Increased Transfer Efficiency from Molecular Photonic Wires on Solid Substrates and Cryogenic Conditions

Dı́az, Sebastián A.; Oliver, Sean M.; Hastman, David A.; Medintz, Igor L.; Vora, Patrick M.

doi:10.1021/acs.jpclett.8b00931

Cited by 14 publications

(29 citation statements)

References 36 publications

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“…The Förster distance ( R 0 ) was estimated using

R_{0} = \sqrt[6]{\frac{9000 \times \ln 10 \times κ_{}^{2} \times Q_{normalD}}{128 \times N_{normalA} \times π^{5} \times n_{normalD}^{4}} \times \int J (λ) normald λ}

where N A is Avogadro's number, n D is the refractive index of the medium, Q D is the donor quantum yield, κ is the relative dipole–dipole orientation of the donor and acceptor, and J (λ) is the donor–acceptor spectral overlap function over all relevant wavelengths. Given the self‐assembled nature of all the QD and downstream DNA structures, a value of 2/3 was utilized for κ 2 as described previously . FRET efficiency ( E FRET ) was estimated using

E_{FRET} (n) = 1 - \frac{I_{DA} (n)}{I_{normalD}}

…”

Section: Methodsmentioning

confidence: 99%

Transducing Protease Activity into DNA Output for Developing Smart Bionanosensors

Bui

Brown

Buckhout‐White

et al. 2019

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DNA can process information through sequence‐based reorganization but cannot typically receive input information from most biological processes and translate that into DNA compatible language. Coupling DNA to a substrate responsive to biological events can address this limitation. A two‐component sensor incorporating a chimeric peptide‐DNA substrate is evaluated here as a protease‐to‐DNA signal convertor which transduces protease activity through DNA gates that discriminate between different input proteases. Acceptor dye‐labeled peptide‐DNAs are assembled onto semiconductor quantum dot (QD) donors as the input gate. Addition of trypsin or chymotrypsin cleaves their cognate peptide sequence altering the efficiency of Förster resonance energy transfer (FRET) with the QD and frees a DNA output which interacts with a tetrahedral output gate. Downstream output gate rearrangement results in FRET sensitization of a new acceptor dye. Following characterization of component assembly and optimization of individual steps, sensor ability to discriminate between the two proteases is confirmed along with effects from joint interactions where potential for cross‐talk is highest. Processing multiple bits of information for a sensing outcome provides more confidence than relying on a single change especially for the discrimination between different targets. Coupling other substrates to DNA that respond similarly could help target other types of enzymes.

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“…The Förster distance ( R 0 ) was estimated using

R_{0} = \sqrt[6]{\frac{9000 \times \ln 10 \times κ_{}^{2} \times Q_{normalD}}{128 \times N_{normalA} \times π^{5} \times n_{normalD}^{4}} \times \int J (λ) normald λ}

E_{FRET} (n) = 1 - \frac{I_{DA} (n)}{I_{normalD}}

…”

Section: Methodsmentioning

confidence: 99%

Transducing Protease Activity into DNA Output for Developing Smart Bionanosensors

Bui

Brown

Buckhout‐White

et al. 2019

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“…Limitations in accessing arrangement of multiple high‐efficiency DNA conjugated FRET donor–acceptor pairs in a sequential manner to create more complex arrangements and cascades has stimulated investigation of alternative fluorophore types going beyond just use of organic dyes or in finding design principles that could overcome these limitations. Some, individual FRET parameters were looked at including: the optimal r DA / R 0 ratio by positioning dyes at different distances; modifying the apparent spectral overlap ( J ) by creating multiacceptor systems, which proportionally increase the FRET acceptor absorption cross‐section and thus R 0 ;53a improving donor QY through attaining cryogenic conditions; and fixing dye dipole orientations into optimal transfer alignments . These studies did indeed show incremental enhancements but were always limited by the characteristic limitations of the heterogeneous FRET mechanism, i.e., the requirement for an energetically downhill arrangement.…”

Section: Fluorescently Labeled Dna Materialsmentioning

confidence: 99%

“…These MPWs allowed for photonic transfer over more than a 31 nm distance with an efficiency of ≈2%, whereas no transfer took place when the repeats were removed. Subsequent studies on structurally similar constructs placed on solid substrates under cryogenic conditions demonstrated that these efficiencies could be increased by ≈3‐fold by minimizing the number of alternative and parasitic relaxation pathways . Work realized by the Hanley group used DNA templates to align fluorescent proteins (monomeric teal fluorescent protein or labeled bovine serum albumin) to also look at HomoFRET transfer, finding that the total fluorescence was not the sum of the individual components and confirming the existence of parasitic traps .…”

