Themed collection Emerging concepts in nucleic acids: structures, functions and applications

Dhiraj Bhatia, Prabal Kumar Maiti, Xiaogang Liu and Arun Richard Chandrasekaran introduce the Nanoscale, Nanoscale Advances and Physical Chemistry Chemical Physics (PCCP) themed collection on DNA and RNA nanotechnology.

DNA computing has emerged as a promising alternative to achieve programmable behaviors in chemistry by repurposing the nucleic acid molecules into chemical hardware upon which synthetic chemical programs can be executed.

DNA-PAINT imaging crucially depends on efficient labeling probes, and this article presents a comprehensive coverage on the variety of binders, various labelling chemistries, and DNA sequence pairs employed for its implementation.

In this minireview, we summarized the recent progress of controllable reconfigurations of complex DNA nanostructures induced by nucleic acid strands, environmental stimuli and enzymatic treatments.

Schematic representation of the effect of nucleases on the stability of a DNA structure, which is shown to break along the edges. This article reviews the uptake of DNA nanostructures into mammalian cells for therapeutic interventions.

The COVID-19 pandemic has emphasized the need for accurate, quick, and portable diagnostic devices at the point of care. First, we reviewed the history of nucleic acid diagnostics, its current state, and an outlook for future developments.

This minireview summarizes the recent advances in stimuli-responsive nucleic acid nanostructures for efficient drug delivery in response to endogenous and exogenous stimuli (redox gradient, pH, nuclease, biomacromolecule, and light).

As an efficient class of hydrogel-based therapeutic drug delivery systems, deoxyribonucleic acid (DNA) hydrogels (particularly DNA nanogels) have attracted massive attention in the last five years.

This review summarizes recent nano-templating approaches based on the combination of DNA and peptides, including strategies to control interactions with biological systems and the use of DNA-peptide conjugates for the generation of new biomaterials.

Since its inception nearly 40 years ago [Kallenbach, et al., Nature, 1983, 305, 829; N. C. Seeman, J. Theoretical Biology, 1982, 99, 237], Nucleic Acid Nanotechnology (NAN) has matured and is beginning to find commercial applications.

A supramolecular approach for the design of assembly–disassembly-driven ¹⁹F ON/OFF nanoparticles, triggered by specific molecular recognition, for the detection of DNA binding cancer biomarkers is reported.

Optimal image reconstruction is an open problem in the field of imaging-by-sequencing. We implement an algorithm that is scalable and robust to different network types by using structural discovery.

Using force tracing and nano-indentation techniques based on atomic force microscopy, the promoting effect of Tf on T7-modified nano-drug transport was investigated at a single-particle and single-cell level in real time.

Flipping bases in-or-out allows DNA nanostructures to continuously morph.

Using fluorescent labelling, graphical inputs in 8-bit monochrome format can be copied as DNA microarrays in 256 colours with high fidelity. This effort highlights the versatility of in situ microarray photolithography for surface patterning.

A highly modular, 4 h-long ‘recombinase amplified CRISPR enhanced chain reaction’ (RACECAR) assay that can detect as little as 40 copies of hepatitis B virus (HBV) genome has been developed.

Sphingomyelin nanoemulsions were covalently conjugated with apMNK2F using a 2-step bioconjugation process. They demonstrated effective intracellular delivery, outperforming free aptamer, resulting in decreased breast cancer cell proliferation.

Gold nanoparticles conjugated with an aptamer are used to stain bacteria cells captured on a filter membrane for total bacterial count measurement.

Simple coarse-grained model with long-range electrostatic interactions providing a nanoscale picture of DNA aggregation–redissolution behaviours controlled by protamine-DNA charge ratios and protamine length in low-salt regime.

We investigated the efficacy of a novel 2D metal oxide-based optical biosensor related to ss-DNA. This study opens the door to the creation of quick, affordable, and highly sensitive diagnostic biosensors to identify a range of pathogenic diseases.

Electrochemical detection of Cu(II) using -PDA- and Au NP mediated DNAzyme activity enhancement.

Ability to control charge transfer in DNA has profound implications in DNA-based electronics for biosensing, data storage and sequencing. We show that the arrangement of bases and their interactions with the Au substrate are critical in tuning the coupling between orbitals.

Top: Schematic of DNA-caged nanoparticle composite formation. Bottom: U87 cells labeled with fluorescent DNA-caged nanoparticles before and after erasing with single stranded DNA. Scale bar = 10 μm.

Redox properties of DNA strands depend on the balance between intramolecular and intermolecular charge delocalization.

Microneedle Arrays (MNAs) can be tunably and electrostatically coated with combinations of adjuvants. Upon treatment, these needles elicit tunable immune cell responses.

Nanopore devices based on graphene and h-BN heterostructures show outstanding electrical and physical characteristics for high throughput label-free DNA sequencing.

In this work, we describe the development of a computational model for arrays of rotary DNA origami elements which can self-organize on a large scale and explore the interesting morphologies and order–disorder transition behavior of these systems.

