fluorescence of [~]40,000 activator sequences. We find the nucleobases at positions 7-12 of the 18-nucleotide-long activator are critical to creating bright NCBs and positions 4-6 and 2-4 are hotspots to generate yellow and red POTs, respectively. Based on these findings, we propose a "zipper bag model" that explains how these hotspots lead to the creation of distinct silver cluster chromophores and contribute to the difference in chromophore chemical yields. Combining high-throughput screening with machine learning algorithms, we establish a pipeline to rationally design bright and multicolor NCBs.

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Kuo, Y.-A., Jung, C., Chen, Y.-A., Kuo, H.-C., Zhao, O. S., Nguyen, T. D., Rybarski, J. R., Hong, S., Chen, Y.-I., Wylie, D. C., Hawkins, J. A., Walker, J. N., Shields, S. W., Brodbelt, J. S., Petty, J. T., Finkelstein, I. J., Yeh, H.-C.. 2021-12-05. Massively Parallel Selection of NanoCluster Beacons. https://doi.org/10.1101/2021.12.04.471212

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