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High-throughput activator sequence selection for silver nanocluster beacons
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Paper Abstract

Invented in 2010, NanoCluster Beacons (NCBs) (1) are an emerging class of turn-on probes that show unprecedented capabilities in single-nucleotide polymorphism (2) and DNA methylation (3) detection. As the activation colors of NCBs can be tuned by a near-by, guanine-rich activator strand, NCBs are versatile, multicolor probes suitable for multiplexed detection at low cost. Whereas a variety of NCB designs have been explored and reported, further diversification and optimization of NCBs require a full scan of the ligand composition space. However, the current methods rely on microarray and multi-well plate selection, which only screen tens to hundreds of activator sequences (4, 5). Here we take advantage of the next-generation-sequencing (NGS) platform for high-throughput, large-scale selection of activator strands. We first generated a ~104 activator sequence library on the Illumina MiSeq chip. Hybridizing this activator sequence library with a common nucleation sequence (which carried a nonfluorescent silver cluster) resulted in hundreds of MiSeq chip images with millions of bright spots (i.e. light-up polonies) of various intensities and colors. With a method termed Chip- Hybridized Associated Mapping Platform (CHAMP) (6), we were able to map these bright spots to the original DNA sequencing map, thus recovering the activator sequence behind each bright spot. After assigning an “activation score” to each “light-up polony”, we used a computational algorithm to select the best activator strands and validate these strands using the traditional in-solution preparation and fluorometer measurement method. By exploring a vast ligand composition space and observing the corresponding activation behaviors of silver clusters, we aim to elucidate the design rules of NCBs.

Paper Details

Date Published: 7 March 2019
PDF: 12 pages
Proc. SPIE 10893, Reporters, Markers, Dyes, Nanoparticles, and Molecular Probes for Biomedical Applications XI, 108930G (7 March 2019); doi: 10.1117/12.2510649
Show Author Affiliations
Yu-An Kuo, The Univ. of Texas at Austin (United States)
Cheulhee Jung, Korea Univ. (Korea, Republic of)
Yu-An Chen, The Univ. of Texas at Austin (United States)
James R. Rybarski, The Univ. of Texas at Austin (United States)
Trung D. Nguyen, The Univ. of Texas at Austin (United States)
Yin-An Chen, The Univ. of Texas at Austin (United States)
Hung-Che Kuo, The Univ. of Texas at Austin (United States)
Oliver S. Zhao, The Univ. of Texas at Austin (United States)
Victor A. Madrid, The Univ. of Texas at El Paso (United States)
Yuan-I Chen, The Univ. of Texas at Austin (United States)
Yen-Liang Liu, The Univ. of Texas at Austin (United States)
John A. Hawkins, The Univ. of Texas at Austin (United States)
Jeffrey T. Petty, Furman Univ. (United States)
Ilya J. Finkelstein, The Univ. of Texas at Austin (United States)
Hsin-Chih Yeh, The Univ. of Texas at Austin (United States)


Published in SPIE Proceedings Vol. 10893:
Reporters, Markers, Dyes, Nanoparticles, and Molecular Probes for Biomedical Applications XI
Samuel Achilefu; Ramesh Raghavachari, Editor(s)

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