FRET efficiency and antenna effect in multi-color DNA origami-based light harvesting systems

Olejko, Lydia; Bald, Ilko

doi:10.1039/c7ra02114c

Cited by 47 publications

(60 citation statements)

References 45 publications

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“…Change in fluorescence of the two fluorophores should report binding between C3 and the FAM-labelled RNA sequences and provide useful indications of the mode of interactions at least by quenching, if not by F€ orster Resonance Energy Transfer (FRET). FAM and Cy3 often act as a Donor-Acceptor couple (Chen et al, 2010;Olejko et al, 2016;Olejko & Bald, 2017;Tsourkas et al, 2003;Zhao et al, 2010), as the fluorescence emission region of FAM (480-600 nm) substantially overlaps with the excitation region of Cy3 (470-570 nm).…”

Section: Conjugate Designmentioning

confidence: 99%

“…Both the nature and the scale of these reciprocal responses from the two fluorophores within the duallylabelled system were somewhat unexpected. FAM and Cy3 have been often used in as a Donor-Acceptor couple in FRET, due to the substantial overlap of the emission spectrum of FAM with the excitation spectrum of Cy3 (Chen et al, 2010;Olejko et al, 2016;Olejko & Bald, 2017;Tsourkas et al, 2003;Zhao et al, 2010). In the case of F€ orster resonance energy transfer from FAM (acting as a Donor) to Cy3 (acting as an Acceptor), the observed decrease of FAM fluorescence is usually coupled with an increase of Cy3 fluorescence.…”

Section: 'Dual Label' Hybridizationmentioning

confidence: 99%

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RNA knockdown by synthetic peptidyl-oligonucleotide ribonucleases: behavior of recognition and cleavage elements under physiological conditions

Gebrezgiabher

Zalloum

Clarke

et al. 2020

Journal of Biomolecular Structure and Dynamics

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Sequence-specific protein-based ribonucleases are not found in nature. Absolute sequence selectivity in RNA cleavage in vivo normally requires multi-component complexes that recruit a guide RNA or DNA for target recognition and a protein-RNA assembly for catalytic functioning (e.g. RNAi molecular machinery, RNase H). Recently discovered peptidyl-oligonucleotide synthetic ribonucleases selectively knock down pathogenic RNAs by irreversible cleavage to offer unprecedented opportunities for control of disease-relevant RNA. Understanding how to increase their potency, selectivity and catalytic turnover will open the translational pathway to successful therapeutics. Yet, very little is known about how these chemical ribonucleases bind, cleave and leave their target. Rational design awaits this understanding in order to control therapy, particularly how to overcome the trade-off between sequence specificity and potency through catalytic turnover. We illuminate this here by characterizing the interactions of these chemical RNases with both complementary and non-complementary RNAs using T m profiles, fluorescence, UV-visible and NMR spectroscopies. Crucially, the level of counter cations, which are tightly-controlled within cellular compartments, also controlled these interactions. The oligonucleotide component dominated interaction between conjugates and complementary targets in the presence of physiological levels of counter cations (K þ), sufficient to prevent repulsion between the complementary nucleic acid strands to allow Watson-Crick hydrogen bonding. In contrast, the positively-charged catalytic peptide interacted poorly with target RNA, when counter cations similarly screened the negatively-charged sugar-phosphate RNA backbones. The peptide only became the key player, when counter cations were insufficient for charge screening; moreover, only under such nonphysiological conditions did conjugates form strong complexes with non-complementary RNAs.