Section: Fluorescently Labeled Dna Materialsmentioning

confidence: 99%

Utilizing the Organizational Power of DNA Scaffolds for New Nanophotonic Applications

Bui

Dı́az

Fontana

et al. 2019

Advanced Optical Materials

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Rapid development of DNA technology has provided a feasible route to creating nanoscale materials. DNA acts as a self‐assembled nanoscaffold capable of assuming any three‐dimensional shape. The ability to integrate dyes and new optical materials such as quantum dots and plasmonic nanoparticles precisely onto these architectures provides new ways to exploit their near‐ and far‐field interactions. A fundamental understanding of these optical processes will help drive development of next‐generation photonic nanomaterials. This review is focused on latest progress in DNA‐based photonic materials and highlights DNA scaffolds for rapidly assembling and prototyping nanoscale optical devices. Three areas are discussed including intrinsically active DNA structures displaying chiral properties, DNA scaffolds hosting plasmonic nanomaterials, and fluorophore‐labeled DNAs that engage in Förster resonance energy transfer and give rise to complex molecular photonic wires. An explanation of what is desired from these optical processes when harnessed sets the tone for what DNA scaffolds are providing toward each focus. Examples from the literature illustrate current progress along with a discussion of challenges to overcome for further improvements. Opportunities to integrate diverse classes of optically active molecules including light‐generating enzymes, fluorescent proteins, nanoclusters, and metal–chelates in new structural combinations on DNA scaffolds are also highlighted.

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“…32,33 This differs from lightharvesting systems where centrosymmetric HomoFRET systems found neutral or increased transfer. 3,4,18 In a recent investigation of MPWs 24 nm in length, which included a long HomoFRET section, the end-to-end efficiencies were observed to be just 6% in poly(vinyl alcohol) (PVA) films, 34 and for similar solution-based MPWs of 30 nm in length, the reported efficiency was 1.7%. 30 From these published works, we developed a hypothesis that HomoFRET would benefit from creating greater density transfer networks by integrating as many dyes as possible.…”

Section: ■ Introductionmentioning

confidence: 99%

DNA Origami Chromophore Scaffold Exploiting HomoFRET Energy Transport to Create Molecular Photonic Wires

Klein

Rolczynski

Oliver

et al. 2020

ACS Appl. Nano Mater.

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DNA-scaffolded molecular photonic wires (MPWs) displaying prearranged donor–acceptor chromophore pairs that engage in extended Förster resonance energy transfer (FRET) cascades represent an emerging nanoscale photonic material with numerous potential applications in data storage, encryption, and communications. For translation to such applications, these devices must first demonstrate robust performance with high transfer efficiencies over extended distances. Here, we report the optimization of FRET in a 6-helix DNA origami architecture supporting a 14-dye site system that contains a central 10-dye homogeneous FRET (HomoFRET) relay span and overall extends over 29 nm in length. Varying the dye density by controlling their presence or absence across all of the individually addressable sites presented an incredibly large optimization space (1024 HomoFRET and 16 384 total permutations). High-throughput experiments, with over 500 measurements of DNA templates assembled in parallel, allowed for the study of HomoFRET transfer as a function of fluorophore density and arrangement. Transfer within solution-phase MPWs initially obtained with steady-state spectroscopy experiments revealed values only reaching ∼1% efficiency. Extensive photophysical characterization, utilizing six different spectroscopic techniques and 11 total methodologies, determined that the diminished FRET efficiency of each individual component step is the principal cause of the limited transfer in solution. Monte Carlo and machine-learning methods provided additional insights into design optimization. A representative MPW set selected based on the previous findings was subsequently characterized in film deposition and also under cryogenic conditions. Under these improved conditions, selected MPWs demonstrated 59 ± 6% energy transport efficiency over a length of 29 nm; this is ∼25% longer and 10-fold more efficient than the previously reported optimized DNA MPWs.

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Increased Transfer Efficiency from Molecular Photonic Wires on Solid Substrates and Cryogenic Conditions

Cited by 14 publications

References 36 publications

Transducing Protease Activity into DNA Output for Developing Smart Bionanosensors

Transducing Protease Activity into DNA Output for Developing Smart Bionanosensors

Utilizing the Organizational Power of DNA Scaffolds for New Nanophotonic Applications

DNA Origami Chromophore Scaffold Exploiting HomoFRET Energy Transport to Create Molecular Photonic Wires

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