Programmable Transformations of DNA Origami Made of Small Modular Dynamic Units

Wang, Dongfang; Yu, Lei; Huang, Chao‐Min; Arya, Gaurav; Chang, Shuai; Ke, Yonggang

doi:10.1021/jacs.0c10576

Cited by 37 publications

(43 citation statements)

References 35 publications

(44 reference statements)

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“…In contrast to amino acids, nucleic acids have relatively simple pairing rules, that is, Watson–Crick base pairing yet can form a diverse array of structures including duplexes, Holliday junctions, and higher-order structures. 35 − 39 Many early, pioneering studies used duplex DNA to template dye aggregates via physisorption. 40 − 42 More recently, an even higher level of precision and versatility has been achieved by covalently tethering dyes to DNA.…”

Section: Introductionmentioning

confidence: 99%

“…Using DNA to template dye aggregates represents an alternative, promising approach. In contrast to amino acids, nucleic acids have relatively simple pairing rules, that is, Watson–Crick base pairing yet can form a diverse array of structures including duplexes, Holliday junctions, and higher-order structures. − Many early, pioneering studies used duplex DNA to template dye aggregates via physisorption. − More recently, an even higher level of precision and versatility has been achieved by covalently tethering dyes to DNA. ,− Such precision and versatility enable the controlled assembly of dye aggregates with distinct packing geometries ,, and dye aggregate networks with a specific number of constituent dyes, ,, facilitating the study of structure–function relationships and design of aggregates with properties custom tailored and optimized for specific applications.…”

Section: Introductionmentioning

confidence: 99%

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Excited-State Lifetimes of DNA-Templated Cyanine Dimer, Trimer, and Tetramer Aggregates: The Role of Exciton Delocalization, Dye Separation, and DNA Heterogeneity

et al. 2021

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DNA-templated molecular (dye) aggregates are a novel class of materials that have garnered attention in a broad range of areas including light harvesting, sensing, and computing. Using DNA to template dye aggregation is attractive due to the relative ease with which DNA nanostructures can be assembled in solution, the diverse array of nanostructures that can be assembled, and the ability to precisely position dyes to within a few Angstroms of one another. These factors, combined with the programmability of DNA, raise the prospect of designer materials custom tailored for specific applications. Although considerable progress has been made in characterizing the optical properties and associated electronic structures of these materials, less is known about their excited-state dynamics. For example, little is known about how the excited-state lifetime, a parameter essential to many applications, is influenced by structural factors, such as the number of dyes within the aggregate and their spatial arrangement. In this work, we use a combination of transient absorption spectroscopy and global target analysis to measure excited-state lifetimes in a series of DNA-templated cyanine dye aggregates. Specifically, we investigate six distinct dimer, trimer, and tetramer aggregates—based on the ubiquitous cyanine dye Cy5—templated using both duplex and Holliday junction DNA nanostructures. We find that these DNA-templated Cy5 aggregates all exhibit significantly reduced excited-state lifetimes, some by more than 2 orders of magnitude, and observe considerable variation among the lifetimes. We attribute the reduced excited-state lifetimes to enhanced nonradiative decay and proceed to discuss various structural factors, including exciton delocalization, dye separation, and DNA heterogeneity, that may contribute to the observed reduction and variability of excited-state lifetimes. Guided by insights from structural modeling, we find that the reduced lifetimes and enhanced nonradiative decay are most strongly correlated with the distance between the dyes. These results inform potential tradeoffs between dye separation, excitonic coupling strength, and excited-state lifetime that motivate deeper mechanistic understanding, potentially via further dye and dye template design.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Excited-State Lifetimes of DNA-Templated Cyanine Dimer, Trimer, and Tetramer Aggregates: The Role of Exciton Delocalization, Dye Separation, and DNA Heterogeneity

et al. 2021

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“…[ 94 ] Reconfiguration of overall dimensions and curvatures of DNA origami is achieved with the use of toehold‐mediated strand displacement. [ 95 ]…”

Section: Ordered Dna Nanoarchitectures Showing Multifunctions For Ddsmentioning

confidence: 99%

DNA‐Based Nanoarchitectures as Eminent Vehicles for Smart Drug Delivery Systems

Komiyama

Shigi

Ariga

2022

Adv Funct Materials

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In order to cure diseases efficiently with minimal side effects in sophisticated medicine, eminent drugs must be selectively delivered to diseased parts and allow to work only there. However, most of drug delivery systems (DDSs) previously proposed are not yet sufficiently selective and effective. This review covers recent developments of DDS in which DNA nanoarchitectures are employed as drug carriers. From short DNA fragments, a variety of complicated nanomedicines are fabricated to show unprecedentedly smart DDS functions. Encapsulated drugs are released mostly through controlled disassembly of DNA nanoarchitectures. Recent attention has been focusing to the use of appropriate stimuli to regulate each process in the DDS (delivery of drug, its release, and others) for further improved therapy. As intracellular stimuli for the regulation, various endogenous compounds (e.g., mRNA and enzymes), which are specifically abundant in target cells, are employed. Alternatively, physical perturbation (e.g., light irradiation) is provided from outside of tissues to control DDS. By combining multiple strategies in terms of new concepts, enormously smart DDSs are being achieved. Further progresses of these approaches in the future are guaranteed by complete freedom of molecular design in DNA nanoarchitectonics.

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“…22 Subsequently, DNA origami nanostructures have emerged as an alternative tool to program chemical reaction networks with nanometer precision and in many cases, absolute control over stoichiometry. 23,24 However, the aforementioned DNA structures do not favor simultaneous reaction of multi-component DNA, thereby limiting the function of chemical reaction networks. Bridge DNA, consisting of a double-stranded middle section and four singlestranded tails (Fig.…”

Section: Introductionmentioning

confidence: 99%