Charge Neutralization Drives the Shape Reconfiguration of DNA Nanotubes

Pi, Li; Zhao, Yan; Liu, Xiaoguo; Sun, Jixue; Xu, Dede; Li, Yang; Li, Qian; Wang, Lihua; Yang, Sichun; Chen, Fan; Lin, Jianping

doi:10.1002/anie.201801498

Cited by 26 publications

(35 citation statements)

References 38 publications

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“…SAXS data first suggested an unexpected slight deformation of TDN structures in solution. By fitting the SAXS data with a combination of normal mode analysis (NMA) and fast-SAXS-pro program, 28,29 we found that the revised TDN molecular structure showed a slight twist, which matched well with the experimental results (c 2 = 7.1, Figures 3A and 3B). The average distance between two base pair increased from 3.40 to 3.55 Å , suggesting stretching of DNA molecules due to their intrinsic elasticity.…”

Section: Saxs and MD Analysis Of The Mechanism For Cap Crystallizationsupporting

confidence: 77%

“…The data were further analyzed by ATASAS 2.7.2 package and Fast-SAXS-Pro. 29 Briefly, the fitting was achieved by initially performing NMA sampling on MD-generated models, and then structural energy minimization, followed by evaluation via goodness-of-fit (denoted by c 2 ) between theoretical and experimental scattering data, where each theoretical SAXS curve was calculated by fast-SAXS-pro, which specially accounts for the hydration characteristic of DNA. The fitting results were also validated by CRYSOL and FoXS.…”

Section: Saxs Characterizationmentioning

confidence: 99%

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DNA Framework-Encoded Mineralization of Calcium Phosphate

Liu

Jing

et al. 2020

Chem

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Calcium phosphate (CaP) nanocrystals with prescribed geometric structures are constructed using various DNA frameworks as templates. Synchrotron small angle X-ray scattering (SAXS) data reveal the initial crystallization process by DNA frameworks. Further experimental studies and theoretical calculations demonstrate that by encoding DNA frameworks via sequence design, one can rationally control the size and shape of CaP nanostructures. These preliminary findings would enlighten the design and applications of DNA framework-encoded biomimetic mineralization and organic-inorganic composite materials.

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Section: Saxs and MD Analysis Of The Mechanism For Cap Crystallizationsupporting

confidence: 77%

Section: Saxs Characterizationmentioning

confidence: 99%

DNA Framework-Encoded Mineralization of Calcium Phosphate

Liu

Jing

et al. 2020

Chem

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“…In summary, we carried out an in situ structural determination of segmented DNA nanotubes through joint experimental and theoretical studies. In particular, our pioneering SAXS studies on assembled DNA nanotubes have provided useful information for the study of DNA nanostructures with conformations more complex than those investigated in previous SAXS studies on uniform DNA nanostructures . This work should also shed light on programmable length control of various DNA nanotubes.…”

Section: Methodsmentioning

confidence: 85%

In‐Situ Configuration Studies on Segmented DNA Origami Nanotubes

et al. 2019

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One-dimensional nanotubes are of considerable interest in materials and biochemical sciences.Aparticular desire is to create DNA nanotubes with user-defined structural features and biological relevance, which will facilitate the application of these nanotubes in the controlled release of drugs,t emplating of other materials into linear arrays and the construction of artificial membrane channels. However,l ittle is knowna bout the structures of assembled DNA nanotubes in solution.H ere we report an in situ exploration of segmented DNA nanotubes, composed of multiple units with set length distributions, by using synchrotron small-angle X-ray scattering (SAXS). Through joint experimental and theoretical studies, we show that the SAXS data are highly informativei nt he context of heterogeneous mixtures of DNA nanotubes. The structural parameters obtained by SAXS are in good agreement with those determined by atomicf orce microscopy (AFM), transmission electron microscopy (TEM), andd ynamic light scattering (DLS). In particular,t he SAXS data revealed important structurali nformation on these DNA nanotubes, such as the in-solution diameters ( % 25 nm), which could be obtained only with difficulty by use of other methods. Our resultsestablish SAXS as areliable structural analysism ethod for long DNA nanotubes and could assist in the rational design of these structures.Genetically encoded nanotubes made from biomacromolecules, such as cytoskeletal filaments, [1] channeling protein nanotubes, [2] and membrane channels, [3] are critical cellular components. They provide structural support for intracellular transport, intercellularc ommunication, and transmembrane ion/molecule channeling. [4,5] Inspired by the natural protein nanotubes widely encountered in vivo, in vitro construction of biomimetic DNA nanotubes has attracted growing interest with the development of structuralD NA nanotechnology. [6][7][8][9][10] In general, at ypical DNA nanotube can be fabricated either by parallel alignmento fD NA duplexes or throughw rapping of DNA tile lattices. [11][12][13] These biomimetic DNA nanotubes have shown great potentiali nawide number of areas, such as cargo delivery, [14] templated arrangement of other materials, artificial membrane channels, and nanoscale reaction containers.Although severalD NA nanotubes have been successfully createdb yu sing rational design, little is knowna bout their structures in solution.C urrently employed characterization methods generally rely on atomic force microscopy (AFM) or transmission electron microscopy (TEM), [15][16][17][18][19] which cannoti nterprett he in situ status of DNA nanotubes very well. Synchrotron small-angle X-ray scattering (SAXS), however,has emerged as ap owerful tool for in situ analysis of DNA nanostructures, especially for DNA nanotubes. SAXS has been used to study the interhelical spacingo fa24-helixb undle of DNA origami and the globalt wisting of planar DNA origami into nanotubes. [20,21] Further,t he positioning of chiral gold nanoparticles (AuNPs) decorated on ...

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“…A ligand‐controlled transporter was demonstrated by using DNA strand displacement to control the opening and closing of a DNA nanopore (Figure h). [21a] Liu et al used charge neutralization to drive the shape reconfiguration of a biomimetic DNA nanochannel . Fisher et al used DNA nanopores to confine and organize disordered nucleoporins that mimicked the central transport channel of nuclear pore complexes .…”

Section: Dna Nanostructures‐confined Lipid Membrane and Transportersmentioning

confidence: 99%

Biomimetic Compartments Scaffolded by Nucleic Acid Nanostructures

Monckton

et al. 2019

Small

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The behaviors of living cells are governed by a series of regulated and confined biochemical reactions. The design and successful construction of synthetic cellular reactors can be useful in a broad range of applications that will bring significant scientific and economic impact. Over the past few decades, DNA self‐assembly has enabled the design and fabrication of sophisticated 1D, 2D, and 3D nanostructures, and is applied to organizing a variety of biomolecular components into prescribed 2D and 3D patterns. In this Concept, the recent and exciting progress in DNA‐scaffolded compartmentalizations and their applications in enzyme encapsulation, lipid membrane assembly, artificial transmembrane nanopores, and smart drug delivery are in focus. Taking advantage of these features promises to deliver breakthroughs toward the attainment of new synthetic and biomimetic reactors.

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Charge Neutralization Drives the Shape Reconfiguration of DNA Nanotubes

Cited by 26 publications

References 38 publications

DNA Framework-Encoded Mineralization of Calcium Phosphate

DNA Framework-Encoded Mineralization of Calcium Phosphate

In‐Situ Configuration Studies on Segmented DNA Origami Nanotubes

Biomimetic Compartments Scaffolded by Nucleic Acid Nanostructures

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