Emerging Biomimetic Applications of DNA Nanotechnology

Green synthesis of zinc oxide nanoparticles using Cnidium monnieri fruit extract: Prescription optimization, Characterization and antifungal activity

Currently, the drugs employed to treat superficial fungal infections are encountering challenges, particularly the rise of drug resistance. Numerous studies have suggested that zinc oxide nanoparticles (ZnO NPs) show promise in the realm of antifungal treatment. Green synthesis makes the preparation of ZnO NPs more environmentally friendly and economical. In order to prepare antifungal active nanoparticles with low economic cost and stable performance, zinc oxide nanoparticles (CM-ZnONPs) were synthesized for the first time in this study using zinc sulfate heptahydrate (ZnSO4·7H2O) with a Cnidium monnieri (L.) Cuss. (C. monnieri) fruit extract as a reducing agent. In this study, the Box-Behnken design method was used to optimize the manufacturing process of CM-ZnONP. Various techniques, including UV-vis, Fourier Transform Infrared Spectroscopy (FTIR) and X-ray Powder Diffraction (XRD) were employed to demonstrate the successful preparation of CM-ZnONPs. The Transmission Electron Microscopy (TEM) analysis indicated that the size of CM-ZnONPs was 53.30 ± 12.89 nm. The dynamic light scattering (DLS) analysis showed the size of 157.7 ± 15.57 nm for CM-ZnONPs, along with an average polydispersity index (PDI) of 0.1791 ± 0.1394. The zone of inhibition of CM-ZnONPs against Candida albicans (C. albicans) was demonstrated to be 17.0 ± 0.8 mm by paper diffusion experiments. The minimum inhibitory concentration (MIC) of CM-ZnONPs against C. albicans was established at 58.59 μg/mL through the microdilution method. In summary, CM-ZnONPs exhibit excellent performance and antifungal activity in various properties. It is expected to be widely produced and used as an effective treatment for superficial fungal infections.

Nature-inspired innovations: unlocking the potential of biomimicry in bionanotechnology and beyond

Bionanotechnology research has surged to the forefront of scientific innovation, propelling the exploration of cutting-edge technologies and interdisciplinary collaboration. Biomimicry, which harnesses nature's ingenuity, drives the development of novel research-based solutions in diverse fields such as vaccines, medicine, and biomedical devices. Nature's role is becoming increasingly pivotal in addressing complex challenges related to environmental conservation, human health, and pandemic preparedness, including those posed by SARS-CoV-2 and other emerging pathogens. Progress in this domain encompasses understanding nature´s mechanisms to develop advanced materials inspired by biological structures. Biomimetic innovations have the potential to revolutionize industries, reduce environmental impacts, and facilitate a more harmonious relationship between humans and nature while considering bioethics, underlining the necessity of conducting responsible research and implementing biomimetic advancements conscientiously. As biomimicry continues to grow, integrating ethical guidelines and policies will ensure these nature-inspired technologies' sustainable development and application, ultimately contributing to a more resilient and adaptive society. This mini-review article broadly overviews bionanotechnology applications based on natural examples.

Research progress of nanoparticles in diagnosis and treatment of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is among the most common malignant liver tumors. Despite progress in anticancer drugs and surgical approaches, early detection of HCC remains challenging, often leading to late-stage diagnosis where rapid disease progression precludes surgical intervention, leaving chemotherapy as the only option. However, the systemic toxicity, low bioavailability, and significant adverse effects of chemotherapy drugs often lead to resistance, rendering treatments ineffective for many patients. This article outlines how nanoparticles, following functional modification, offer high sensitivity, reduced drug toxicity, and extended duration of action, enabling precise targeting of drugs to HCC tissues. Combined with other therapeutic modalities and imaging techniques, this significantly enhances the diagnosis, treatment, and long-term prognosis of HCC. The advent of nanomedicine provides new methodologies and strategies for the precise diagnosis and integrated treatment of HCC.

