Self-assembly of DNA parallel double-crossover motifs.

DNA double-crossover motifs, including parallel and antiparallel crossovers, serve as the structural foundation for the creation of diverse nanostructures and dynamic devices in DNA nanotechnology. Parallel crossover motifs have unique advantages over the widely used antiparallel crossover design but have not developed as substantially due to the difficulties in assembly. Here we created 29 designs of parallel double-crossover motifs varying in hybridization pathways, central domain lengths, and crossover locations to investigate their assembly mechanism. Arrays were successfully formed in four distinct designs, and large tubular structures were obtained in seven designs with predefined pathways and central domains appoximately 16 nucleotides in length. The nanotubes obtained from parallel crossover design showed improved nuclease resistance than the ones from the antiparallel counterpart design. Overall, our study provides a basis for the development of generalized assembly rules of DNA parallel crossover systems and opens new opportunities for their potential use in biological systems.

19F NMR ON/OFF nanoparticles: a universal approach for the specific detection of DNA-binding cancer biomarkers.

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. The key to our design strategy is the characteristic 19F NMR signal of the probe, which completely vanishes in the aggregated state due to the shortening of T2 relaxation. However, molecular recognition of DNA by the cancer biomarkers through specific molecular recognition results in the disassembly of the nanoparticles, which causes the restoration of the characteristic 19F signal of the probe. The universal nature of the approach is demonstrated through the selective detection of various cancer biomarkers including miRNA, ATP, thrombin, and telomerase.

Nucleic acid paranemic structures: a promising building block for functional nanomaterials in biomedical and bionanotechnological applications.

Over the past few decades, DNA has been recognized as a powerful self-assembling material capable of crafting supramolecular nanoarchitectures with quasi-angstrom precision, which promises various applications in the fields of materials science, nanoengineering, and biomedical science. Notable structural features include biocompatibility, biodegradability, high digital encodability by Watson-Crick base pairing, nanoscale dimension, and surface addressability. Bottom-up fabrication of complex DNA nanostructures relies on the design of fundamental DNA motifs, including parallel (PX) and antiparallel (AX) crossovers. However, paranemic or PX motifs have not been thoroughly explored for the construction of DNA-based nanostructures compared to AX motifs. In this review, we summarize the developments of PX-based DNA nanostructures, highlight the advantages as well as challenges of PX-based assemblies, and give an overview of the structural and chemical features that lend their utilization in a variety of applications. The works presented cover PX-based DNA nanostructures in biological systems, dynamic systems, and biomedical contexts. The possible future advances of PX structures and applications are also summarized, discussed, and postulated.

Galactose Grafted Two-Dimensional Nanosheets as a Scaffold for the In Situ Synthesis of Silver Nanoparticles: A Potential Catalyst for the Reduction of Nitroaromatics.

Two major hurdles in NP-based catalysis are the aggregation of the NPs and their recycling. Immobilization of NPs onto a 2D support is the most promising strategy to overcome these difficulties. Herein, amphiphilicity-driven self-assembly of galactose-hexaphenylbenzene-based amphiphiles into galactose-decorated 2D nanosheet is reported. The extremely dense decoration of reducing sugar on the surface of the sheets is used for the in situ synthesis and immobilization of ultrafine catalytically active AgNPs by using Tollens' reaction. The potential of the system as a catalyst for the reduction of various nitroaromatics is demonstrated. Enhanced catalytic activity is observed for the immobilized AgNPs when compared to the corresponding discrete AgNPs. Recovery of the catalytic system from the reaction mixture by ultrafiltration and its subsequent recycling for several cycles without dropping its activity is shown. This is the first report demonstrating the in situ synthesis and immobilization of ultrafine AgNPs onto a 2D nanosheet that exhibits excellent catalytic performance for the reduction of nitroaromatics.

Biotin-decorated NIR-absorbing nanosheets for targeted photodynamic cancer therapy.

