Overcoming aggregation-induced quenching in DNA-assembled rhodamine dimers

Collective effects in molecular aggregates, such as absorption band narrowing and superradiance, are fundamentally interesting and can be leveraged to enhance function. There are lesser well-known collective effects, such as aggregation-induced quenching (AIQ), that can frustrate fundamental studies and inhibit function. In this work, we use DNA to assemble rhodamine aggregates that are either susceptible to or that overcome AIQ. Specifically, we use four-way DNA junctions to assemble dimers of ethyl and azetidinyl rhodamine derivatives. Using steady-state and transient optical spectroscopy, we show that certain configurations either permit or inhibit AIQ. We provide structural insight into the dimer packing and surrounding environment <i>via</i> a combination of optical simulations, <i>ab initio</i> calculations, and molecular dynamics simulations. Our results suggest it may be possible to use biomolecules, such as DNA, to tailor the environment of molecular aggregates and thereby overcome and better understand AIQ.

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Publication Details

Journal
Physical Chemistry Chemical Physics
Published
2025-01-01
DOI
https://doi.org/10.1039/d5cp00595g
Citations
3
Primary Topic
Advanced biosensing and bioanalysis techniques
Type
article
Field-Weighted Citation Impact
2.42

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article

Overcoming aggregation-induced quenching in DNA-assembled rhodamine dimers

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3 citations
Physical Chemistry Chemical Physics
Advanced biosensing and bioanalysis techniques
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article

Overcoming aggregation-induced quenching in DNA-assembled rhodamine dimers

Maia Ketteridge, Ryan Rau, Jeunghoon Lee, Bernard Yurke, Paul Cavanaugh, Austin Biaggne, Matthew S. Barclay, Ryan D. Pensack, Paul H. Davis, Simon K. Roy, Jacob C. Dean, Daniel B. Turner, William B. Knowlton, Lan Li
article en
3 citations

Abstract

Collective effects in molecular aggregates, such as absorption band narrowing and superradiance, are fundamentally interesting and can be leveraged to enhance function. There are lesser well-known collective effects, such as aggregation-induced quenching (AIQ), that can frustrate fundamental studies and inhibit function. In this work, we use DNA to assemble rhodamine aggregates that are either susceptible to or that overcome AIQ. Specifically, we use four-way DNA junctions to assemble dimers of ethyl and azetidinyl rhodamine derivatives. Using steady-state and transient optical spectroscopy, we show that certain configurations either permit or inhibit AIQ. We provide structural insight into the dimer packing and surrounding environment <i>via</i> a combination of optical simulations, <i>ab initio</i> calculations, and molecular dynamics simulations. Our results suggest it may be possible to use biomolecules, such as DNA, to tailor the environment of molecular aggregates and thereby overcome and better understand AIQ.

Physical Chemistry Chemical PhysicsVol. 27(30)
Southern Utah University (US), Micron (United States) (US), Boise State University (US), Center for Advanced Energy Studies (US)
Office of Naval Research, National Institute of General Medical Sciences, Basic Energy Sciences
Openalex Percentile: Top 11%
Advanced biosensing and bioanalysis techniques
2.42
DOIOpen Access PDFOpenAlex
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