Polymerase-Based Signal Delay for Temporally Regulating DNA Involved Reactions, Programming Dynamic Molecular Systems, and Biomimetic Sensing

Complex temporal molecular signals play a pivotal role in the intricate biological pathways of living organisms, and cells exhibit the ability to transmit and receive information by intricately managing the temporal dynamics of their signaling molecules. Although biomimetic molecular networks are successfully engineered outside of cells, the capacity to precisely manipulate temporal behaviors remains limited. In this study, the catalysis activity of isothermal DNA polymerase (DNAP) through combined use of molecular dynamics simulation analysis and fluorescence assays is first characterized. DNAP-driven delay in signal strand release ranged from 100 to 102 min, which is achieved through new strategies including the introduction of primer overhangs, utilization of inhibitory reagents, and alteration of DNA template lengths. The results provide a deeper insight into the underlying mechanisms of temporal control DNAP-mediated primer extension and DNA strand displacement reactions. Then, the regulated DNAP catalysis reactions are applied in temporal modulation of downstream DNA-involved reactions, the establishment of dynamic molecular signals, and the generation of barcodes for multiplexed detection of target genes. The utility of DNAP-based signal delay as a dynamic DNA nanotechnology extends beyond theoretical concepts and achieves practical applications in the fields of cell-free synthetic biology and bionic sensing.

Structures and dynamics of 8-oxo-7,8-dihydro-2'-deoxyguanosine in neutral and basic aqueous solutions by spectroscopy

8-oxo-7,8-dihydro-2'-dexyoguanine (8-oxo-dG) can be tautomerized to a 6-enolate,8-keto tautomer through nearby-NH deprotonation at elevated pH. In this work, the N3-protonated 8-oxo-dG tautomers in deuterated pH-buffer solutions were studied using steady-state UV/Vis, FTIR, and ultrafast two-dimensional IR spectroscopies. The presence of 6,8-diketo and C6-anionic tautomers at neutral to basic conditions (pD = 7.4-12.0) was revealed by UV/Vis and FTIR results and was further confirmed by 2D IR signals in both diagonal and off-diagonal regions. However, the C6-enol tautomer, which may be an intermediate during the transition from 6,8-diketo to C6-enolate,C8-keto, was not observed appreciably due to its extreme low population. Furthermore, the neutral-to-anionic tautomeric transition of N3H-8-oxo-dG studied in this work occurs under more basic conditions than the N1H-8-oxo-dG reported previously, showing a higher pKa value for N3H than N1H. Finally, vibrational relaxation of the carbonyl stretching mode was found to be both molecular site dependent and pD dependent for 8oxo-dG. Taken together, this work shows that the ultrafast infrared spectroscopic method is effective for examining tautomers and their dynamics in nucleic acids.

Self-Replicating DNA-Based Nanoassemblies

The properties of DNA that make it an effective genetic material also allow it to be ideal for programmed self-assembly. Such DNA-programmed assembly has been utilized to construct responsive DNA origami and wireframe nanoassemblies, yet replicating these hybrid nanomaterials remains challenging. Here we report a strategy for replicating DNA wireframe nanoassemblies using the isothermal ligase chain reaction lesion-induced DNA amplification (LIDA). We designed a triangle wireframe structure that can be formed in one step by ring-closing of its linear analog. Introducing a small amount of the wireframe triangle to an excess of the linear analog and complementary fragments, one of which contains a destabilizing abasic lesion, leads to rapid, sigmoidal self-replication of the wireframe triangle via cross-catalysis. Using the same cross-catalytic strategy we also demonstrate rapid self-replication of a hybrid wireframe triangle containing synthetic vertices as well as the self-replication of circular DNA. This work reveals the suitability of isothermal ligase chain reactions such as LIDA to self-replicate complex DNA architectures, opening the door to incorporating self-replication, a hallmark of life, into biomimetic DNA nanotechnology.