Targeted photodynamic therapy (PDT) is one of the promising approaches for the selective killing of cancerous cells without affecting the normal cells, and hence designing new strategies for targeted PDT is extremely important. Herein we report the design and synthesis of a new class of nanosheets derived from the self-assembly of the iodo-BODIPY-biotin conjugate as a photosensitizer for targeted PDT applications. The nanosheet exhibits a high extinction coefficient in the NIR region, high singlet oxygen efficiency, no toxicity in the dark and cell targeting ligands (biotin) on the surface, which are necessary features required for an ideal photosensitizer. Overexpression of sodium-dependent multivitamin transporters (SMVTs) in HeLa and A549 (biotin receptor positive cell lines) is explored for the selective uptake of the nanophotosensitizer through receptor mediated endocytosis (interaction between biotin and SMVT). Control experiments using a biotin receptor negative cell line (WI-38) are also carried out to confirm that the specific interaction between the SMVTs and biotin is mainly responsible for the selective uptake of the photosensitizer. Efficient killing of cancerous cells is demonstrated upon light irradiation through the generation of singlet oxygen and other reactive oxygen species around the cellular environment.

DNA-π Amphiphiles: A Unique Building Block for the Crafting of DNA-Decorated Unilamellar Nanostructures.

The unparalleled ability of DNA to recognize its complementary strand through Watson and Crick base pairing is one of the most reliable molecular recognition events found in natural systems. This highly specific sequence information encoded in DNA enables it to be a versatile building block for bottom-up self-assembly. Hence, the decoration of functional nanostructures with information-rich DNA is extremely important as this allows the integration of other functional molecules onto the surface of the nanostructures through DNA hybridization in a highly predictable manner. DNA amphiphiles are a class of molecular hybrids where a short hydrophilic DNA is conjugated to a hydrophobic moiety. Since DNA amphiphiles comprise DNA as the hydrophilic segment, their self-assembly in aqueous medium always results in the formation of nanostructures with shell made of DNA. This clearly suggests that self-assembly of DNA amphiphiles is a straightforward strategy for the ultradense decoration of a nanostructure with DNA. However, initial attempts toward the design of DNA amphiphiles were primarily focused on long flexible hydrocarbon chains as the hydrophobic moiety, and it has been demonstrated in several examples that they typically self-assemble into DNA-decorated micelles (spherical or cylindrical). Hence, molecular level control over the self-assembly of DNA amphiphiles and achieving diverse morphologies was extremely challenging and unrealized until recently.In this Account, we summarize our recent efforts in the area of self-assembly of DNA amphiphiles and narrate the remarkable effect of the incorporation of a large π-surface as the hydrophobic domain in the self-assembly of DNA amphiphiles. Self-assembly of DNA amphiphiles with flexible hydrocarbon chains as the hydrophobic moiety is primarily driven by the hydrophobic effect. The morphology of such nanostructures is typically predicted based on the volume ratio of hydrophobic to hydrophilic segments. However, control over the self-assembly and prediction of the morphology become increasingly challenging when the hydrophobic moieties can interact with each other through other noncovalent interactions. In this Account, the unique self-assembly behaviors of DNA-π amphiphiles, where a large π-surface acts as the hydrophobe, are described. Due to the extremely strong π-π stacking in aqueous medium, the assembly of the amphiphile is found to preferably proceed in a lamellar fashion (bilayer) and hence the morphology of the nanostructures can easily be tuned by the structural modification of the π-surface. Design principles for crafting various DNA-decorated lamellar nanostructures including unilamellar vesicles, two-dimensional (2D) nanosheets, and helically twisted nanoribbons by selecting suitable π-surfaces are discussed. Unilamellar vesicular nanostructures were achieved by using linear oligo(phenylene ethynylene) (OPE) as the hydrophobic segment, where lamellar assembly undergoes folding to form unilamellar vesicles. The replacement of OPE with a strongly π-stacking hydrophobe such as hexabenzocoronene (HBC) or tetraphenylethylene (TPE) provides extremely strong π-stacking compared to OPE, which efficiently directed the 2D growth for the lamellar assembly and led to the formation of 2D nanosheets. A helical twist in the lamella was achieved by the replacement of HBC with hexaphenylbenzene (HPB), which is the twisted analogue of HBC, directing the assembly into helically twisted nanoribbons. The most beneficial structural feature of this kind of nanostructure is the extremely dense decoration of their surface with ssDNA, which can further be used for DNA-directed organization of other functional nanomaterials. By exploring this, their potential as a nanoscaffold for predefined assembly of plasmonic nanomaterials into various plasmonic 1D, 2D, and 3D nanostructures through DNA hybridization is discussed. Moreover, the design of pH-responsive DNA-based vesicles and their application as a nanocarrier for payload delivery is also demonstrated.

