Cracking the Color Code of DNA-stabilized Metal Nanoclusters with Rapid Optical Array Characterization and Machine Learning

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Technical Abstract Elisabeth Gwinn of the University of California, Santa Barbara is supported by an award from the Computational and Data Driven Materials Research program for research to combine computational machine learning tools with strategic data obtained from fast, array format optical characterization, with the goal of discovering and developing a versatile new class of photonic nanomaterial. Specifically, the work will investigate fluorescent, DNA-stabilized, few-atom metal nanoclusters, or DNA-mNCs. DNA-mNCs based on silver clusters are already beginning to be used in innovative imaging, molecular logic, and selective sensor applications. The recent discovery of copper-based DNA-mNCs suggests that the formation of fluorescent clusters in DNA hosts may generalize to other coinage metals.The PI's prior work revealed the special sensitivity of silver cluster fluorescence to the sequence and secondary structure of the host DNA. Studies of small sets of various DNA strands have found DNA-AgNCs with fluorescence colors spanning 500 - 900 nm. Together with the compact sizes of DNA-mNCs, which are compatible with the finest resolutions accessed by DNA nanotechnology, this wide color space may open new arenas beyond current solution applications, in nanoscale photonic arrays for information processing and signaling of biochemical and physical events. However, there is essentially no current understanding of how the properties of DNA-mNCs relate to the sequence of the host DNA. Even for the relatively well-studied DNA-AgNCs, there are no identified sequence motifs that govern fluorescence color, brightness or stability. This is despite the fundamental importance of these properties to all applications, and to the underlying materials science. But, only ~100 strands have been examined as potential hosts for chemically stable DNA-AgNCs. This is a miniscule sampling of the space of possible sequences. This research aims to crack the code for the sequence characteristics that govern the properties of DNA-mNCs, by applying machine learning tools to much larger, strategically selected data sets. The data will be acquired by robotic synthesis and rapid array optical characterization of Ag-based DNA-mNCs. Strand selection will leverage the knowledge of DNA-AgNCs developed in the PI's prior work. To elucidate the role of the specific metal from which the cluster is formed, experiments on other coinage metals, including copper, will also be made.The undergraduate and graduate students who participate in the work will be trained in advanced techniques encompassing materials science, computer science and nanotechnology. High school students will be exposed to aspects of the work through UCSB's School for Scientific Thought (SST).Non-Technical AbstractThis work focuses on tiny clusters composed of just a few atoms of metal, that are made stable in water by wrapping the clusters up in short strands of DNA. It has been known for many years that "bare" clusters made of a few metal atoms have very interesting optical properties. In particular, they can be fluorescent, meaning that the clusters emit photons after they are placed in an excited state. These DNA-encapsulated, few-atom metal nanoclusters may have many potential uses, such as fluorescent sensing of toxic ions and of targeted DNA and RNA strands. The most fascinating and potentially useful feature of these materials is the fact that different DNA sequences can produce clusters of different color. Cracking the code for the DNA sequence characteristics that govern this color is the focus of this work. The primary focus will be on silver clusters, building on previous work, but to elucidate the role of the specific metal from which the cluster is formed, experiments on other metals, including copper, will also be carried out. The undergraduate and graduate students who participate in the work will be trained in advanced techniques encompassing materials science, computer science and nanotechnology. High school students will be exposed to aspects of the work through UCSB's School for Scientific Thought (SST).