Assembly and optically triggered disassembly of lipid-DNA origami fibers

The co-assembly of lipids and other compounds has recently gained increasing interest. Here, we report the formation of stimuli-responsive lipid-DNA origami fibers through the electrostatic co-assembly of cationic lipids and 6-helix bundle (6HB) DNA origami. The photosensitive lipid degrades when exposed to UV-A light, which allows a photoinduced, controlled release of the 6HBs from the fibers. The presented complexation strategy may find uses in developing responsive nanomaterials e.g. for therapeutics.

Sensing and manipulating single lipid vesicles using dynamic DNA nanotechnology

Natural and artificial lipid vesicles have been widely involved in nano-delivery, bio-analysis and diagnosis. For sensing and manipulating single lipid vesicles, dynamic DNA reactions were constructed inside or on the surface of lipid vesicles. In this review, we interpreted various ways of integrating lipid vesicles and dynamic DNA nanotechnology by summarizing the latest reports in bio-analysis and biomimetic cell research.

Biomimetic cell membrane-coated poly(lactic-co-glycolic acid) nanoparticles for biomedical applications

Poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) are commonly used for drug delivery because of their favored biocompatibility and suitability for sustained and controlled drug release. To prolong NP circulation time, enable target-specific drug delivery and overcome physiological barriers, NPs camouflaged in cell membranes have been developed and evaluated to improve drug delivery. Here, we discuss recent advances in cell membrane-coated PLGA NPs, their preparation methods, and their application to cancer therapy, management of inflammation, treatment of cardiovascular disease and control of infection. We address the current challenges and highlight future research directions needed for effective use of cell membrane-camouflaged NPs.

Interplay of the mechanical and structural properties of DNA nanostructures determines their electrostatic interactions with lipid membranes

Nucleic acids and lipids function in close proximity in biological processes, as well as in nanoengineered constructs for therapeutic applications. As both molecules carry a rich charge profile, and frequently coexist in complex ionic solutions, the electrostatics surely play a pivotal role in interactions between them. Here we discuss how each component of a DNA/ion/lipid system determines its electrostatic attachment. We examine membrane binding of a library of DNA molecules varying from nanoengineered DNA origami through plasmids to short DNA domains, demonstrating the interplay between the molecular structure of the nucleic acid and the phase of lipid bilayers. Furthermore, the magnitude of DNA/lipid interactions is tuned by varying the concentration of magnesium ions in the physiologically relevant range. Notably, we observe that the structural and mechanical properties of DNA are critical in determining its attachment to lipid bilayers and demonstrate that binding is correlated positively with the size, and negatively with the flexibility of the nucleic acid. The findings are utilized in a proof-of-concept comparison of membrane interactions of two DNA origami designs - potential nanotherapeutic platforms - showing how the results can have a direct impact on the choice of DNA geometry for biotechnological applications.

Modulation of Biofilm Mechanics by DNA Structure and Cell Type

Deoxyribonucleic acid (DNA) evolved as a tool for storing and transmitting genetic information within cells, but outside the cell, DNA can also serve as “construction material” present in microbial biofilms or various body fluids, such as cystic fibrosis, sputum, and pus. In the present work, we investigate the mechanics of biofilms formed from Pseudomonas aeruginosa Xen 5, Staphylococcus aureus Xen 30, and Candida albicans 1408 using oscillatory shear rheometry at different levels of compression and recreate these mechanics in systems of entangled DNA and cells. The results show that the compression-stiffening and shear-softening effects observed in biofilms can be reproduced in DNA networks with the addition of an appropriate number of microbial cells. Additionally, we observe that these effects are cell-type dependent. We also identify other mechanisms that may significantly impact the viscoelastic behavior of biofilms, such as the compression-stiffening effect of DNA cross-linking by bivalent cations (Mg²⁺, Ca²⁺, and Cu²⁺) and the stiffness-increasing interactions of P. aeruginosa Xen 5 biofilm with Pf1 bacteriophage produced by P. aeruginosa. This work extends the knowledge of biofilm mechanobiology and demonstrates the possibility of modifying biopolymers toward obtaining the desired biophysical properties.

