Proximity-Induced H-Aggregation of Cyanine Dyes on DNA-Duplexes

Nicoli, Francesca; Roos, Matthias; Hemmig, Elisa A.; Antonio, Marco Di; Vivie‐Riedle, Regina de; Liedl, Tim

doi:10.1021/acs.jpca.6b10939

Cited by 74 publications

(87 citation statements)

References 55 publications

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“…In this work, we studied the absorption and CD spectra of a (Cy3) 2 dimers attached to DNA using flexible linkers (58). However, those studies did not account for the influence of the vibrational states of the cyanine chromophores, which led to claims of solely J-type and H-type dimer conformations, respectively.…”

Section: Discussionmentioning

confidence: 99%

Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA

Kringle

Sawaya

Widom

et al. 2018

The Journal of Chemical Physics

133

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Understanding the properties of electronically interacting molecular chromophores, which involve internally coupled electronic-vibrational motions, is important to the spectroscopy of many biologically relevant systems. Here we apply linear absorption, circular dichroism, and two-dimensional fluorescence spectroscopy to study the polarized collective excitations of excitonically coupled cyanine dimers (Cy3) that are rigidly positioned within the opposing sugar-phosphate backbones of the double-stranded region of a double-stranded (ds)-single-stranded (ss) DNA fork construct. We show that the exciton-coupling strength of the (Cy3)-DNA construct can be systematically varied with temperature below the ds-ss DNA denaturation transition. We interpret spectroscopic measurements in terms of the Holstein vibronic dimer model, from which we obtain information about the local conformation of the (Cy3) dimer, as well as the degree of static disorder experienced by the Cy3 monomer and the (Cy3) dimer probe locally within their respective DNA duplex environments. The properties of the (Cy3)-DNA construct we determine suggest that it may be employed as a useful model system to test fundamental concepts of protein-DNA interactions and the role of electronic-vibrational coherence in electronic energy migration within exciton-coupled bio-molecular arrays.

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Section: Discussionmentioning

confidence: 99%

Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA

Kringle

Sawaya

Widom

et al. 2018

The Journal of Chemical Physics

133

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“…As shown in Figure a, the intensity of the hypsochromic peak at around 512 nm increases with increasing Cy3 surface grafting density on virus surface. This phenomenon of the Cy3 dye is ascribed to increased interactions between adjacent dye molecules via π‐orbital stacking, which form H‐aggregates in solution . We then sought to study how the increased interactions among neighboring Cy3 dyes change the quantum yield of the dye.…”

Section: Methodsmentioning

confidence: 99%

“…This phenomenon of the Cy3 dye is ascribed to increased interactions between adjacent dye molecules via π-orbital stacking, which form H-aggregates in solution. [28,29] We then sought to study how the increased interactions among neighboring Cy3 dyes change the quantum yield of the dye. By varying the optical densities at 532 nm (the excitation wavelength), we measured the fluorescence and the results are summarized in Figure 4b.…”

Section: Doi: 101002/smll201901233mentioning

confidence: 99%

M13 Virus‐Based Framework for High Fluorescence Enhancement

Huang

deQuilettes

et al. 2019

Small

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Fluorescence imaging is a powerful tool for studying biologically relevant macromolecules, but its applicability is often limited by the fluorescent probe, which must demonstrate both high site‐specificity and emission efficiency. In this regard, M13 virus, a versatile biological scaffold, has previously been used to both assemble fluorophores on its viral capsid with molecular precision and to also target a variety of cells. Although M13‐fluorophore systems are highly selective, these complexes typically suffer from poor molecular detection limits due to low absorption cross‐sections and moderate quantum yields. To overcome these challenges, a coassembly of the M13 virus, cyanine 3 dye, and silver nanoparticles is developed to create a fluorescent tag capable of binding with molecular precision with high emissivity. Enhanced emission of cyanine 3 of up to 24‐fold is achieved by varying nanoparticle size and particle‐fluorophore separation. In addition, it is found that the fluorescence enhancement increases with increasing dye surface density on the viral capsid. Finally, this highly fluorescent probe is applied for in vitro staining of E. coli. These results demonstrate an inexpensive framework for achieving tuned fluorescence enhancements. The methodology developed in this work is potentially amendable to fluorescent detection of a wide range of M13/cell combinations.

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“…1a). Upon conjugation to antibodies the absorption spectra display an increase in absorption at 610 nm with increasing DOL indicating dimer formation between Al647 molecules 38,39 . Multiple-Cy5-labeled antibodies exhibit a more pronounced dimer-shoulder at ~600 nm and accordingly also a lower fluorescence intensity indicating stronger fluorophore interactions ( Supplementary Fig.…”

Section: Fluorescence Quenching In Multiple-labeled Antibodiesmentioning

confidence: 99%

Multiple-labeled antibodies behave like single emitters in photoswitching buffer

Helmerich

Beliu

Sauer

2020

Preprint

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The degree of labeling (DOL) of antibodies has so far been optimized for high brightness and specific and efficient binding. The influence of the DOL on the blinking performance of antibodies used in direct stochastic optical reconstruction microscopy (dSTORM) has so far attained limited attention. Here, we investigated the spectroscopic characteristics of IgG antibodies labeled at DOLs of 1.1- 8.3 with Alexa Fluor 647 (Al647) at the ensemble and single-molecule level. Multiple-Al647-labeled antibodies showed weak and strong quenching interactions in aqueous buffer but could all be used for dSTORM imaging with spatial resolutions of ∼ 20 nm independent of the DOL. Photon antibunching experiments in aqueous buffer demonstrate that the emission of multiple-Al647-labeled antibodies switches from classical to non-classical light in photoswitching buffer. We developed a model that explains the observed blinking of multiple-labeled antibodies and can be used advantageously to develop improved fluorescent probes for dSTORM experiments.

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Proximity-Induced H-Aggregation of Cyanine Dyes on DNA-Duplexes

Cited by 74 publications

References 55 publications

Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA

Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA

M13 Virus‐Based Framework for High Fluorescence Enhancement

Multiple-labeled antibodies behave like single emitters in photoswitching buffer

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