Living Supramolecular Polymerization of DNA

Lanier, Laura; Bermudez, Harry

doi:10.1002/marc.201800342

Cited by 8 publications

(4 citation statements)

References 33 publications

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“…We used agarose gel electrophoresis to survey how temperature and divalent-cation (i.e., Mg 2+ ) concentration influenced qualitative distributions of ribbon lengths. With slats at 0.2 µM each and the seed at 2 nM, we grew ribbons for 16 19,20). We define "optimal" growth conditions as those producing the longest ribbons with the most uniform length distributions, as evidenced by a tight, slowly Monomers with a higher coordination number (2n) have more sustained kinetic barriers to spontaneous nucleation under increasingly irreversible growth conditions, with a theoretical comparison of square-tile (ST) nanotubes, hexagonal-tile (HT) nanotubes, and crisscross-slat (CS) ribbons that have identical free energies G(A) for nucleation at near-reversible ε → 0 conditions.…”

Section: Resultsmentioning

confidence: 99%

Robust nucleation control via crisscross polymerization of highly coordinated DNA slats

et al. 2021

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Natural biomolecular assemblies such as actin filaments or microtubules can exhibit all-or-nothing polymerization in a kinetically controlled fashion. The kinetic barrier to spontaneous nucleation arises in part from positive cooperativity deriving from joint-neighbor capture, where stable capture of incoming monomers requires straddling multiple subunits on a filament end. For programmable DNA self-assembly, it is likewise desirable to suppress spontaneous nucleation to enable powerful capabilities such as all-or-nothing assembly of nanostructures larger than a single DNA origami, ultrasensitive detection, and more robust algorithmic assembly. However, existing DNA assemblies use monomers with low coordination numbers that present an effective kinetic barrier only for slow, near-reversible growth conditions. Here we introduce crisscross polymerization of elongated slat monomers that engage beyond nearest neighbors which sustains the kinetic barrier under conditions that promote fast, irreversible growth. By implementing crisscross slats as single-stranded DNA, we attain strictly seed-initiated nucleation of crisscross ribbons with distinct widths and twists.

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Section: Resultsmentioning

confidence: 99%

Robust nucleation control via crisscross polymerization of highly coordinated DNA slats

et al. 2021

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“…Supramolecular DNA assembly is a new facet of DNA research that combines DNA building blocks with synthetic organic, inorganic or polymeric structures. [ 109 ] This assembly creates new opportunities for applications in supramolecular chemistry, materials science, structural DNA nanotechnology, molecular biology, [ 110 ] catalysis and medicine. [ 105 ] For example, DNA walkers utilize the interaction between DNase and DNA molecules to make the assembled DNA nanomaterials travel along a track and release fluorescent signals to achieve rapid amplification of the detected signals.…”

Section: Form and Structure Of Dna‐based Materialsmentioning

confidence: 99%

DNA‐Based Materials Inspired by Natural Extracellular DNA

Qin

Wang

Zhang

et al. 2023

Adv Funct Materials

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The advent of biotechnology has expedited the understanding of the biochemistry of deoxyribonucleic acids (DNA). In the past, DNA are thought to be present only in cell nucleus as bearers of the genetic code. With the identification of extracellular DNA in circulating body fluids, DNA are now utilized, at least experimentally, for diagnosis and treatment of diseases. Extracellular DNA of host origin trigger immune responses, and are closely linked to autoimmune disease, cancer-related inflammation, bacteria adhesion and thrombosis. Recent advancements in DNA nanotechnology have led to the development of a series of DNA-based materials for treating diseases because of their structural programmability. Current discussions on biosafety and immunogenicity of artificial DNA materials are insufficient. This issue severely restricts the clinical translation of these novel biotechnologies. The present review attempts to bridge the gap between natural extracellular DNA and their derivatives, DNA-based materials. The pathological attributes of endogenous extracellular DNA motivate the design of targeting DNA materials. In addition, the fate of exogenous DNA in the host inspires the optimization of DNA materials in reducing immune rejection. These bioinspired strategies provide the blueprint for utilizing DNA materials in the management of diseases that are currently challenging to diagnose or treat.

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“…Random repeat oligomerization involves the assembly of numerous overlapping DNA fragments followed by post-synthetic determination of gene molecular weight. [47][48][49][50][51][52] This approach is wellsuited for generating libraries of minimal consensus repeat proteins with varying numbers of tandem repeats. Recursive directional ligation involves the construction of modular genes that are iteratively assembled using compatible but non-regenerable restriction sites.…”

Section: Introductionmentioning

confidence: 99%

Monomer‐scale design of functional protein polymers using consensus repeat sequences

Chang

Huang

Danielle

2021

Journal of Polymer Science

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Protein-based polymers possess chemically defined sequences that can encode diverse properties and functions into a new class of biopolymeric materials.However, sequence variation that emerges from evolution can obscure the sequence-function relationships of naturally derived polymers. One strategy to clarify these relationships is to identify common sequences between proteins with similar functions. These conserved sequences often emerge from repeat proteins, and "consensus repeat sequences" provide a convenient platform for systematic investigations of biopolymer sequence-property relationships. In this review, we highlight recent approaches to engineer tunable polymeric materials using monomer-scale design of consensus repeat proteins. We explore established and emerging protein-based materials with mechanical resilience, thermodynamic phase behavior, chemical responsiveness, biomolecular transport, and hierarchical structure. Overall, recent advances in the monomer-scale design of repetitive protein polymers present exciting fundamental and translational opportunities for polymer scientists and engineers.

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Living Supramolecular Polymerization of DNA

Cited by 8 publications

References 33 publications

Robust nucleation control via crisscross polymerization of highly coordinated DNA slats

Robust nucleation control via crisscross polymerization of highly coordinated DNA slats

DNA‐Based Materials Inspired by Natural Extracellular DNA

Monomer‐scale design of functional protein polymers using consensus repeat sequences

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