Orthogonal Enzyme-Driven Timers for DNA Strand Displacement Reactions

Here, we demonstrate a strategy to rationally program a delayed onset of toehold-mediated DNA strand displacement reactions (SDRs). The approach is based on blocker strands that efficiently inhibit the strand displacement by binding to the toehold domain of the target DNA. Specific enzymatic degradation of the blocker strand subsequently enables SDR. The kinetics of the blocker enzymatic degradation thus controls the time at which the SDR starts. By varying the concentration of the blocker strand and the concentration of the enzyme, we show that we can finely tune and modulate the delayed onset of SDR. Additionally, we show that the strategy is versatile and can be orthogonally controlled by different enzymes each specifically targeting a different blocker strand. We designed and established three different delayed SDRs using RNase H and two DNA repair enzymes (formamidopyrimidine DNA glycosylase and uracil-DNA glycosylase) and corresponding blockers. The achieved temporal delay can be programed with high flexibility without undesired leak and can be conveniently predicted using kinetic modeling. Finally, we show three possible applications of the delayed SDRs to temporally control the ligand release from a DNA nanodevice, the inhibition of a target protein by a DNA aptamer, and the output signal generated by a DNA logic circuit.

Prospects and challenges of dynamic DNA nanostructures in biomedical applications

The physicochemical nature of DNA allows the assembly of highly predictable structures via several fabrication strategies, which have been applied to make breakthroughs in various fields. Moreover, DNA nanostructures are regarded as materials with excellent editability and biocompatibility for biomedical applications. The ongoing maintenance and release of new DNA structure design tools ease the work and make large and arbitrary DNA structures feasible for different applications. However, the nature of DNA nanostructures endows them with several stimulus-responsive mechanisms capable of responding to biomolecules, such as nucleic acids and proteins, as well as biophysical environmental parameters, such as temperature and pH. Via these mechanisms, stimulus-responsive dynamic DNA nanostructures have been applied in several biomedical settings, including basic research, active drug delivery, biosensor development, and tissue engineering. These applications have shown the versatility of dynamic DNA nanostructures, with unignorable merits that exceed those of their traditional counterparts, such as polymers and metal particles. However, there are stability, yield, exogenous DNA, and ethical considerations regarding their clinical translation. In this review, we first introduce the recent efforts and discoveries in DNA nanotechnology, highlighting the uses of dynamic DNA nanostructures in biomedical applications. Then, several dynamic DNA nanostructures are presented, and their typical biomedical applications, including their use as DNA aptamers, ion concentration/pH-sensitive DNA molecules, DNA nanostructures capable of strand displacement reactions, and protein-based dynamic DNA nanostructures, are discussed. Finally, the challenges regarding the biomedical applications of dynamic DNA nanostructures are discussed.

Green porous benzamide-like nanomembranes for hazardous cations detection, separation, and concentration adjustment

