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

Mastracco, Peter; Copp, Stacy M.

doi:10.1039/d3cc02890a

Cited by 6 publications

(3 citation statements)

References 124 publications

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“…High-throughput screening of DNA-AgNCs for other properties, like fluorescence decay time or optically activated delayed fluorescence, has not yet been realized. In the high-throughput screening setup, a pipetting robot is often used to synthesize the DNA-AgNCs, which are subsequently analyzed on well plate readers with steady state ultraviolet (UV) excitation for the recording of emission spectra. − In this approach, the DNA-AgNCs are excited through their DNA-related UV band rather than their AgNC-related visible/near-infrared (Vis/NIR) band …”

Section: Principle Of White Light Excitation For Screening Of Dna-agncsmentioning

confidence: 99%

Fluorescence Screening of DNA-AgNCs with Pulsed White Light Excitation

Liisberg,

Vosch

2024

Nano Lett.

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DNA-stabilized silver nanoclusters (DNA-AgNCs) are a class of fluorophores with interesting photophysical properties dominated by the choice of DNA sequence. Screening methods with ultraviolet excitation and steady state well plate readers have previously been used for deepening the understanding between DNA sequence and emission color of the resulting DNA-AgNCs. Here, we present a new method for screening DNA-AgNCs by using pulsed white light excitation (λ ex ≈ 490−900 nm). By subtraction and time gating we are able to circumvent the dominating scatter of the white excitation light and extract both temporally and spectrally resolved emission of DNA-AgNCs over the visible to near-infrared range. Additionally, we are able to identify weak long-lived emission, which is often buried underneath the intense nanosecond fluorescence. This new approach will be useful for future screening of DNA-AgNCs (or other novel emissive materials) and aid machine-learning models by providing a richer training data set.

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Section: Principle Of White Light Excitation For Screening Of Dna-agncsmentioning

confidence: 99%

Fluorescence Screening of DNA-AgNCs with Pulsed White Light Excitation

Liisberg,

Vosch

2024

Nano Lett.

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“…25−28 A recent review summarizes machine learning-guided design of Ag N -DNAs. 29 This approach has dramatically expedited Ag N -DNA discovery, generating hundreds of new emitters and significantly expanding the palette of NIR Ag N -DNAs. In a sense, these high-throughput studies have "opened Pandora's box," enabling the discovery of numerous Ag N -DNAs that have been studied in recent works, including several NIR Ag N -DNAs with exceptional optical properties.…”

Section: Introductionmentioning

confidence: 99%

“…This is because the combinatorically large space of DNA sequences and the complex connection between sequence and Ag N -DNA color makes it challenging to design Ag N -DNA templates purely by conventional intuition-based approaches or simple combinatorial experimental screening. Our work pioneered high-throughput experimentation together with machine learning to decode the relationship behind sequence and color and thereby design new DNA templates for Ag N -DNAs with targeted fluorescence colors. − A recent review summarizes machine learning-guided design of Ag N -DNAs . This approach has dramatically expedited Ag N -DNA discovery, generating hundreds of new emitters and significantly expanding the palette of NIR Ag N -DNAs.…”

Section: Introductionmentioning

confidence: 99%

An Atom-Precise Understanding of DNA-Stabilized Silver Nanoclusters

Gonzàlez-Rosell,

Copp

2024

Acc. Chem. Res.

