DNA-mediated excitonic upconversion FRET switching

Kellis, Donald L.; Rehn, Sarah M.; Cannon, Brittany L.; Davis, Paul H.; Graugnard, Elton; Lee, Jeunghoon; Yurke, Bernard; Knowlton, William B.

doi:10.1088/1367-2630/17/11/115007

Cited by 10 publications

(18 citation statements)

References 76 publications

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“…According to Kasha's molecular exciton model, the strength of excitonic coupling can be quantitatively described with an exciton hopping parameter, J m,n [26]. The creation of excitons with strong excitonic coupling is the foundation of the development of such applications as organic photoswitches [27][28][29][30][31][32], light harvesting [33], and emerging quantum information systems [34,35]. Control over intermolecular distances between dyes and their respective orientation, as well as the number of dyes per aggregate, is key in harnessing molecular excitons.…”

Section: Introductionmentioning

confidence: 99%

Photocrosslinking Probes Proximity of Thymine Modifiers Tethering Excitonically Coupled Dye Aggregates to DNA Holliday Junction

et al. 2022

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A DNA Holliday junction (HJ) has been used as a versatile scaffold to create a variety of covalently templated molecular dye aggregates exhibiting strong excitonic coupling. In these dye-DNA constructs, one way to attach dyes to DNA is to tether them via single long linkers to thymine modifiers incorporated in the core of the HJ. Here, using photoinduced [2 + 2] cycloaddition (photocrosslinking) between thymines, we investigated the relative positions of squaraine-labeled thymine modifiers in the core of the HJ, and whether the proximity of thymine modifiers correlated with the excitonic coupling strength in squaraine dimers. Photocrosslinking between squaraine-labeled thymine modifiers was carried out in two distinct types of configurations: adjacent dimer and transverse dimer. The outcomes of the reactions in terms of relative photocrosslinking yields were evaluated by denaturing polyacrylamide electrophoresis. We found that for photocrosslinking to occur at a high yield, a synergetic combination of three parameters was necessary: adjacent dimer configuration, strong attractive dye–dye interactions that led to excitonic coupling, and an A-T neighboring base pair. The insight into the proximity of dye-labeled thymines in adjacent and transverse configurations correlated with the strength of excitonic coupling in the corresponding dimers. To demonstrate a utility of photocrosslinking, we created a squaraine tetramer templated by a doubly crosslinked HJ with increased thermal stability. These findings provide guidance for the design of HJ-templated dye aggregates exhibiting strong excitonic coupling for exciton-based applications such as organic optoelectronics and quantum computing.

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Section: Introductionmentioning

confidence: 99%

Photocrosslinking Probes Proximity of Thymine Modifiers Tethering Excitonically Coupled Dye Aggregates to DNA Holliday Junction

et al. 2022

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“…The absence of cyclic fatigue is most likely attributed to superior cyclic fatigue resistance of the diarylethene photochromic nucleotide ,, as well as the photostability (Supporting Information S1) of the chromophore selection . While future studies will be required to examine the overall reliability of our all-optical excitonic switch, the preliminary results for the all-optical excitonic switch demonstrate exceptional cyclic fatigue resistance in the liquid and solid phases, as well as over 2 orders of magnitude greater cycling when compared to other DNA scaffolded FRET-based excitonic switches. ,,,,, …”

Section: Resultsmentioning

confidence: 97%

“…49 While future studies will be required to examine the overall reliability of our all-optical excitonic switch, the preliminary results for the all-optical excitonic switch demonstrate exceptional cyclic fatigue resistance in the liquid and solid phases, as well as over 2 orders of magnitude greater cycling when compared to other DNA scaffolded FRET-based excitonic switches. 7,13,16,18,45,46…”

Section: Resultsmentioning

confidence: 99%

“…Targeting the above-described challenges, various FRET-based excitonic devices have been developed, typically with donor/acceptor chromophore pairs self-assembled onto static or dynamic DNA scaffolds. These include switches, ,, logic gates, , and energy ratchet switches . However, the switching processes employed in these devices require aqueous solutions with chemical compositions that enable DNA duplex dissociation via DNA strand invasion, DNA-intercalation, or chromophore modulation. − Furthermore, these switching processes have rate-limiting steps such as strand displacement, mass transport, and reducing agent diffusion, which lead to challenges including cyclic fatigue and long cycle times (Supporting Information S1).…”