Green biomaterials play a crucial role in the diagnosis and treatment of diseases as well as health-related problem-solving. Typically, biocompatibility, biodegradability, and mechanical strength are requirements centered on biomaterial engineering. However, in-hospital therapeutics require an elaborated synthesis of hybrid and complex nanomaterials capable of mimicking cellular behavior. Accumulation of hazardous cations like K+ in the inner and middle ear may permanently damage the ear system. We synthesized nanoplatforms based on Allium noeanum to take the first steps in developing biological porous nanomembranes for hazardous cation detection in biological media. The 1,1,1-tris[[(2'-benzyl-amino-formyl)phenoxy]methyl]ethane (A), 4-amino-benzo-hydrazide (B), and 4-(2-(4-(3-carboxy-propan-amido)benzoyl)hydrazineyl)-4-oxobutanoic acid (B1) were synthesized to obtain green ligands based on 4-X-N-(…(Y(hydrazine-1-carbonyl)phenyl)benzamide, with X denoting fluoro (B2), methoxy (B3), nitro (B4), and phenyl-sulfonyl (B5) substitutes. The chemical structure of ligand-decorated adenosine triphosphate (ATP) molecules (S-ATP) was characterized by FTIR, XRD, AFM, FESEM, and TEM techniques. The cytotoxicity of the porous membrane was patterned by applying different cell lines, including HEK-293, PC12, MCF-7, HeLa, HepG2, and HT-29, to disclose their biological behavior. The morphology of cultured cells was monitored by confocal laser scanning microscopy. The sensitivity of S-ATP to different cations of Na+, Mg2+, K+, Ba2+, Zn2+, and Cd2+ was evaluated by inductively coupled plasma atomic emission spectroscopy (ICP-AES) in terms of extraction efficiency (η). For pH of 5.5, the η of A-based S-ATP followed the order Na+ (63.3%) > Mg2+ (62.1%) > Ba2+ (7.6%) > Ca2+ (5.5%); while for pH of 7.4, Na+ (37.0%) > Ca2+ (33.1%) > K+ (25.7%). The heat map of MTT and dose-dependent evaluations unveiled acceptable cell viability of more than 90%. The proposed green porous nanomembranes would pave the way to use multifunctional green porous nanomembranes in biological membranes.

DNA Nanodevice as a Co-delivery Vehicle of Antisense Oligonucleotide and Silver Ions for Selective Inhibition of Bacteria Growth

DNA nanostructures possess unique programmability and addressability and exhibit a wide variety of potential applications. Recently, they demonstrated their ability to be ideal carriers of antibacterial drugs. In this study, the first use of a DNA six-helix bundle (6HB) nanostructure to co-deliver antisense oligonucleotide (ASO) and silver ions is reported. Although 6HB with Ag⁺ shows excellent antibacterial effect against both Gram-negative Escherichia coli and Gram-positive Staphylococcus aureus, 6HB with ASO selectively inhibits S. aureus. Furthermore, 6HB with both Ag⁺ and ASO exhibits enhanced antibacterial efficacy on S. aureus, probably through two sequential activities. Specifically, Ag⁺-modified 6HB greatly delays bacterial growth by destroying its cell walls, whereas 6HB conjugated with ASO targeting the ftsZ gene of S. aureus effectively inhibits its growth in the logarithmic growth phase by inhibiting the expression of the ftsZ gene. Moreover, this synergistic antibacterial treatment shows excellent biosafety with human normal liver cell L02. This co-delivery system by DNA nanostructures provides a promising platform for antibacterial therapeutics.

Deoxyribonucleic acid anchored on cell membranes for biomedical application

Engineering cellular membranes with functional molecules provides an attractive strategy to manipulate cellular behaviors and functionalities. Currently, synthetic deoxyribonucleic acid (DNA) has emerged as a promising molecular tool to engineer cellular membranes for biomedical applications due to its molecular recognition and programmable properties. In this review, we summarized the recent advances in anchoring DNA on the cellular membranes and their applications. The strategies for anchoring DNA on cell membranes were summarized. Then their applications, such as immune response activation, receptor oligomerization regulation, membrane structure mimicking, cell-surface biosensing, and construction of cell clusters, were listed. The DNA-enabled intelligent systems which were able to sense stimuli such as DNA strands, light, and metal ions were highlighted. Finally, insights regarding the remaining challenges and possible future directions were provided.

Chiral 3D DNA origami structures for ordered heterologous arrays

The DNA origami technique allows the facile design and production of three-dimensional shapes from single template strands of DNA. These can act as functional devices with multiple potential applications but are constrained by practical limitations on size. Multi-functionality could be achieved by connecting together distinct DNA origami modules in an ordered manner. Arraying of non-identical, three-dimensional DNA origamis in an ordered manner is challenging due for example, to a lack of compatible rotational symmetries. Here we show that we can design and build ordered DNA structures using non-identical 3D building blocks by using DNA origami snub-cubes in left-handed and right-handed forms. These can be modified such that one form only binds to the opposite-handed form allowing regular arrays wherein building blocks demonstrate alternating chirality.

