Leveraging DNA Origami to Study Phagocytosis Miller, Wyatt D; Kern, Nadja; Douglas, Shawn M ...
Methods in molecular biology (Clifton, N.J.),
2023, Letnik:
2654
Journal Article
Many plasma membrane receptors and ligands form nanoscale clusters on the plasma membrane surface. However, methods for directly and precisely manipulating nanoscale protein localization are limited, ...making understanding the effects of this clustering difficult. DNA origami allows precise control over nanoscale protein localization with high fidelity and adaptability. Here, we describe how we have used this technique to study how nanoscale protein clustering affects phagocytosis. We provide protocols for conjugating DNA origami structures to supported lipid bilayer-coated beads to assay phagocytosis and planar glass coverslips for TIRF microscopy. The core aspects of this protocol can be translated to study other immune signaling pathways and should enable the implementation of previously inaccessible investigations.
DNA nanostructures with programmable nanoscale patterns has been achieved in the past decades, and molecular information coding (MIC) on those designed nanostructures has gained increasing attention ...for information security. However, achieving steganography and cryptography synchronously on DNA nanostructures remains a challenge. Herein, we demonstrated MIC in a reconfigurable DNA origami domino array (DODA), which can reconfigure intrinsic patterns but keep the DODA outline the same for steganography. When a set of keys (DNA strands) are added, the cryptographic data can be translated into visible patterns within DODA. More complex cryptography with the ASCII code within a programmable 6×6 lattice is demonstrated to demosntrate the versatility of MIC in the DODA. Furthermore, an anti‐counterfeiting approach based on conformational transformation‐mediated toehold strand displacement reaction is designed to protect MIC from decoding and falsification.
The DNA Code: A novel steganography and cryptography molecular information coding (MIC) strategy in a reconfigurable DNA origami domino array (DODA) is demonstrated. This strategy opens new opportunities for high‐density information storage and information security against decoding, duplication, and forgery, overcoming the key difficulties in MIC technologies.
DNA Origami: The Art of Folding DNA Saccà, Barbara; Niemeyer, Christof M.
Angewandte Chemie (International ed.),
January 2, 2012, Letnik:
51, Številka:
1
Journal Article
Recenzirano
The advent of DNA origami technology greatly simplified the design and construction of nanometer‐sized DNA objects. The self‐assembly of a DNA‐origami structure is a straightforward process in which ...a long single‐stranded scaffold (often from the phage M13mp18) is folded into basically any desired shape with the help of a multitude of short helper strands. This approach enables the ready generation of objects with an addressable surface area of a few thousand nm2 and with a single “pixel” resolution of about 6 nm. The process is rapid, puts low demands on experimental conditions, and delivers target products in high yields. These features make DNA origami the method of choice in structural DNA nanotechnology when two‐ and three‐dimensional objects are desired. This Minireview summarizes recent advances in the design of DNA origami nanostructures, which open the door to numerous exciting applications.
Know when to fold ′em: As in the ancient art of paper folding, where a single sheet of paper is modeled into beautiful shapes, DNA origami technology allows nanoscale‐addressable objects to be created from one single strand of DNA (see picture).
Molecular chirality is a geometric property that is of great importance in chemistry, biology, and medicine. Recently, plasmonic nanostructures that exhibit distinct chiroptical responses have ...attracted tremendous interest, given their ability to emulate the properties of chiral molecules with tailored and pronounced optical characteristics. However, the optical chirality of such human‐made structures is in general static and cannot be manipulated postfabrication. Herein, different concepts to reconfigure the chiroptical responses of plasmonic nano‐ and micro‐objects are outlined. Depending on the utilized strategies and stimuli, the chiroptical signature, the 3D structural conformation, or both can be reconfigured. Optical devices based on plasmonic nanostructures with reconfigurable chirality possess great potential in practical applications, ranging from polarization conversion elements to enantioselective analysis, chiral sensing, and catalysis.
The chiroptical response of artificial metal nanostructures can be manipulated postfabrication. Different approaches to reconfigure the chiroptical spectral signature, the structural conformation of the plasmonic systems, or both, are presented. The discussed concepts have the potential to serve as key elements in future optical systems and chiral sensing.
3D DNA Origami Crystals Zhang, Tao; Hartl, Caroline; Frank, Kilian ...
