Lipid‐Bilayer‐Spanning DNA Nanopores with a Bifunctional Porphyrin Anchor

Burns, Jonathan R.; Göpfrich, Kerstin; Wood, James W.; Thacker, Vivek V.; Stulz, Eugen; Keyser, Ulrich F.; Howorka, Stefan

doi:10.1002/anie.201305765

Cited by 200 publications

(275 citation statements)

References 54 publications

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“…9,14,19,24 The potential of mediating the assembly of nucleic acid objects on a surface has recently been exploited by using chemically modified nucleic acids that are bound or grafted to a solid surface or a bilayer. 25–34 This opens up new possibilities to use biomolecules to construct functional nanostructured surfaces with applications in, for example, bio analytical and diagnostic devices. However, previous studies mainly involve hybridization of short modified DNA or RNA oligomers, e.g.…”

Section: Introductionmentioning

confidence: 99%

Assembly of RNA nanostructures on supported lipid bilayers

et al. 2015

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The assembly of nucleic acid nanostructures with controlled size and shape has large impact in the fields of nanotechnology, nanomedicine and synthetic biology. The directed arrangement of nanostructures at interfaces is important for many applications. In spite of this, the use of laterally mobile lipid bilayers to control RNA three-dimensional nanostructure formation on surfaces remains largely unexplored. Here, we direct the self-assembly of RNA building blocks into three-dimensional structures of RNA on fluid lipid bilayers composed of cationic 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) or mixtures of zwitterionic 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) and cationic sphingosine. We demonstrate the stepwise supramolecular assembly of discrete building blocks through specific and selective RNA-RNA interactions, based on results from quartz crystal microbalance with dissipation (QCM-D), ellipsometry, fluorescence recovery after photobleaching (FRAP) and total internal reflection fluorescence microscopy (TIRF) experiments. The assembly can be controlled to give a densely packed single layer of RNA polyhedrons at the fluid lipid bilayer surface. We show that assembly of the 3D structure can be modulated by sequence specific interactions, surface charge and changes in the salt composition and concentration. In addition, the tertiary structure of the RNA polyhedron can be controllably switched from an extended structure to one that is dense and compact. The versatile approach to building up three-dimensional structures of RNA does not require modification of the surface or the RNA molecules, and can be used as a bottom-up means of nanofabrication of functionalized bio-mimicking surfaces.

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Section: Introductionmentioning

confidence: 99%

Assembly of RNA nanostructures on supported lipid bilayers

et al. 2015

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“…[2] Because of the endogenous nature and high programmability of DNA, self-assembled DNA nanotubes have attracted intense interest. [3] These DNA nanotubes, when appropriately modified, can be readily inserted into membranes [4] to function as biomimetic channels. Molecular dynamics (MD) simulations have also revealed interesting properties, [5] including ion flow and gating-like behaviors in these DNA-based nanochannels.…”

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confidence: 99%

Charge Neutralization Drives the Shape Reconfiguration of DNA Nanotubes

Zhao

Liu

et al. 2018

Angew Chem Int Ed

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Reconfiguration of membrane protein channels for gated transport is highly regulated under physiological conditions. However, a mechanistic understanding of such channels remains challenging owing to the difficulty in probing subtle gating-associated structural changes. Herein, we show that charge neutralization can drive the shape reconfiguration of a biomimetic 6-helix bundle DNA nanotube (6HB). Specifically, 6HB adopts a compact state when its charge is neutralized by Mg2+; whereas Na+ switches it to the expanded state, as revealed by MD simulations, small-angle X-ray scattering (SAXS), and FRET characterization. Furthermore, partial neutralization of the DNA backbone charges by chemical modification renders 6HB compact and insensitive to ions, suggesting an interplay between electrostatic and hydrophobic forces in the channels. This system provides a platform for understanding the structure-function relationship of biological channels and designing rules for the shape control of DNA nanostructures in biomedical applications.

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“…Two porphyrin-based hydrophobic tags also anchored negatively charged DNA nanostructure (artificial transmembrane channel) into the hydrophobic core of lipid bilayers. 375 Furthermore, a membrane-spanning DNA nanopore was prepared also from a bundle of six DNA duplexes which were folded from six DNA strands. 376 This hollow nanobarrel had a channel width of approximately 2 nm, the outer diameter 5.5 nm, and the height 14 nm.…”

Section: Determination Of Dna Nanostructures In Solutionsmentioning

confidence: 99%

Chemistry Can Make Strict and Fuzzy Controls for Bio-Systems: DNA Nanoarchitectonics and Cell-Macromolecular Nanoarchitectonics

Komiyama

Yoshimoto

Sisido

et al. 2017

Bulletin of the Chemical Society of Japan

275

131

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In this review, we introduce two kinds of bio-related nanoarchitectonics, DNA nanoarchitectonics and cellmacromolecular nanoarchitectonics, both of which are basically controlled by chemical strategies. The former DNA-based approach would represent the precise nature of the nanoarchitectonics based on the strict or "digital" molecular recognition between nucleic bases. This part includes functionalization of single DNAs by chemical means, modification of the main-chain or side-chain bases to achieve stronger DNA binding, DNA aptamers and DNAzymes. It also includes programmable assemblies of DNAs (DNA Origami) and their applications for delivery of drugs to target sites in vivo, sensing in vivo, and selective labeling of biomaterials in cells and in animals. In contrast to the digital molecular recognition between nucleic bases, cell membrane assemblies and their interaction with macromolecules are achieved through rather generic and "analog" interactions such as hydrophobic effects and electrostatic forces. This cell-macromolecular nanoarchitectonics is discussed in the latter part of this review. This part includes bottom-up and top-down approaches for constructing highly organized cell-architectures with macromolecules, for regulating cell adhesion pattern and their functions in twodimension, for generating three-dimensional cell architectures on micro-patterned surfaces, and for building synthetic/natural macromolecular modified hybrid biointerfaces.

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Lipid‐Bilayer‐Spanning DNA Nanopores with a Bifunctional Porphyrin Anchor

Abstract: Holding tight: An artificial membrane nanopore assembled from DNA oligonucleotides carries porphyrin tags (red), which anchor the nanostructure into the lipid bilayer. The porphyrin moieties also act as fluorescent dyes to aid the microscopic visualization of the DNA nanopore.

Cited by 200 publications

References 54 publications

Assembly of RNA nanostructures on supported lipid bilayers

Assembly of RNA nanostructures on supported lipid bilayers

Charge Neutralization Drives the Shape Reconfiguration of DNA Nanotubes

Chemistry Can Make Strict and Fuzzy Controls for Bio-Systems: DNA Nanoarchitectonics and Cell-Macromolecular Nanoarchitectonics

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