Programming cell communications with pH-responsive DNA nanodevices

DNA nanoswitches on cell surfaces could respond to changes of pH under physiological conditions by switching from a three-chain structure to a double-chain structure, thus connecting another set of cells modified with complementary single-stranded DNA. This pH-triggered cell communication offers a promising approach for cell-based therapy under a tumor microenvironment.

Recent Progress of DNA Nanostructures on Amphiphilic Membranes

Employing DNA nanostructures mimicking membrane proteins on artificial amphiphilic membranes have been widely developed to understand the structures and functions of the natural membrane systems. In this review, the recent developments in artificial systems constructed by amphiphilic membranes and DNA nanostructures are summarized. First, the preparations and properties of the amphipathic bilayer models are introduced. Second, the interactions are discussed between the membrane and the DNA nanostructures, as well as their coassembly behaviors. Next, the alternative systems related to membrane protein-mediated signal transmission, selective distribution, transmembrane channels, and membrane fusion are also introduced. Moreover, the constructions of membrane skeleton protein-mimicking DNA nanostructures are also highlighted.

Organizing Multi-Enzyme Systems into Programmable Materials for Biocatalysis

Significant advances in enzyme discovery, protein and reaction engineering have transformed biocatalysis into a viable technology for the industrial scale manufacturing of chemicals. Multi-enzyme catalysis has emerged as a new frontier for the synthesis of complex chemicals. However, the in vitro operation of multiple enzymes simultaneously in one vessel poses challenges that require new strategies for increasing the operational performance of enzymatic cascade reactions. Chief among those strategies is enzyme co-immobilization. This review will explore how advances in synthetic biology and protein engineering have led to bioinspired co-localization strategies for the scaffolding and compartmentalization of enzymes. Emphasis will be placed on genetically encoded co-localization mechanisms as platforms for future autonomously self-organizing biocatalytic systems. Such genetically programmable systems could be produced by cell factories or emerging cell-free systems. Challenges and opportunities towards self-assembling, multifunctional biocatalytic materials will be discussed.

Biocompatible exosomes nanodrug cargo for cancer cell bioimaging and drug delivery

Therapy against cancer remains a daunting issue for human health, despite remarkable innovations in many areas of pathology. In situ biosynthesized nanoclusters bestow a novel remedy for carcinogenic cell imaging. Exosomes have received special attention as an efficient tool for the diagnosis of various diseases, including cancers. All types of cells (healthy or diseased) generate exosomes, making them significantly unique for relevant disease diagnosis and treatment. In this contribution, we exploit the possibility of utilizing the exosomes to facilitate chemotherapeutics, viz. the combination of doxorubicin (Dox) and biosynthesized silver nanoclusters in cancer cells. Our study showed a new facile way for bioimaging of cancer cells using biosynthesized silver-DNA nanoclusters, and thus further targeting cancer cells using the relevant cancer exosomes as drug delivery cargo. After isolating exosomes from neoplastic cells, i.e. HeLa, loaded with the drug, and treating other neoplastic cells with cargo-loaded isolated exosomes, we found that cargo-loaded isolated exosomes can readily enter into the targeted cancer cells and efficiently kill these neoplastic cells. This raises the possibility of acting as a novel facile modality for target cancer theranostics with high efficiency and biocompability.

DNA-Origami-Templated Growth of Multilamellar Lipid Assemblies

Lipids are important building blocks in cellular compartments, and therefore their self-assembly into well-defined hierarchical structures has gained increasing interest. Cationic lipids and unstructured DNA can co-assemble into highly ordered structures (lipoplexes), but potential applications of lipoplexes are still limited. Using scaffolded DNA origami nanostructures could aid in resolving these drawbacks. Here, we have complexed DNA origami together with a cationic lipid 1,2-dioleoly-3-trimethylammonium-propane (DOTAP) and studied their self-assembly driven by electrostatic and hydrophobic interactions. The results suggest that the DNA origami function as templates for the growth of multilamellar lipid structures and that the DNA origami are embedded in the formed lipid matrix. Furthermore, the lipid encapsulation was found to significantly shield the DNA origami against nuclease digestion. The presented complexation strategy is suitable for a wide range of DNA-based templates and could therefore find uses in construction of cell-membrane-associated components.

