Toward Precise Manipulation of DNA–Protein Hybrid Nanoarchitectures

Abstract

Nucleic acids and proteins are the two primary building materials of living organisms. Over the past decade, artificial DNA–protein hybrid structures have been pursued for a wide range of applications. DNA nanotechnology, in particular, has dramatically expanded nanoscale molecule engineering and contributed to the spatial arrangement of protein components. Strategies for designing site‐specific coupling of DNA oligomers to proteins are needed in order to allow for precise control over stoichiometry and position. Efforts have also been focused on coassembly of protein–DNA complexes by engineering their fundamental molecular recognition interactions. This Concept focuses on the precise manipulation of DNA–protein nanoarchitectures. Particular attention is paid to site‐selectivity within DNA–protein conjugates, regulation of protein orientation using DNA scaffolds, and coassembly principles upon unique structural motifs. Current challenges and future directions are also discussed in the design and application of DNA–protein nanoarchitectures.

Molecular goniometers for single-particle cryo-electron microscopy of DNA-binding proteins

“…In principle, RNAs can bind to the DNA stage directly via hybridization, or by docking to RNA-binding moieties that attach to the DNA stage. In addition to studying natural targets, our goniometers may be useful for de novo design of small DNA-binding proteins to enable and accelerate the molecular design of hybrid architectures 18 , such as DNA origami structures decorated with proteins that carry out binding or catalysis.…”

DNA Origami-Enabled Biosensors

“…Later, DNA origami-based nanostructure gradually turned to application fields. In addition, there are some excellent reviews that summarize the advancement of DNA origami in application, such as in precise manipulation of chemical and enzymatic reactions, assembly of plasmonic antennas, drug delivery, biocomputing, three-dimensional lattice engineering of nanoparticles (NPs), nanofabrication in surface engineering [22][23][24][25][26][27] and so on. This review covers several signal readout strategies that are widely used in DNA origami-enabled biosensors and presents the sensing mechanism, potential, and challenge in practical application.…”

Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering

“…"HUH-tag" fusion proteins are emerging as a versatile bioconjugation platform to covalently link proteins to DNA, combining the diverse functionality of proteins with the programmability of DNA 4 . HUH-tag applications have permeated into technologies such as DNA origami scaffolded protein assembly [5][6][7][8] , receptor-specific cell targeting by adeno-associated virus 9 , aptamer-based sandwich detection 10 , directed nanoparticle drug-delivery via DNA aptamers 11 , and CRISPR-Cas9 genome engineering 12,13 , mainly due to their ability to form robust covalent adducts under physiologic conditions. Rather than relying on expensive nucleic acid modifications such as the SNAP-tag 14 , CLIP-tag 15 , and Halo-tag 16 systems, HUH-tags rely on an inherent ssDNA binding moiety that promotes the catalysis of a transesterification reaction resulting in a stable phosphotyrosine adduct 1 .…”