Phototheranostic DNA micelles from the self-assembly of DNA-BODIPY amphiphiles for the thermal ablation of cancer cells.

Design of phototheranostic agents in a single step approach is one of the challenges in cancer therapy. Herein, a one-step strategy based on amphiphilicity-driven self-assembly of DNA-BODIPY amphiphiles for the design of a new class of micelles, which offer all three phototheranostic functions, is reported. These include (i) strong emission at NIR (φf = 30%) for imaging, (ii) high photothermal conversion (η = 52%) for PTT and (iii) an ssDNA-based shell for the integration of cell targeting moieties. Selective uptake of DNA micelles into a target cancer cell and its killing by laser irradiation (635 nm) are also demonstrated. Furthermore, the excellent biocompatibility, ultrasmall nanosize and high stability of DNA micelles are promising for in vivo applications.

Efficient Capturing of Polycyclic Aromatic Micropollutants From Water Using Physically Crosslinked DNA Nanoparticles.

Design and synthesis of physically (non-covalently) cross-linked nanoparticles through host-guest interaction between ß-CD and adamantane is reported. Specific molecular recognition between ß-CD functionalized branched DNA nanostructures (host) and a star-shaped adamantyl-terminated 8-arm poly(ethylene glycol) polymer (guest) is explored for the design of the nanoparticles. The most remarkable structural features of DNA nanoparticles include their excellent biocompatibility and the possibility of various non-covalent interactions with both hydrophobic and hydrophilic organic molecules. Potential of DNA nanoparticles for the rapid and efficient capture of various micropollutants typically present in water including carcinogens (hydrophobic micropollutants), organic dyes (hydrophilic), and pharmaceutical molecules (hydrophilic) is also demonstrated. The capture of micropollutants by DNA nanoparticles is attributed to the various non-covalent interactions between DNA nanoparticles and the micropollutants. Our results clearly suggest that DNA based nanomaterials would be an ideal candidate for the capturing and removal of both hydrophilic and hydrophobic micropollutants typically present in water.

Galactose-Grafted 2D Nanosheets from the Self-Assembly of Amphiphilic Janus Dendrimers for the Capture and Agglutination of Escherichia coli.

High aspect ratio, sugar-decorated 2D nanosheets are ideal candidates for the capture and agglutination of bacteria. Herein, the design and synthesis of two carbohydrate-based Janus amphiphiles that spontaneously self-assemble into high aspect ratio 2D sheets are reported. The unique structural features of the sheets include the extremely high aspect ratio and dense display of galactose on the surface. These structural characteristics allow the sheet to act as a supramolecular 2D platform for the capture and agglutination of E. coli through specific multivalent noncovalent interactions, which significantly reduces the mobility of the bacteria and leads to the inhibition of their proliferation. Our results suggest that the design strategy demonstrated here can be applied as a general approach for the crafting of biomolecule-decorated 2D nanosheets, which can perform as 2D platforms for their interaction with specific targets.