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Section: Conjugate Designmentioning

confidence: 99%

Section: 'Dual Label' Hybridizationmentioning

confidence: 99%

RNA knockdown by synthetic peptidyl-oligonucleotide ribonucleases: behavior of recognition and cleavage elements under physiological conditions

Gebrezgiabher

Zalloum

Clarke

et al. 2020

Journal of Biomolecular Structure and Dynamics

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“…Furthermore, the DNA origami technique has also been exploited to self-assemble fluorophore systems for fabrication of artificial light harvesting antennas. 28 , 30 , 31 …”

Section: Dna Origami For Hybrid Photonic Structuresmentioning

confidence: 99%

DNA Origami Route for Nanophotonics

et al. 2018

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The specificity and simplicity of the Watson–Crick base pair interactions make DNA one of the most versatile construction materials for creating nanoscale structures and devices. Among several DNA-based approaches, the DNA origami technique excels in programmable self-assembly of complex, arbitrary shaped structures with dimensions of hundreds of nanometers. Importantly, DNA origami can be used as templates for assembly of functional nanoscale components into three-dimensional structures with high precision and controlled stoichiometry. This is often beyond the reach of other nanofabrication techniques. In this Perspective, we highlight the capability of the DNA origami technique for realization of novel nanophotonic systems. First, we introduce the basic principles of designing and fabrication of DNA origami structures. Subsequently, we review recent advances of the DNA origami applications in nanoplasmonics, single-molecule and super-resolution fluorescent imaging, as well as hybrid photonic systems. We conclude by outlining the future prospects of the DNA origami technique for advanced nanophotonic systems with tailored functionalities.

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“…While MCSs tend to have inherent structural heterogeneity, the distributions of structural parameters of those systems were not considered in previous studies. [7,[28][29][30][31][32]37] Structural heterogeneity can originate from both (i) the rapid structural fluctuation of orientation factor and interchromophore distance around each of their average values and (ii) the static distribution of structural parameters such as D-A distance and orientation factor of all donors. To consider the structural heterogeneity of MCSs, we performed the simulations for calculating FRET in the model MCSs while considering two cases for each of Δ DA (and Δ DD ) and 2 , which are two major parameters that govern FRET , resulting in four cases in total.…”

Section: Calculation Of Fret For Model Multichromophore Systemsmentioning

confidence: 99%

“…[7,28] However, the influence of D-D energy transfer on FRET in MCSs has been controversial. For example, Olejko and Bald [29] studied the effect of the number of donors (n D ) on FRET using the DNA origami structure as a scaffold for donors and acceptors. By varying n D from one to four, they found that FRET barely changes with n D although the amount of harvested energy increases with n D .…”

Section: Introductionmentioning

confidence: 99%

Enhancement of Energy Transfer Efficiency with Structural Control of Multichromophore Light‐Harvesting Assembly

Lee

Kim

et al. 2020

Advanced Science

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Multichromophore systems (MCSs) are envisioned as building blocks of molecular optoelectronic devices. While it is important to understand the characteristics of energy transfer in MCSs, the effect of multiple donors on energy transfer has not been understood completely, mainly due to the lack of a platform to investigate such an effect systematically. Here, a systematic study on how the number of donors (n D) and interchromophore distances affect the efficiency of energy transfer (FRET) is presented. Specifically, FRET is calculated for a series of model MCSs using simulations, a series of multiporphyrin dendrimers with systematic variation of n D and interdonor distances is synthesized, and FRET s of those dendrimers using transient absorption spectroscopy are measured. The simulations predict FRET in the multiporphyrin dendrimers well. In particular, it is found that FRET is enhanced by donor-to-donor energy transfer only when structural heterogeneity exists in an MCS, and the relationships between the FRET enhancement and the structural parameters of the MCS are revealed.

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FRET efficiency and antenna effect in multi-color DNA origami-based light harvesting systems

Cited by 47 publications

References 45 publications

RNA knockdown by synthetic peptidyl-oligonucleotide ribonucleases: behavior of recognition and cleavage elements under physiological conditions

RNA knockdown by synthetic peptidyl-oligonucleotide ribonucleases: behavior of recognition and cleavage elements under physiological conditions

DNA Origami Route for Nanophotonics

Enhancement of Energy Transfer Efficiency with Structural Control of Multichromophore Light‐Harvesting Assembly

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