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Nucleic acids are emerging as powerful and functional biomaterials due to their molecular recognition ability, programmability, and ease of synthesis and chemical modification. Various types of nucleic acids have been used as gene regulation tools or therapeutic agents for the treatment of human diseases with genetic disorders. Nucleic acids can also be used to develop sensing platforms for detecting ions, small molecules, proteins, and cells. Their performance can be improved through integration with other organic or inorganic nanomaterials. To further enhance their biological properties, various chemically modified nucleic acid analogues can be generated by modifying their phosphodiester backbone, sugar moiety, nucleobase, or combined sites. Alternatively, using nucleic acids as building blocks for self-assembly of highly ordered nanostructures would enhance their biological stability and cellular uptake efficiency. In this review, we will focus on the development and biomedical applications of structural and functional natural nucleic acids, as well as the chemically modified nucleic acid analogues over the past ten years. The recent progress in the development of functional nanomaterials based on self-assembled DNA-based platforms for gene regulation, biosensing, drug delivery, and therapy will also be presented. We will then summarize with a discussion on the advanced development of nucleic acid research, highlight some of the challenges faced and propose suggestions for further improvement.

Targeted transcriptional modulation in the central nervous system (CNS) can be achieved by adeno-associated virus (AAV) delivery of CRISPR activation (CRISPRa) and interference (CRISPRi) transgenes. To enable AAV packaging, we constructed minimal CRISPRa and CRISPRi transgenes by fusing catalytically inactive Staphylococcus aureus Cas9 (dSaCas9) to the transcriptional activator (VP64 and VP160) and repressor (KRAB and SID4X) domains along with truncated regulatory elements. We then evaluated the performance of these constructs in two reporter assays (bioluminescent and fluorescent), five endogenous genes (Camk2a, Mycn, Nrf2, Keap1, and PDGFRA), and two cell lines (neuro-2a [N2a] and U87) by targeting the promoter and/or enhancer regions. To enable systemic delivery of AAVs to the CNS, we have also generated an AAV1-PHP.B by inserting a 7-mer PHP.B peptide on AAV1 capsid. We showed that AAV1-PHP.B can efficiently cross the blood-brain barrier (BBB) and be taken up by the brain tissue upon lateral tail vein injection in mice. Importantly, a single-dose intravenous administration of AAV1-PHP.B expressing CRISPRa was shown to achieve targeted transgene activation in the mouse brain. This proof-of-concept study will contribute to the development of a non-invasive, specific and potent AAV-CRISPR system for correcting transcriptional misregulation in broad brain areas and multiple neuroanatomical structures., Graphical Abstract

Time-resolved fluorescence is a widely adopted technique for DNA detection due to its high sensitivity and selectivity. However, due to stringent requirements on optics and electronics, instrumentation with time-resolved capability is bulky and expensive, prohibiting their use in portable and point-of-care applications. In this work, a fully-integrated DNA biosensor based on liquid-core waveguide (LCW) optics for fluorescence lifetime analysis is presented. The DNA biosensor encompasses all-custom bioassay, optics and electronics into a microsystem, delivering a near sample-to-answer level of integration. Lifetime, rather than intensity, is exploited as the analytical signal from the V-carbazole probe for the first time. Excitation propagation within the LCW is investigated both analytically and in simulations to achieve high excitation rejection and low temporal dispersion, enabling the proposed LCW-based system with much smaller instrumentation size to deliver comparable lifetime measurement accuracy to traditional systems. Detection of DNA down to 15 base pairs at a low detection limit of 1.38 nM demonstrates the high applicability of the proposed biosensor for compact, application-specific, and low-cost diagnostics devices.

Guanine tracts of human telomeric DNA sequences are known to fold into eight different four-stranded structures that vary by the conformation of guanine nucleotides arranged in the stack of G-tetrads in their core and by different kinds and orders of connecting loops, called G-quadruplexes. Here, we present a novel G-quadruplex structure formed in K+ solution by a human telomeric variant d[(GGGTTA)2GGGTTTGGG], htel21T18. This variant DNA is located in the subtelomeric regions of human chromosomes 8, 11, 17, and 19 as well as in the DNase hypersensitive region and in the subcentromeric region of chromosome 5. Interestingly, single A18T substitution that makes htel21T18 different from the human telomeric sequence results in the formation of a three-layer chair-type G-quadruplex, a fold previously unknown among human telomeric repeats, with two loops interacting through the reverse Watson–Crick A6·T18 base pair. The loops are edgewise; glycosidic conformation of guanines is syn·anti·syn·anti around each tetrad, and each strand of the core has two antiparallel adjacent strands. Our results expand the repertoire of known G-quadruplex folding topologies and may provide a potential target for structure-based anticancer drug design.

