Single-Molecule Multivalent Interactions Revealed by Plasmon-Enhanced Fluorescence

Kasper R. Okholm; Sjoerd W. Nooteboom; Johan Nygaard Vinther; Vincenzo Lamberti; Swayandipta Dey; Ebbe Sloth Andersen; Peter Zijlstra; Duncan S. Sutherland

doi:10.1021/acsnano.4c12600

Single-Molecule Multivalent Interactions Revealed by Plasmon-Enhanced Fluorescence

Kasper R. Okholm, Sjoerd W. Nooteboom, Johan Nygaard Vinther, Vincenzo Lamberti, Swayandipta Dey, Ebbe Sloth Andersen, Peter Zijlstra^*, Duncan S. Sutherland^*

^*Corresponding author for this work

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

Abstract

Multivalency as an interaction principle is widely utilized in nature. It enables specific and strong binding by multiple weak interactions through enhanced avidity and is a core process in immune recognition and cellular signaling, which is also a current concept in drug design. Here, we use the high signals from plasmon-enhanced fluorescence of nanoparticles to extract binding kinetics and dynamics of multivalent interactions on the single-molecule level and in real time. We study mono-, bi-, and trivalent binding interactions using a DNA Holliday Junction as a model construct with programmable valency and introduce a step-binding model for binding kinetics relevant for structured macromolecules by including an experimentally extractable binding restriction term ω to quantify the effects from conformation, steric effects, and rigidity. We used this approach to explore how length and flexibility of the DNA ligands affect binding restriction and binding strength, where the overall binding strength decreased with spacer length. For trivalent systems, increasing spacer length additionally activated binding in the trivalent state, giving insight into the design of multivalent drug or targeting moieties. By systematically changing the receptor density, we explored the binding super selectivity of the multivalent HJ at the single-molecule level. We find a polynomial behavior of the trivalent binding strength that clearly shows receptor-density-dependent selective binding. Interestingly, we could exploit the rapidly decaying near fields of the plasmon that induce a strong dependence of the signal on the position of the dye to observe binding dynamics during single multivalent binding events.

Original language	English
Journal	ACS Nano
Volume	18
Issue	52
Pages (from-to)	35429-35442
Number of pages	14
ISSN	1936-0851
DOIs	https://doi.org/10.1021/acsnano.4c12600
Publication status	Published - Dec 2024

Keywords

DNA nanotechnology
fluorescence enhancement
multivalency
plasmonic nanoparticles
single-molecule fluorescence

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10.1021/acsnano.4c12600

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title = "Single-Molecule Multivalent Interactions Revealed by Plasmon-Enhanced Fluorescence",

abstract = "Multivalency as an interaction principle is widely utilized in nature. It enables specific and strong binding by multiple weak interactions through enhanced avidity and is a core process in immune recognition and cellular signaling, which is also a current concept in drug design. Here, we use the high signals from plasmon-enhanced fluorescence of nanoparticles to extract binding kinetics and dynamics of multivalent interactions on the single-molecule level and in real time. We study mono-, bi-, and trivalent binding interactions using a DNA Holliday Junction as a model construct with programmable valency and introduce a step-binding model for binding kinetics relevant for structured macromolecules by including an experimentally extractable binding restriction term ω to quantify the effects from conformation, steric effects, and rigidity. We used this approach to explore how length and flexibility of the DNA ligands affect binding restriction and binding strength, where the overall binding strength decreased with spacer length. For trivalent systems, increasing spacer length additionally activated binding in the trivalent state, giving insight into the design of multivalent drug or targeting moieties. By systematically changing the receptor density, we explored the binding super selectivity of the multivalent HJ at the single-molecule level. We find a polynomial behavior of the trivalent binding strength that clearly shows receptor-density-dependent selective binding. Interestingly, we could exploit the rapidly decaying near fields of the plasmon that induce a strong dependence of the signal on the position of the dye to observe binding dynamics during single multivalent binding events.",