Light-Controlled, Toehold-Mediated Logic Circuit for Assembly of DNA Tiles

Inspired by cytoskeletal structures that respond sensitively to environmental changes and chemical inputs, we report a strategy to trigger and finely control the assembly of stimulus-responsive DNA nanostructures with light under isothermal conditions. The strategy is achieved via integrating an upstream light-controlled, toehold-mediated DNA strand displacement circuit with a downstream DNA tile self-assembly process. By rationally designing an upstream DNA strand module, we further transform the upstream DNA strand displacement circuit to an "AND gate" circuit to control the assembly of DNA nanostructures. This example represents the demonstration of the spatial and temporal assembly of DNA nanostructures using a noninvasive chemical input. Such a light-controlled DNA logic circuit not only adds a new element to the tool box of DNA nanotechnology but also inspires us to assemble complex and responsive nanostructures.

DNA logic circuits based on FokI enzyme regulation

A series of DNA logic devices was constructed based on the allosteric strategy of the enzyme-assisted cleavage regulation system, which are simple in scale, modular, and work efficiently.

Solid-phase synthesis and structural characterisation of phosphoroselenolate-modified DNA: a backbone analogue which does not impose conformational bias and facilitates SAD X-ray crystallography

Oligodeoxynucleotides incorporating internucleotide phosphoroselenolate linkages have been prepared under solid-phase synthesis conditions using dimer phosphoramidites. These dimers were constructed following the high yielding Michaelis-Arbuzov (M-A) reaction of nucleoside H-phosphonate derivatives with 5'-deoxythymidine-5'-selenocyanate and subsequent phosphitylation. Efficient coupling of the dimer phosphoramidites to solid-supported substrates was observed under both manual and automated conditions and required only minor modifications to the standard DNA synthesis cycle. In a further demonstration of the utility of M-A chemistry, the support-bound selenonucleoside was reacted with an H-phosphonate and then chain extended using phosphoramidite chemistry. Following initial unmasking of methyl-protected phosphoroselenolate diesters, pure oligodeoxynucleotides were isolated using standard deprotection and purification procedures and subsequently characterised by mass spectrometry and circular dichroism. The CD spectra of both modified and native duplexes derived from self-complementary sequences with A-form, B-form or mixed conformational preferences were essentially superimposable. These sequences were also used to study the effect of the modification upon duplex stability which showed context-dependent destabilisation (-0.4 to -3.1 °C per phosphoroselenolate) when introduced at the 5'-termini of A-form or mixed duplexes or at juxtaposed central loci within a B-form duplex (-1.0 °C per modification). As found with other nucleic acids incorporating selenium, expeditious crystallisation of a modified decanucleotide A-form duplex was observed and the structure solved to a resolution of 1.45 Å. The DNA structure adjacent to the modification was not significantly perturbed. The phosphoroselenolate linkage was found to impart resistance to nuclease activity.

