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Review
, 11, 124-140
eCollection

Molecular Architectonics of DNA for Functional Nanoarchitectures

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Review

Molecular Architectonics of DNA for Functional Nanoarchitectures

Debasis Ghosh et al. Beilstein J Nanotechnol.

Abstract

DNA is the key biomolecule central to almost all processes in living organisms. The eccentric idea of utilizing DNA as a material building block in molecular and structural engineering led to the creation of numerous molecular-assembly systems and materials at the nanoscale. The molecular structure of DNA is believed to have evolved over billions of years, with structure and stability optimizations that allow life forms to sustain through the storage and transmission of genetic information with fidelity. The nanoscale structural characteristics of DNA (2 nm thickness and ca. 40-50 nm persistence length) have inspired the creation of numerous functional patterns and architectures through noncovalent conventional and unconventional base pairings as well as through mutual templating-interactions with small organic molecules and metal ions. The recent advancements in structural DNA nanotechnology allowed researchers to design new DNA-based functional materials with chemical and biological properties distinct from their parent components. The modulation of structural and functional properties of hybrid DNA ensembles of small functional molecules (SFMs) and short oligonucleotides by adapting the principles of molecular architectonics enabled the creation of novel DNA nanoarchitectures with potential applications, which has been termed as templated DNA nanotechnology or functional DNA nanoarchitectonics. This review highlights the molecular architectonics-guided design principles and applications of the derived DNA nanoarchitectures. The advantages and ability of functional DNA nanoarchitectonics to overcome the trivial drawbacks of classical DNA nanotechnology to fulfill realistic and practical applications are highlighted, and an outlook on future developments is presented.

Keywords: DNA nanotechnology; functional DNA nanoarchitectonics; functional small molecules; molecular architectonics; nucleic acids; templated coassembly.

Figures

Figure 1
Figure 1
Illustration of conventional (WC) and unconventional (non-WC) hydrogen bonding interactions between the nucleobases to form canonical (DNA duplex) and noncanonical hybrid DNA ensembles through the assembly of DNA or DNA with SFMs/metal ions. The brick image has been adopted with permission from [17], copyright 2012 American Association for the Advancement of Science.
Figure 2
Figure 2
Molecular design and engineering of DNA nanoarchitectures using different types of DNA modules. The 2D DNA origami, hollow 3D DNA origami, single-stranded tile assembly, and lattice structures are adopted with permission from [37], copyright 2018 Wiley and Sons. The DNA double-crossover foundation and holiday junction structure have been reproduced with permission from [8], copyright 2016 Royal Society of Chemistry, [34], copyright 1993 American Chemical Society. The DNA nanorobot structure has been adopted with permission from [9], copyright 2012 American Association for the Advancement of Science. The first image on the left side of drug and gene delivery has been adopted with permission from [53], copyright 2012 American Chemical Society.
Figure 3
Figure 3
Schematic representation of DNA tetrahedron-based electroluminescence biosensor platforms. The image has been adapted with permission from [69], copyright 2017 American Chemical Society.
Figure 4
Figure 4
a) Schematic representation of mutually templated double-helical zipper assemblies of APA and dBn (B: nucleobases T, A, or G; n =10, 20) via canonical and noncanonical hydrogen bonding interactions. b) pH-dependent CD measurement of double-helical zipper ensembles. c) AFM image of double-helical zipper assembly nanofiber dT20–(APA)20–dT20 and its height profile data (5 nm, inset), typical thickness 4.5 nm. Fig. 4–c has been adapted with permission from [18], copyright 2015 Royal Society of Chemistry.
Figure 5
Figure 5
a) Mutually templated coassembly of BNA and dTn (n = 6, 10, 20) to form a BNAn–dTn hybrid ensemble, and displacement of BNA from Hg(II), followed by the formation of a metallo-DNA duplex. b) FESEM images of 2D nanoarchitectures (nanosheets) of BNAn–dTn coassembly and 1D tapes of BNA. c) Schematic representation of a FET device of BNAn–dTn fabricated for conductometric sensing of Hg(II) with ultrasensitive sensitivity (0.1 nM, 0.02 ppb). Fig. 5–c has been adapted with permission from [20], copyright 2016 American Chemical Society.
Figure 6
Figure 6
Molecular structures of nucleobase-tethered NDI molecules (NDI-AA and NDI-TT) and their assembly, coassembly, and templated coassembly with PNA clamps. Adapted with permission from [75], copyright 2013 Royal Society of Chemistry.
Figure 7
Figure 7
a) Zn(II)-cyclen-tethered NDI and DPP SFMs. b) DPP–dT40 and NDI–dT40 multichromophore arrays over a gold electrode via coimmobilizing donor–acceptor units. c) Random assembly of a DPP–NDI–dT40 multichromophore array over a gold electrode. d) Formation of a metallo-DNA duplex through T–Hg(II)–T interactions, maintaining the 2:1 molar ratio of T and Hg(II). Fig. 7–c has been adapted with permission from [84], copyright 2015 Wiley and Sons, and Fig. 7 has been adapted from [86], copyright 2006 American Chemical Society.
Figure 8
Figure 8
a) Schematic representation of a porphyrin-appended DNA nanopore base lipid anchor. b) AFM image of a nanopore assembly. c) Schematic design of a membrane-spanning porphyrin-tagged DNA duplex. d) Fluorescence confocal image highlighting the interaction of porphyrin-tethered DNA with lipid membrane. e) Molecular dynamics simulation to analyze steady-state local densities of porphyrin–DNA-anchored lipid chains and their current flow. Fig. 8 and Fig. 8 were adapted from [93], distributed under a Creative Commons Attribution license, copyright 2013 by the authors. Fig. 8–e was adapted with permission from [94], copyright 2016 American Chemical Society.

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