“Printing” DNA Strand Patterns on Small Molecules with Control of Valency, Directionality, and Sequence

Trinh, Tuan; Saliba, Daniel; Liao, Chenyi; Rochambeau, Donatien de; Prinzen, Alexander L.; Li, Jianing; Sleiman, Hanadi F.

doi:10.1002/anie.201809251

Cited by 14 publications

(11 citation statements)

References 54 publications

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“…We prepared molecular cores with discrete, but variable, numbers of reactive handles for the covalent functionalization of DNA strands. Specifically, a series of azide-bearing molecules was synthesized and conjugated with dibenzocyclooctyne (DBCO)-modified DNA strands via copper-free “click” chemistry to yield small-molecule–DNA hybrids (SMDHs), − which have been utilized for directing the assembly of discrete nanostructures, − extended arrays, and networks, − as well as for studying the cellular uptake properties of multivalent DNA architectures. , We hypothesized that these molecularly defined, multivalent DNA architectures would function as highly mobile EEs when co-assembled with PAEs, yielding superlattices with phase symmetries defined by the PAE sublattices. Furthermore, by precisely tuning numerous structural factors, such as the EE valency, EE dispersity, and EE-to-PAE ratio, colloidal crystals with predictable thermal stabilities and lattice symmetries could be synthesized.…”

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confidence: 99%

Electron-Equivalent Valency through Molecularly Well-Defined Multivalent DNA

2021

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Oligonucleotide-functionalized nanoparticles (NPs), also known as "programmable atom equivalents" (PAEs), have emerged as a class of versatile building blocks for generating colloidal crystals with tailorable structures and properties. Recent studies have shown that, at small size and low DNA grafting density, PAEs can also behave as "electron equivalents" (EEs), roaming through and stabilizing a complementary PAE sublattice. However, it has been challenging to obtain a detailed understanding of EE-PAE interactions and the underlying colloidal metallicity because there is inherent polydispersity in the number of DNA strands on the surfaces of these NPs; thus, the structural uniformity and tailorability of NP-based EEs are somewhat limited. Herein, we report a strategy for synthesizing colloidal crystals where the EEs are templated by small molecules, instead of NPs, and functionalized with a precise number of DNA strands. When these molecularly precise EEs are assembled with complementary NP-based PAEs, X-ray scattering and electron microscopy reveal the formation of three distinct "metallic" phases. Importantly, we show that the thermal stability of these crystals is dependent on the number of sticky ends per EE, while lattice symmetry is controlled by the number and orientation of EE sticky ends on the PAEs. Taken together, this work introduces the notion that, unlike conventional electrons, EEs that are molecular in origin can have a defined valency that can be used to influence and guide specific phase formation.

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confidence: 99%

Electron-Equivalent Valency through Molecularly Well-Defined Multivalent DNA

2021

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“…The hydrogen bonds between base pairs (A-T and C-G) were easily destroyed at high temperature, which restricted the applications of branched DNA nanostructures in PCR. To address this problem, some organic molecules were introduced to covalently link branched DNA for the construction of thermostable DNA nanostructures. − Marx groups proposed a method of using covalently cross-linked branched DNA as primers, and constructed 3D DNA network through branched PCR amplification. ,, The branched primers with organic molecules as cores were formed by standard solid phase synthesis, whose length influenced the meshes of DNA network. The method provided a strategy for the addition of chemically modified nucleotides in PCR.…”

Section: Construction Of Branched Dna Building-blocksmentioning

confidence: 99%

DNA Functional Materials Assembled from Branched DNA: Design, Synthesis, and Applications

et al. 2020

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DNA is traditionally known as a central genetic biomolecule in living systems. From an alternative perspective, DNA is a versatile molecular building-block for the construction of functional materials, in particular biomaterials, due to its intrinsic biological attributes, molecular recognition capability, sequence programmability, and biocompatibility. The topologies of DNA building-blocks mainly include linear, circular, and branched types. Branched DNA recently has been extensively employed as a versatile building-block to synthesize new biomaterials, and an assortment of promising applications have been explored. In this review, we discuss the progress on DNA functional materials assembled from branched DNA. We first briefly introduce the background information on DNA molecules and sketch the development history of DNA functional materials constructed from branched DNA. In the second part, the synthetic strategies of branched DNA as building-blocks are categorized into base-pairing assembly and chemical bonding. In the third part, construction strategies for the branched DNA-based functional materials are comprehensively summarized including tile-mediated assembly, DNA origami, dynamic assembly, and hybrid assembly. In the fourth part, applications including diagnostics, protein engineering, drug and gene delivery, therapeutics, and cell engineering are demonstrated. In the end, an insight into the challenges and future perspectives is provided. We envision that branched DNA functional materials can not only enrich the DNA nanotechnology by ingenious design and synthesis but also promote the development of interdisciplinary fields in chemistry, biology, medicine, and engineering, ultimately addressing the growing demands on biological and medical-related applications in the real world.

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“…Indeed, the outstanding advantages of DNA have previously been demonstrated in templating synthetic reactions and influencing the rates of monocatalytic processes. DNA has long been used as a template to accelerate bond formation in a variety of reactions − and to bring substrates proximal to catalysts. − DNA has also been used as a scaffold to activate monocatalysts − and to influence monocatalytic processes for asymmetric synthesis. − Conformational switching of DNA has been used to regulate catalytic activity of monocatalytic gold bound to DNA, catalytic activity of a PNA-peptide hybrid, to activate heme-catalyzed peroxidation, , and to alter the distance between two enzymes in a cascade reaction. , However, to the best of our knowledge, DNA-scaffolded synergistic catalysis has not been demonstrated, and more broadly, no scaffolded synergistic catalysis has been performed that incorporates the advantages of DNA (convergent synthesis, precise positioning, and switching in response to stimuli). Here, we report the DNA-scaffolded Cu/TEMPO oxidation of alcohols.…”

Section: Introductionmentioning

confidence: 99%

DNA-Scaffolded Synergistic Catalysis

et al. 2021

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We report DNA-scaffolded synergistic catalysis, a concept that combines the diverse reaction scope of synergistic catalysis with the ability of DNA to precisely preorganize abiotic groups and undergo stimuli-triggered conformational changes. As an initial demonstration of this concept, we focus on Cu-TEMPO-catalyzed aerobic alcohol oxidation, using DNA as a scaffold to hold a copper cocatalyst and an organic radical cocatalyst (TEMPO) in proximity. The DNA-scaffolded catalyst maintained a high turnover number upon dilution and exhibited 190-fold improvement in catalyst turnover number relative to the unscaffolded cocatalysts. By incorporating the cocatalysts into a DNA hairpin-containing scaffold, we demonstrate that the rate of the synergistic catalytic reaction can be controlled through a reversible DNA conformational change that alters the distance between the cocatalysts. This work demonstrates the compatibility of synergistic catalytic reactions with DNA scaffolding, opening future avenues in reaction discovery, sensing, responsive materials, and chemical biology.

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“Printing” DNA Strand Patterns on Small Molecules with Control of Valency, Directionality, and Sequence

Cited by 14 publications

References 54 publications

Electron-Equivalent Valency through Molecularly Well-Defined Multivalent DNA

Electron-Equivalent Valency through Molecularly Well-Defined Multivalent DNA

DNA Functional Materials Assembled from Branched DNA: Design, Synthesis, and Applications

DNA-Scaffolded Synergistic Catalysis

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