Advanced materials (Weinheim)
30, Številka:
28
Journal Article
Recenzirano
Odprti dostop
3D crystals assembled entirely from DNA provide a route to design materials on a molecular level and to arrange guest particles in predefined lattices. This requires design schemes that provide high ...rigidity and sufficiently large open guest space. A DNA‐origami‐based “tensegrity triangle” structure that assembles into a 3D rhombohedral crystalline lattice with an open structure in which 90% of the volume is empty space is presented here. Site‐specific placement of gold nanoparticles within the lattice demonstrates that these crystals are spacious enough to efficiently host 20 nm particles in a cavity size of 1.83 × 105 nm3, which would also suffice to accommodate ribosome‐sized macromolecules. The accurate assembly of the DNA origami lattice itself, as well as the precise incorporation of gold particles, is validated by electron microscopy and small‐angle X‐ray scattering experiments. The results show that it is possible to create DNA building blocks that assemble into lattices with customized geometry. Site‐specific hosting of nano objects in the optically transparent DNA lattice sets the stage for metamaterial and structural biology applications.
A DNA‐origami‐based triangle structure assembles into a 3D rhombohedral crystalline lattice. The accurate assembly of the DNA origami lattice itself as well as the precise incorporation of gold particles is demonstrated by electron microscopy and small‐angle X‐ray scattering experiments.
The chiral state of a molecule plays a crucial role in molecular recognition and biochemical reactions. Because of this and owing to the fact that most modern drugs are chiral, the sensitive and ...reliable detection of the chirality of molecules is of great interest to drug development. The majority of naturally occurring biomolecules exhibit circular dichroism (CD) in the UV range. Theoretical studies and several experiments have demonstrated that this UV-CD can be transferred into the plasmonic frequency domain when metal surfaces and chiral biomolecules are in close proximity. Here, we demonstrate that the CD transfer effect can be drastically enhanced by placing chiral molecules, here double-stranded DNA, inside a plasmonic hotspot. By using different particle types (gold, silver, spheres, and rods) and by exploiting the versatility of DNA origami, we were able to systematically study the impact of varying particle distances on the CD transfer efficiency and to demonstrate CD transfer over the whole optical spectrum down to the near-infrared. For this purpose, nanorods were also placed upright on DNA origami sheets, forming strong optical antennas. Theoretical models, demonstrating the intricate relationships between molecular chirality and achiral electric fields, support our experimental findings. From both experimental measurements and theoretical considerations, we conclude that the transferred CD is most intensive for systems with strong plasmonic hotspots, as we find them in relatively small gaps (5–12 nm) between spherical nanoparticles and preferably between the tips of nanorods.
DNA nanotechnology allows for the creation of three-dimensional structures at nanometer scale. Here, we use DNA to build the largest synthetic pore in a lipid membrane to date, approaching the ...dimensions of the nuclear pore complex and increasing the pore-area and the conductance 10-fold compared to previous man-made channels. In our design, 19 cholesterol tags anchor a megadalton funnel-shaped DNA origami porin in a lipid bilayer membrane. Confocal imaging and ionic current recordings reveal spontaneous insertion of the DNA porin into the lipid membrane, creating a transmembrane pore of tens of nanosiemens conductance. All-atom molecular dynamics simulations characterize the conductance mechanism at the atomic level and independently confirm the DNA porins’ large ionic conductance.
Application of DNA origami in nanobiomedicine Wang, J; Zhang, P; Xia, Q ...
Nan fang yi ke da xue xue bao = Journal of Southern Medical University,
06/2021, Letnik:
41, Številka:
6
Journal Article
Metallic nanocube ensembles exhibit tunable localized surface plasmon resonance to induce the light manipulation at the subwavelength scale. Nevertheless, precisely control anisotropic metallic ...nanocube ensembles with relative spatial directionality remains a challenge. Here, we report a DNA origami based nanoprinting (DOBNP) strategy to transfer the essential DNA strands with predefined sequences and positions to the surface of the gold nanocubes (AuNCs). These DNA strands ensured the specific linkages between AuNCs and gold nanoparticles (AuNPs) that generating the stereo‐controlled AuNC‐AuNP nanostructures (AANs) with controlled geometry and composition. By anchoring the single dye molecule in hot spot regions, the dramatic enhanced electromagnetic field aroused stronger surface enhanced Raman scattering (SERS) signal amplification. Our approach opens the opportunity for the fabrication of stereo‐controlled metal nanostructures for designing highly sensitive photonic devices.
DNA origami‐based nanoprinting can transfer DNA strands with predefined sequences and positions to gold nanocube surfaces to create the stereo‐controlled metallic nanostructures with controlled geometry and composition. By anchoring the single dye molecule in hot spot regions, the dramatic enhanced electromagnetic field aroused stronger SERS signal amplification.
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