Fabrication of DNA/Quantum Dot (QD) complexes making use of electrostatic adsorption forces has advantages of the cost-efficiency and simplicity. To obtain aggregation-free complexes, high molecular weight polymers or the purposefully designed ligands are commonly employed as a bridge between DNA and QDs, which limits their applications in practice. In this work, DNA/QDs complexes were obtained using electrostatic adsorption between cysteamine stabilized CdTe QDs and self-assembled DNA nanocages. Zeta potential, dynamic light scattering and gel electrophoresis measurements demonstrated their aggregation-free state, different from the cases where single-stranded and double-stranded DNAs were used. The appearance of aggregation-free complexes in the case of DNA nanocages was ascribed to their 3D rigid structure. Forster resonance energy transfer (FRET) was demonstrated for the complexes of Cy3 labeled DNA nanocages and QDs, pointing out on the close proximity of these building blocks.

A DNA tetrahedron as the most classical and simplest three-dimensional DNA nanostructure has been widely utilized in biomedicine and biosensing. However, the existing assembly approaches usually require harsh thermal annealing conditions, involve the formation of unwanted by-products, and have poor size control. Herein, a facile strategy to fabricate a discrete DNA tetrahedron as a single, thermodynamically stable product in a quantitative yield at room temperature is reported. This system does not require a DNA trigger or thermal annealing treatment to initiate self-assembly. This DNA tetrahedron was made of three chemically ligated triangular-shaped DNAs in unconventional ladder-like arrangements, with measured heights of ∼4.16 ± 0.04 nm, showing extra protections for enzymatic degradation in biological environment. They show substantial cellular uptake in different cell lines via temperature, energy-dependent and clathrin-mediated endocytosis pathways. These characteristics allow our DNA tetrahedron to be used as vehicles for the delivery of very small and temperature-sensitive cargos. This novel assembly strategy developed for DNA tetrahedra could potentially be extended to other highly complex polyhedra; this indicated its generalizability.

The rapidly emerging DNA nanotechnology began with pioneer Seeman’s hypothesis that DNA not only can carry genetic information but also can be used as molecular organizer to create well-designed and controllable nanomaterials for applications in materials science, nanotechnology, and biology. DNA-based self-assembly represents a versatile system for nanoscale construction due to the well-characterized conformation of DNA and its predictability in the formation of base pairs. The structural features of nucleic acids form the basis of constructing a wide variety of DNA nanoarchitectures with well-defined shapes and sizes, in addition to controllable permeability and flexibility. More importantly, self-assembled DNA nanostructures can be easily functionalized to construct artificial functional systems with nanometer scale precision for multipurposes. Apparently scientists envision artificial DNA-based nanostructures as tool for drug loading andin vivotargeted delivery because of their abilities in selective encapsulation and stimuli-triggered release of cargo. Herein, we summarize the strategies of creating multidimensional self-assembled DNA nanoarchitectures and review studies investigating their stability, toxicity, delivery efficiency, loading, and control release of cargos in addition to their site-specific targeting and delivery of drug or cargo molecules to cellular systems.

We demonstrate an all-optical method for magnetic sensing of individual molecules in ambient conditions at room temperature. Our approach is based on shallow nitrogen-vacancy (NV) centers near the surface of a diamond crystal, which we use to detect single paramagnetic molecules covalently attached to the diamond surface. The manipulation and readout of the NV centers is all-optical and provides a sensitive probe of the magnetic field fluctuations stemming from the dynamics of the electronic spins of the attached molecules. As a specific example, we demonstrate detection of a single paramagnetic molecule containing a gadolinium (Gd$^{3+}$) ion. We confirm single-molecule resolution using optical fluorescence and atomic force microscopy to co-localize one NV center and one Gd$^{3+}$-containing molecule. Possible applications include nanoscale and in vivo magnetic spectroscopy and imaging of individual molecules.