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Metrics & More Article Recommendations CONSPECTUS: DNA-stabilized silver nanoclusters (Ag N -DNAs) are sequence-encoded fluorophores. Like other noble metal nanoclusters, the optical properties of Ag N -DNAs are dictated by their atomically precise sizes and shapes. What makes Ag N -DNAs unique is that nanocluster size and shape are controlled by nucleobase sequence of the templating DNA oligomer. By choice of DNA sequence, it is possible to synthesize a wide range of Ag N -DNAs with diverse emission colors and other intriguing photophysical properties. Ag N -DNAs hold significant potential as "programmable" emitters for biological imaging due to their combination of small molecular-like sizes, bright and sequence-tuned fluorescence, low toxicities, and cost-effective synthesis. In particular, the potential to extend Ag N -DNAs into the second near-infrared region (NIR-II) is promising for deep tissue imaging, which is a major area of interest for advancing biomedical imaging. Achieving this goal requires a deep understanding of the structure−property relationships that govern Ag N -DNAs in order to design Ag N -DNA emitters with sizes and geometries that support NIR-II emission. In recent years, major advances have been made in understanding the structure and composition of Ag N -DNAs, enabling new insights into the correlation of nanocluster structure and photophysical properties. These advances have hinged on combined innovations in mass characterization and crystallography of compositionally pure Ag N -DNAs, together with combinatorial experiments and machine learning-guided design. A combined approach is essential due to the major challenge of growing suitable Ag N -DNA crystals for diffraction and to the labor-intensive nature of preparing and solving the molecular formulas of atomically precise Ag N -DNAs by mass spectrometry. These approaches alone are not feasibly scaled to explore the large sequence space of DNA oligomer templates for Ag N -DNAs. This account describes recent fundamental advances in Ag N -DNA science that have been enabled by high throughput synthesis and fluorimetry together with detailed analytical studies of purified Ag N -DNAs. First, short introductions to nanocluster chemistry and Ag N -DNA basics are presented. Then, we review recent large-scale studies that have screened thousands of DNA templates for Ag N -DNAs, leading to discovery of distinct classes of these emitters with unique cluster core compositions and ligand chemistries. In particular, the discovery of a new class of chloride-stabilized Ag N -DNAs enabled the first ab initio calculations of Ag N -DNA electronic structure and present new approaches to stabilize these emitters in biologically relevant conditions. Near-infrared (NIR) emissive Ag N -DNAs are also found to exhibit diverse structures and properties. Finally, we conclude by highlighting recent proof-of-principle demonstrations of NIR Ag N -DNAs for targeted fluorescence imaging. Continued efforts may future push Ag N -DNAs into the tissue transparency window...

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Hydration Sensitive Orthogonal Dual Emission of a DNA‐Stabilized Silver Nanocluster

Liisberg,

Rück,

Romolini

et al. 2024

Advanced Optical Materials

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DNA‐stabilized silver nanoclusters (DNA‐AgNCs) are a class of emitters that have primarily been studied for their molecular‐like photophysical properties with ns‐lived fluorescence. However, µs‐lived luminescence has recently been reported for an increasing number of DNA‐AgNCs, but little is still known about the origin of the long‐lived emission. To deepen the understanding of the long‐lived state, (DNA)2‐[Ag11]7+, an emitter with short‐ and long‐lived dual emission, is studied. By examining crystals of (DNA)2‐[Ag11]7+, it is found that the fluorescence and luminescence transitions are orthogonal to each other, which implies that components orthogonal to the long axis of the AgNC, such as the nucleobases, contribute significantly to the polarization character of the long‐lived luminescent state. The effect of the hydration level on the dual emission of dried (DNA)2‐[Ag11]7+ droplets is also investigated, and it is found that water drastically reduces emission from the long‐lived state and causes a redshift of the emission. Finally, an unusual excitation intensity‐dependent response of dried (DNA)2‐[Ag11]7+ droplets is noticed. This is ascribed to the heterogeneous local environment of the amorphous solid resulting in different conformations of (DNA)2‐[Ag11]7+ with different optically activated delayed fluorescence probabilities. The presented results provide new key insights into the nature of the long‐lived state of DNA‐AgNCs.

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

Abstract: 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...

Cited by 6 publications

References 124 publications

Fluorescence Screening of DNA-AgNCs with Pulsed White Light Excitation

Fluorescence Screening of DNA-AgNCs with Pulsed White Light Excitation

An Atom-Precise Understanding of DNA-Stabilized Silver Nanoclusters

Hydration Sensitive Orthogonal Dual Emission of a DNA‐Stabilized Silver Nanocluster

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