Controlling aggregation of cholesterol-modified DNA nanostructures

DNA nanotechnology allows for the design of programmable DNA-built nanodevices which controllably interact with biological membranes and even mimic the function of natural membrane proteins. Hydrophobic modifications, covalently linked to the DNA, are essential for targeted interfacing of DNA nanostructures with lipid membranes. However, these hydrophobic tags typically induce undesired aggregation eliminating structural control, the primary advantage of DNA nanotechnology. Here, we study the aggregation of cholesterol-modified DNA nanostructures using a combined approach of non-denaturing polyacrylamide gel electrophoresis, dynamic light scattering, confocal microscopy and atomistic molecular dynamics simulations. We show that the aggregation of cholesterol-tagged ssDNA is sequence-dependent, while for assembled DNA constructs, the number and position of the cholesterol tags are the dominating factors. Molecular dynamics simulations of cholesterol-modified ssDNA reveal that the nucleotides wrap around the hydrophobic moiety, shielding it from the environment. Utilizing this behavior, we demonstrate experimentally that the aggregation of cholesterol-modified DNA nanostructures can be controlled by the length of ssDNA overhangs positioned adjacent to the cholesterol. Our easy-to-implement method for tuning cholesterol-mediated aggregation allows for increased control and a closer structure-function relationship of membrane-interfacing DNA constructs - a fundamental prerequisite for employing DNA nanodevices in research and biomedicine.

Chemistries for DNA Nanotechnology

The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.

DNA Origami Nanoarrays for Multivalent Investigations of Cancer Cell Spreading with Nanoscale Spatial Resolution and Single-Molecule Control

We present a strategy for the fabrication of biomimetic nanoarrays, based on the use of DNA origami, that permits the multivalent investigation of ligand-receptor molecule interactions in cancer cell spreading, with nanoscale spatial resolution and single-molecule control. We employed DNA origami to control the nanoscale spatial organization of integrin- and epidermal growth factor (EGF)-binding ligands that modulate epidermal cancer cell behavior. By organizing these multivalent DNA nanostructures in nanoarray configurations on nanopatterned surfaces, we demonstrated the cooperative behavior of integrin and EGF ligands in the spreading of human cutaneous melanoma cells: this cooperation was shown to depend on both the number and ratio of the selective ligands employed. Notably, the multivalent biochips we have developed allowed for this cooperative effect to be demonstrated with single-molecule control and nanoscale spatial resolution. By and large, the platform presented here is of general applicability for the study, with molecular control, of different multivalent interactions governing biological processes from the function of cell-surface receptors to protein-ligand binding and pathogen inhibition.

DNA Origami as Seeds for Promoting Protein Crystallization

This study reports the first experimental evidence of DNA origami as a seed resulting in the increase in probability of protein crystallization. Using the DNA origami constructed from long single-stranded M13 DNA scaffolds folded with short single-stranded DNA staples, it was found that the addition of the DNA origami in concentrations of 2-6 nM to mixtures of a well-characterized protein (catalase) solution (1.0-7.0 mg/mL) resulted in a higher proportion of mixtures with successful crystallization, up to 11× greater. The improvement in crystallization is evident particularly for mixtures with low concentrations of catalase (<5 mg/mL). DNA origami in different conformations of a flat rectangular sheet and a tubular hollow cylinder were examined. Both conformations improved the crystallization as compared to control experiments without M13 DNA or nonfolded M13 DNA but exhibited little difference in the extent of protein crystallization improvement. This work confirms the predictions of the potential use of DNA origami to promote protein crystallization, with potential application to systems with limited protein availability or difficulty in crystallization.

Stimuli-Responsive DNA-Switchable Biointerfaces

Switchable interfaces, also known as smart interfaces, can alter their macroscopic properties in response to external stimuli. Compared to an artificial switchable interface, DNA-based switchable biointerfaces have high diversity, uniformity, reproducibility, and functionality and are easily designed and developed with atomic precision because the sequence of the DNA strand strictly governs the structural and active properties of its assembly. Moreover, various structures such as double strands based on the Watson-Crick base-pairing rule, G-quadruplexes, i-Motifs, triplexes, and parallel-stranded duplexes exist between or among DNA strands to enrich the structures of DNA biointerfaces. In this article, the design, stimulus responses, and applications of switchable DNA biointerfaces were discussed in terms of single-switch, dual-response, and sequential operation. The applications related to sensing, imaging, delivery, logic gates, and nanomechines were introduced in terms of the design and construction of DNA biointerfaces. Future directions and challenges were also outlined for this rapidly emerging field.