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confidence: 99%

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An All-Optical Excitonic Switch Operated in the Liquid and Solid Phases

et al. 2019

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The excitonic circuitry found in photosynthetic organisms suggests an alternative to electronic circuits, but the assembly of optically active molecules to fabricate even simple excitonic devices has been hampered by the limited availability of suitable molecular scale assembly technologies. Here we have designed and operated a hybrid all-optical excitonic switch comprised of donor/acceptor chromophores and photochromic nucleotide modulators assembled with nanometer scale precision using DNA nanotechnology. The all-optical excitonic switch was operated successfully in both liquid and solid phases, exhibiting high ON/OFF switching contrast with no apparent cyclic fatigue through nearly 200 cycles. These findings, combined with the switch’s small footprint and volume, estimated low energy requirement, and potential ability to switch at speeds in the 10s of picoseconds, establish a prospective pathway forward for all-optical excitonic circuits.

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“…The quantum yield of this process heavily depends on the dopant concentrations and the size of the crystal but is typically below 1% . Despite this, UCNPs have been used extensively as RET donors to both organic chromophores and quantum dots due to their anti‐Stokes emission that favorably separates the excitation and observation bands, as well as their near‐infrared (NIR) absorption that allows for deeper penetration in biological tissues. Very little work, however, has utilized UCNPs as FRET acceptors.…”

Section: Introductionmentioning

confidence: 99%

Upconverting Nanoparticle Relays for Resonance Energy Transfer Networks

LaBoda

Dwyer

2016

Adv Funct Materials

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wileyonlinelibrary.comvariety of mechanisms such as DNA strand displacement, [ 3,[6][7][8] excited singlet saturation, [ 9,10 ] and optochemically accessed dark states of standard chromophores. [11][12][13][14][15][16][17] To store state in these networks, researchers have developed RET based fl ip-fl ops [ 16 ] and write-once polychromatic RET based storage devices with densities 1000 times greater than current standards. [ 18 ] Tying all of these circuit elements together is an impressive array of RET wires that can transport excitons through geometrically complex DNA nanostructures spanning more than 20 nm in length. [19][20][21][22][23][24] Given these extensive contributions, it is clear that the foundations for building more complex RET circuits have already been established.Despite these advances in essential circuit elements, the intrinsic energy loss of these networks currently prohibits large scale circuit fabrication. Energy loss is defi ned as the red-shifting Stokes effect that excitons incur as they traverse a set of RET donor-acceptor pairs. Once in the excited state, vibrational relaxation forces each fl uorophore's emission spectrum to be red-shifted with respect to its excitation spectrum. This shift requires an acceptor's excitation spectrum be lower in energy than its donor. Accordingly, as an exciton traverses any RET network from input to output it loses energy. Without a way to restore this energy, the output of one network cannot act as the input to a subsequent network, thereby prohibiting the cascading of independently designed RET networks to form larger circuitry. In certain cases, it may be possible to design an entire set of cascaded logic operations as a single RET network ensuring that the design does not violate this downhill energy fl ow; however, such solutions cannot be scaled to fabricate arbitrarily large circuits. Instead, we have engineered a device that will restore the energy of the excitons as they transition from one network to the next. This concept is analogous to a buffer in digital logic that decouples two networks and restores the signal between them. To achieve this restoration, we explored the use of upconversion.Upconverting processes combine many low energy inputs to form high energy outputs. The most commonly utilized upconversion processes rely entirely on far-fi eld interactions, e.g., multiphoton excitation of fl uorophores or excited state absorption in upconverting laser media. Such far-fi eld mechanisms, however, are unfi t for restoring energy in RET Networks of fl uorophores arranged at the nanoscale can perform basic computation using resonance energy transfer (RET) to transport and manipulate information in the form of excitons. As excitons travel through RET circuits, they are red-shifted due to vibrational energy loss at each transfer event. This loss prohibits RET circuits from being cascaded to form larger, more computationally complex systems. To address this issue, a nanoassembly capable of converting three or more low energy excitons into a si...

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DNA-mediated excitonic upconversion FRET switching

Cited by 10 publications

References 76 publications

Photocrosslinking Probes Proximity of Thymine Modifiers Tethering Excitonically Coupled Dye Aggregates to DNA Holliday Junction

Photocrosslinking Probes Proximity of Thymine Modifiers Tethering Excitonically Coupled Dye Aggregates to DNA Holliday Junction

An All-Optical Excitonic Switch Operated in the Liquid and Solid Phases

Upconverting Nanoparticle Relays for Resonance Energy Transfer Networks

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