Correlative light and electron microscopy promises to combine molecular specificity with nanoscale imaging resolution. However, there are substantial technical challenges including reliable co-registration of optical and electron images, and rapid optical signal degradation under electron beam irradiation. Here, we introduce a new approach to solve these problems: imaging of stable optical cathodoluminescence emitted in a scanning electron microscope by nanoparticles with controllable surface chemistry. We demonstrate well-correlated cathodoluminescence and secondary electron images using three species of semiconductor nanoparticles that contain defects providing stable, spectrally-distinguishable cathodoluminescence. We also demonstrate reliable surface functionalization of the particles. The results pave the way for the use of such nanoparticles for targeted labeling of surfaces to provide nanoscale mapping of molecular composition, indicated by cathodoluminescence colour, simultaneously acquired with structural electron images in a single instrument.

A novel series of monodisperse, multi-dipolar zigzag oligoaryleneethynylenes DA(n) and D-Ar-A(n), bearing electron-donating dibenzothiophene and electron-accepting dibenzothiophene dioxide as arenes, with up to six charge-transfer (dipolar) units have been designed and synthesized by palladium-catalyzed Sonogashira coupling reactions. The linear and nonlinear optical properties of these multi-dipolar oligoaryleneethynylenes can easily be modified or enhanced by incorporating/extending with various central aryleneethynyl moieties such as phenylethynyl, oligo(9,9-dibutylfluorenyl)ethynyl, and oligothienylethynyl within the donor-acceptor units. Interestingly, the absorption and emission of these zigzag oligoaryleneethynylenes are not dependent on the number of covalently linked dipolar chromophores; however, the fluorescence quantum efficiencies consistently decrease with increased number of covalently linked dipolar units. These zigzag oligoaryleneethynylenes exhibit a linear increase in the two-photon absorption (TPA) cross-sections with increased number of covalently linked dipolar units without red-shifting the absorption and emission spectra. In addition, very large TPA cross-sections in the femtosecond regime (sigma(800) = 1306 GM in DMF or sigma(750) = 1522 GM in CH(2)Cl(2)) were obtained for D-TF-A(4) despite the moderate strength of the donor-acceptor pair. Our results suggest that the TPA properties of these zigzag oligoaryleneethynylenes including TPA wavelength and TPA cross-section can easily be tuned by means of modifying the central aryleneethynylene units and increasing the number of dipolar units, respectively. This approach provides an alternative means to tune or enhance the TPA cross-section at a specific wavelength.

A novel series of oligophenylene OPP(n)-substituted calix[4]crown-4s bearing up to three phenylene units, 1a-d, has been efficiently synthesized by means of either microwave-assisted or silver(I) ion-assisted Pd-catalyzed Suzuki cross-coupling of tetraiodocalix[4]crown-4 and the corresponding oligophenylboronic acids. Complexation of OPP(n)-substituted calix[4]crown-4s with silver (I) ion was substantiated by 1H NMR spectroscopic and high-resolution ESI- or MALDI-TOF- MS studies. The weak binding affinities of OPP(n)-substituted calix[4]crown-4s for silver (I) ion, which were estimated from 1H NMR titrations with binding association in the range of 30-90 M(-1), allows reversible disassembling in the presence of KI at ambient temperature. Remarkably, the single-crystal X-ray structures of OPP(n)-calix[4]crown-4.Ag+ complexes indicate the atypical silver (I) ion-crown ether binding mode resulting in the formation of rigid nanocones with volume created up to approximately 1500 A(3). Our results suggested that despite the weak binding affinity of crown ether ligands for silver (I) ion, this weak interaction is still be useful as a tool to construct supramolecular architectures.

[reaction: see text] A facile and efficient protocol for the synthesis of oligophenylene OPP(n)-substituted calix[4]arenes (with n up to 4) via iodo-substituted oligoarylcalix[4]arenes has been developed. The cooperation effect of the proximate fluoroionophores in hexylsulfanyl end-capped OPP(n)-substituted calix[4]arene assemblies leads to metal ion binding enhancement.