DNA-stabilized silver nanoclusters (AgN-DNAs) are a class of nanomaterials comprised of 10-30 silver atoms held together by short synthetic DNA template strands. AgN-DNAs are promising biosensors and fluorophores due to their small sizes, natural compatibility with DNA, and bright fluorescence---the property of absorbing light and re-emitting light of a different color. The sequence of the DNA template acts as a "genome" for AgN-DNAs, tuning the size of the encapsulated silver nanocluster, and thus its fluorescence color. However, current understanding of the AgN-DNA genome is still limited. Only a minority of DNA sequences produce highly fluorescent AgN-DNAs, and the bulky DNA strands and complex DNA-silver interactions make it challenging to use first principles chemical calculations to understand and design AgN-DNAs. Thus, a major challenge for researchers studying these nanomaterials is to develop methods to employ observational data about studied AgN-DNAs to design new nanoclusters for targeted applications.
In this work, we present an approach to design AgN-DNAs by employing variational autoencoders (VAEs) as generative models. Specifically, we employ an LSTM-based β-VAE architecture and regularize its latent space to correlate with AgN-DNA properties such as color and brightness. The regularization is adaptive to skewed sample distributions of available observational data along our design axes of properties. We employ our model for design of AgN-DNAs in the near-infrared (NIR) band, where relatively few AgN-DNAs have been observed to date. Wet lab experiments validate that when employed for designing new AgN-DNAs, our model significantly shifts the distribution of AgN-DNA colors towards the NIR while simultaneously achieving bright fluorescence. This work shows that VAE-based generative models are well-suited for the design of AgN-DNAs with multiple targeted properties, with significant potential to advance the promising applications of these nanomaterials for bioimaging, biosensing, and other critical technologies.
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High-throughput activator sequence selection for silver nanocluster beacons
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.
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- Award ID(s):
- 1757885
- NSF-PAR ID:
- 10343198
- Editor(s):
- Achilefu, Samuel; Raghavachari, Ramesh
- Date Published:
- Journal Name:
- High-throughput activator sequence selection for silver nanocluster beacons DOI number
- Page Range / eLocation ID:
- 18
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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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 polar opposite twins (POTs), it is difficult to discover new POT‐NCBs using the conventional low‐throughput characterization approaches. Here, a high‐throughput selection method is reported that takes advantage of repurposed next‐generation‐sequencing chips to screen the activation fluorescence of ≈40 000 activator sequences. It is found that 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–orange and red POTs, respectively. Based on these findings, a “zipper‐bag” model is proposed that can explain how these hotspots facilitate the formation of distinct silver cluster chromophores and alter their chemical yields. Combining high‐throughput screening with machine‐learning algorithms, a pipeline is established to design bright and multicolor NCBs in silico.
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Sequence-encoded biomolecules such as DNA and peptides are powerful programmable building blocks for nanomaterials. This paradigm is enabled by decades of prior research into how nucleic acid and amino acid sequences dictate biomolecular interactions. The properties of biomolecular materials can be significantly expanded with non-natural interactions, including metal ion coordination of nucleic acids and amino acids. However, these approaches present design challenges because it is often not well-understood how biomolecular sequence dictates such non-natural interactions. This Feature Article presents a case study in overcoming challenges in biomolecular materials with emerging approaches in data mining and machine learning for chemical design. We review progress in this area for a specific class of DNA-templated metal nanomaterials with complex sequence-to-property relationships: DNA-stabilized silver nan- oclusters (AgN-DNAs) with bright, sequence-tuned fluorescence colors and promise for biophotonics applications. A brief overview of machine learning concepts is presented, and high-throughput experimental synthesis and characterization of AgN-DNAs are discussed. Then, recent progress in machine learning-guided design of DNA sequences that select for specific AgN-DNA fluorescence properties is reviewed. We conclude with emerging opportunities in machine learning-guided design and discovery of AgN-DNAs and other sequence-encoded biomolecular nanomaterials.more » « less
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.1117/12.2510649