Dimeric cyanostilbenes exhibit contrasting fluorescence responses towards heparin (emission enhancement) and DNA (emission quenching). Furthermore, efficient light-harvesting systems were fabricated by exploiting the heparin-based co-assemblies.

By tuning the ionic conditions, plus-shaped, blunt-ended DNA-origami lattices are driven to self-assemble elongated, ordered structures: adding Ni²⁺ triggers the formation of ribbon-shaped 2D-lattices, which roll into 3D-tubes at higher Ni²⁺ concentrations.

Three-dimensional DNA nanocages have attracted significant attention for various biomedical applications including targeted bioimaging in vivo.

We introduce a new DNA-based approach to systematically investigate the bulk properties of crosslinked semiflexible DNA-based polymer networks as a model for natural biopolymer networks, by stepwise altering the binding affinity of the crosslinkers.

Here we proposed a new strategy combining the nanopore series circuit and the current clamp to get the voltage trace across the nanopore, hence producing a voltage blockade signal when DNA translocate. This signal exhibits an intriguing charging and discharging phenomenon.

Design of G-Quadruplex based plasmonic sensor has been demonstrated for the specific SERS based detection of single Thioflavin T molecule using DNA origami-assembled Au nanobipyramid nanoantenna.

OWL2 sensor uses T2 and T4 arms for unwinding folded analytes, short P-strand for specific recognition of single base variations and an analyte-independent universal molecular beacon (UMB) probe for cost efficient analysis of any ssDNA or RNA.

Combining experimental and computational design, the length and flexibility of wireframe DNA nanotubes are modulated with minimal design alterations.

Terpyridine Zn(II) complex has good AIE and three-photon absorption activity, and the ultra-bright fluorescence induced by the aggregation state of Zn complex can assist the multi-photon and super-resolution imaging of nuclear RNA.

We present the self-assembly of DNA nanostars having three, four and five arms into a gel phase using a bead-spring coarse-grained model.

DNA sequences of ideal and natural geometries are examined, studying their charge transport properties as mutation detectors.

Our work focuses on the structural and energetic analysis of promoters and exon–intron boundaries within DNA using Molecular Dynamics simulation-based parameters mapped over trinucleotides and tetranucleotides.

Controlling exciton coupling in DNA templated dye aggregates is achieved by modifying sterics and hydrophobicity of Cy5-R dyes (varying the 5,5′-substituents). We conclude that sterics play the main role in orientation and coupling strength.

Using a reconfigurable DNA origami device, we study the bending of DNA by a bending protein. To this end, we used transmission electron microscopy to directly observe the structural reconfiguration of the origami devices caused by the protein.

The intercalation of the chemotherapeutic drug terpyridine-platinum within the G-quadruplex structure of DNA sensitizes cancer cells to the low energy electrons produced by ionizing radiation during radiotherapy.

Cell behavior is determined by a variety of properties of the extracellular environment like ligand spacing, nanotopography, and matrix stiffness.

Nucleic acids and lipids function in close proximity in biological processes, as well as in nanoengineered constructs for therapeutic applications.

A self-assembled block copolymer is used to create nanoscale arrays of gold dots for selective self-assembly of DNA origami and directed placement of gold nanorods for nanoelectronics applications.

We present the functionalization of a model DNA cage, tetrahedron with a cationic lipid, DOTMA; demonstrating enhancement in cellular uptake of DNA nanocages by minimizing the negative charge and increasing hydrophobic surface mediated internalization.

Schematic diagram of a new method for analyzing interactions between DNA and its ligands based on surface-enhanced Raman spectroscopy (SERS) combined with molecular dynamics simulations.

This work presents the developed a multi-component DNA origami 6-bar mechanism that can be assembled into tubes with reconfigurable cross-sections, bridging complex shape transformations of DNA devices to micron-scale assemblies.

An intelligent, autocatalytic, DNAzyme biocircuit based on a CD/AM nanodevice was constructed for precise sensing and logical calculation of intracellular microRNAs.

By use of colloidal stamps, several functional DNA patches were patterned at the surface of particles. The produced DNA-patchy particles are ideal candidates to act as advanced designer building blocks to self-assemble next generation materials.

DNA epigenetic modification 5-formylcytosine (^5fC) confers unique and specific conformational changes to duplex DNA.

The study of biologically relevant molecules and their interaction with external stimuli on a single molecular scale is of high importance due to the availability of distributed rather than averaged information.

Sustainable antibacterial hydrogel from hybridization mediated self-assembly of DNA Quantum Dot and genomic DNA extracted from onion.

Parallel DNA circuits are constructed using autocatalytic strand displacement reactions and measured using a nanopore multiplexed sensing platform.

While polyvalent metal ions and heating can both degrade nucleic acids, we herein report that a combination of them leads to stabilization.

The self-assembly of colloidal diamond (CD) crystals is considered as one of the most coveted goals of nanotechnology, both from the technological and fundamental points of view.

DNA-assisted selective electrofusion (DASE) combines the efficiency of standard electrofusion with the selectivity of DNA-mediated interactions. Here we apply DASE to induce the fusion between giant lipid vesicles and E. coli derived spheroplasts.