Passivating Nucleobases Bring Charge Transfer Character to Optically Active Transitions in Small Silver Nanoclusters

Beyond nature's base pairs: machine learning-enabled design of DNA-stabilized silver nanoclusters

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 nanoclusters (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.

Hg2+ Detection with Rational Design of DNA-Templated Fluorescent Silver Nanoclusters

Atomically precise silver nanoclusters (AgNCs) are small nanostructures consisting of only a few atoms of silver. The combination of AgNCs with cytosine-rich single-stranded oligonucleotides results in DNA-templated silver nanoclusters (DNA-AgNCs). DNA-AgNCs are highly luminescent and can be engineered with reproducible and unique fluorescent properties. Furthermore, using nucleic acids as templates for the synthesis of AgNCs provides additional practical benefits by expanding optical activity beyond the visible spectral range and creating the possibility for color tunability. In this study, we explore DNA oligonucleotides designed to fold into hairpin-loop (HL) structures which modulate optical properties of AgNCs based on the size of the loop containing different number of cytosines (HL-CN). Depending on the size of the loop, AgNCs can be manufactured to have either single or multiple emissive states. Such hairpin-loop structures provide an additional stability for AgNCs and further control over the base composition of the loop, allowing for the rational design of AgNCs’ optical properties. We demonstrate the potential of AgNCs in detecting Hg2+ by utilizing the HL-C13 design and its variants HL-T2C11, HL-T4C9, and HL-T6C7. The replacement of cytosines with thymines in the loop was intended to serve as an additional sink for mercury ions extending the detectable range of Hg2+. While AgNC@HL-T0C13 exhibits an interpretable quenching curve, AgNC@HL-T6C7 provides the largest detectable range of Hg2+. The results presented herein suggest that it is possible to use a rational design of DNA-AgNCs based on the composition of loop sequence in HL structures for creating biosensors to detect heavy metals, particularly Hg2+.

DNA-Templated Fluorescent Silver Nanoclusters Inhibit Bacterial Growth While Being Non-Toxic to Mammalian Cells

Silver has a long history of antibacterial effectiveness. The combination of atomically precise metal nanoclusters with the field of nucleic acid nanotechnology has given rise to DNA-templated silver nanoclusters (DNA-AgNCs) which can be engineered with reproducible and unique fluorescent properties and antibacterial activity. Furthermore, cytosine-rich single-stranded DNA oligonucleotides designed to fold into hairpin structures improve the stability of AgNCs and additionally modulate their antibacterial properties and the quality of observed fluorescent signals. In this work, we characterize the sequence-specific fluorescence and composition of four representative DNA-AgNCs, compare their corresponding antibacterial effectiveness at different pH, and assess cytotoxicity to several mammalian cell lines.