Building machines with DNA molecules

Ramezani, Hamid; Dietz, Hendrik

doi:10.1038/s41576-019-0175-6

Cited by 250 publications

(225 citation statements)

References 169 publications

(232 reference statements)

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“…rogrammable self-assembly with DNA is a route to nanofabrication [1][2][3][4][5][6][7][8] with applications emerging in a variety of fields 9,10 . The self-assembly reactions of such objects can yield monodisperse products 11 and the underlying design concepts in principle enable specifying target structures with chemical accuracy on the level of single bases, within objects designed to contain several thousand bases.…”

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confidence: 99%

Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution

et al. 2020

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The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is folded by many short DNA oligonucleotides, can be employed to make objects comprising hundreds of unique DNA strands and thousands of base pairs, thus in principle providing many degrees of freedom for modelling complex objects of defined 3D shapes and sizes. Here, we address the problem of accurate structural validation of DNA objects in solution with cryo-EM based methodologies. By taking into account structural fluctuations, we can determine structures with improved detail compared to previous work. To interpret the experimental cryo-EM maps, we present molecular-dynamics-based methods for building pseudo-atomic models in a semi-automated fashion. Among other features, our data allows discerning details such as helical grooves, single-strand versus double-strand crossovers, backbone phosphate positions, and single-strand breaks. Obtaining this higher level of detail is a step forward that now allows designers to inspect and refine their designs with base-pair level interventions.

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Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution

et al. 2020

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“…Comparing this to silicon-based computation, although many challenges in designing computation devices, aptamer-based hydrogels logic circuits are still developing with great rapidity, due to their stability, biocompatibility, and predictable structure (143)(144)(145)(146). Yin et al (147) exploited a hydrogel structure based on hybridization behavior between crosslinker strands with aptamer sequences of ATP and cocaine molecules onto polymer chains.…”

Section: Aptamer-based Hydrogels For Logic Devicesmentioning

confidence: 99%

“…Schematic Illustration of the four-input concatenated logic gates based on target-catalyzed DNA four-way junctions. Reprinted with permission from Ramezani and Dietz(143). Copyright (2015) American Chemical Society.…”

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Design, Bioanalytical, and Biomedical Applications of Aptamer-Based Hydrogels

Wang

et al. 2020

Front. Med.

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Aptamers are special types of single-stranded DNA generated by a process called systematic evolution of ligands by exponential enrichment (SELEX). Due to significant advances in the chemical synthesis and biotechnological production, aptamers have gained considerable attention as versatile building blocks for the next generation of soft materials. Hydrogels are high water-retainable materials with a three-dimensional (3D) polymeric network. Aptamers, as a vital element, have greatly expanded the applications of hydrogels. Due to their biocompatibility, selective binding, and molecular recognition, aptamer-based hydrogels can be utilized for bioanalytical and biomedical applications. In this review, we focus on the latest strategies of aptamer-based hydrogels in bioanalytical and biomedical applications. We begin this review with an overview of the underlying design principles for the construction of aptamer-based hydrogels. Next, we will discuss some bioanalytical and biomedical applications of aptamer-based hydrogel including biosensing, target capture and release, logic devices, gene and cancer therapy. Finally, the recent progress of aptamer-based hydrogels is discussed, along with challenges and future perspectives.

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“…The DNA origami folding method [40][41][42][43] takes advantage of the unique and inherent building properties of DNA molecules, and has proven to be an extremely versatile engineering tool, 44,45 especially when combined to model membranes. [46][47][48][49][50][51] Seminal studies recently granted us better overview on how to efficiently attach cholesteryl-modified DNA origami to membranes 52,53 and investigate diffusion.…”

Section: Introductionmentioning

confidence: 99%