keywords = "DNA nanotechnology, fluorescence enhancement, multivalency, plasmonic nanoparticles, single-molecule fluorescence",

author = "Okholm, {Kasper R.} and Nooteboom, {Sjoerd W.} and Vinther, {Johan Nygaard} and Vincenzo Lamberti and Swayandipta Dey and Andersen, {Ebbe Sloth} and Peter Zijlstra and Sutherland, {Duncan S.}",

note = "Publisher Copyright: {\textcopyright} 2024 The Authors. Published by American Chemical Society.",

year = "2024",

month = dec,

doi = "10.1021/acsnano.4c12600",

language = "English",

volume = "18",

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journal = "ACS Nano",

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T1 - Single-Molecule Multivalent Interactions Revealed by Plasmon-Enhanced Fluorescence

AU - Okholm, Kasper R.

AU - Nooteboom, Sjoerd W.

AU - Vinther, Johan Nygaard

AU - Lamberti, Vincenzo

AU - Dey, Swayandipta

AU - Andersen, Ebbe Sloth

AU - Zijlstra, Peter

AU - Sutherland, Duncan S.

PY - 2024/12

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N2 - Multivalency as an interaction principle is widely utilized in nature. It enables specific and strong binding by multiple weak interactions through enhanced avidity and is a core process in immune recognition and cellular signaling, which is also a current concept in drug design. Here, we use the high signals from plasmon-enhanced fluorescence of nanoparticles to extract binding kinetics and dynamics of multivalent interactions on the single-molecule level and in real time. We study mono-, bi-, and trivalent binding interactions using a DNA Holliday Junction as a model construct with programmable valency and introduce a step-binding model for binding kinetics relevant for structured macromolecules by including an experimentally extractable binding restriction term ω to quantify the effects from conformation, steric effects, and rigidity. We used this approach to explore how length and flexibility of the DNA ligands affect binding restriction and binding strength, where the overall binding strength decreased with spacer length. For trivalent systems, increasing spacer length additionally activated binding in the trivalent state, giving insight into the design of multivalent drug or targeting moieties. By systematically changing the receptor density, we explored the binding super selectivity of the multivalent HJ at the single-molecule level. We find a polynomial behavior of the trivalent binding strength that clearly shows receptor-density-dependent selective binding. Interestingly, we could exploit the rapidly decaying near fields of the plasmon that induce a strong dependence of the signal on the position of the dye to observe binding dynamics during single multivalent binding events.

AB - Multivalency as an interaction principle is widely utilized in nature. It enables specific and strong binding by multiple weak interactions through enhanced avidity and is a core process in immune recognition and cellular signaling, which is also a current concept in drug design. Here, we use the high signals from plasmon-enhanced fluorescence of nanoparticles to extract binding kinetics and dynamics of multivalent interactions on the single-molecule level and in real time. We study mono-, bi-, and trivalent binding interactions using a DNA Holliday Junction as a model construct with programmable valency and introduce a step-binding model for binding kinetics relevant for structured macromolecules by including an experimentally extractable binding restriction term ω to quantify the effects from conformation, steric effects, and rigidity. We used this approach to explore how length and flexibility of the DNA ligands affect binding restriction and binding strength, where the overall binding strength decreased with spacer length. For trivalent systems, increasing spacer length additionally activated binding in the trivalent state, giving insight into the design of multivalent drug or targeting moieties. By systematically changing the receptor density, we explored the binding super selectivity of the multivalent HJ at the single-molecule level. We find a polynomial behavior of the trivalent binding strength that clearly shows receptor-density-dependent selective binding. Interestingly, we could exploit the rapidly decaying near fields of the plasmon that induce a strong dependence of the signal on the position of the dye to observe binding dynamics during single multivalent binding events.

KW - DNA nanotechnology

KW - fluorescence enhancement

KW - multivalency

KW - plasmonic nanoparticles

KW - single-molecule fluorescence

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JO - ACS Nano

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ER -

Single-Molecule Multivalent Interactions Revealed by Plasmon-Enhanced Fluorescence

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