DNA-Decorated, Helically Twisted Nanoribbons: A Scaffold for the Fabrication of One-Dimensional, Chiral, Plasmonic Nanostructures.

Crafting of chiral plasmonic nanostructures is extremely important and challenging. DNA-directed organization of nanoparticle on a chiral template is the most appealing strategy for this purpose. Herein, we report a supramolecular approach for the design of DNA-decorated, helically twisted nanoribbons through the amphiphilicity-driven self-assembly of a new class of amphiphiles derived from DNA and hexaphenylbenzene (HPB). The ribbons are self-assembled in a lamellar fashion through the hydrophobic interactions of HPB. The transfer of molecular chirality of ssDNA into the HPB core results in the bias of one of the chiral propeller conformations for HPB and induces a helical twist into the lamellar packing, and leads to the formation of DNA-wrapped nanoribbons with M-helicity. The potential of the ribbon to act as a reversible template for the 1D chiral organization of plasmonic nanomaterials through DNA hybridization is demonstrated.

Self-Assembly of an Aptamer-Decorated, DNA-Protein Hybrid Nanogel: A Biocompatible Nanocarrier for Targeted Cancer Therapy.

Nanocarrier-based chemotherapy is one of the most efficient approaches for the treatment of cancer, and hence, the design of new nanocarriers is very important. Herein, the design of a new class of physically cross-linked nanoparticles (nanogel) solely made of biomolecules including DNA, protein, and biotin as a nanocarrier for the targeted cancer therapy is reported. A specific molecular recognition interaction between biotin and streptavidin is explored for the cross-linking of a DNA nanostructure for the crafting of a nanogel. The most unique structural features of nanogels include the following: (i) excellent biocompatibility, (ii) decoration of the nanogel surface with biotin and streptavidin randomly that allowed the integration of aptamer DNA onto the surface of the nanostructure through the biotin-streptavidin interaction, (iii) high doxorubicin encapsulation efficacy through the intercalation of doxorubicin inside the DNA duplex, and (iv) stimuli responsiveness. The selective uptake of a doxorubicin-loaded nanogel by aptamer-receptor-positive cell lines (CCRF-CEM and HeLa) and its delivery inside the target cells are demonstrated. The selective uptake of the nanogel by CCRF-CEM and HeLa cells is attributed to the specific interaction between the aptamer DNA decorated on the surface of the nanogel with the PTK7 receptor overexpressed on CCRF-CEM and HeLa cell lines. These results imply that the nanogel obtained from the self-assembly of biomolecules would be ideal for the crafting of nanocarriers for targeted cargo delivery applications.

Self-assembly of DNA-tetraphenylethylene amphiphiles into DNA-grafted nanosheets as a support for the immobilization of gold nanoparticles: a recyclable catalyst with enhanced activity.

Preventing the aggregation of NPs and their recovery are the two major hurdles in NP based catalysis. Immobilization of NPs on a support has proven to be a promising strategy to overcome these difficulties. Herein we report the design of high aspect ratio two-dimensional (2D) crystalline DNA nanosheets formed from the amphiphilicity-driven self-assembly of DNA-tetraphenylethylene amphiphiles and also demonstrate the potential of DNA nanosheets for the immobilization of catalytically active NPs. The most remarkable feature of this approach is the high loading of NPs in a non-aggregated manner, and hence exhibiting enhanced catalytic activity. Recycling of NP loaded nanosheets for several cycles without reduction in catalytic efficiency by simple ultrafiltration is also demonstrated.

Copper(I)-catalyzed cascade sulfonimidate to sulfonamide rearrangement: synthesis of imidazo[1,2-a][1,4]diazepin-7(6H)-one.

A novel strategy of copper(I)-catalyzed cascade intramolecular nucleophilic attack on N-sulfonylketenimine followed by rearrangement of sulfonimidates to sulfonamides resulting in a library of substituted 8,9-dihydro-5H-imidazo[1,2-a][1,4]diazepin-7(6H)-ones has been developed.