Search

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.

Aptamers are exciting smart molecular probes for specific recognition of disease biomarkers. A number of strategies have been developed to convert target-aptamer binding into physically detectable signals. Since the aptamer sequence was first discovered, a large variety of aptamer-based biosensors have been developed, with considerable attention paid to their potential applications in clinical diagnostics. So far, a variety of techniques in combination with a wide range of functional nanomaterials have been used for the design of aptasensors to further improve the sensitivity and detection limit of target determination. In this paper, the advantages of aptamers over traditional antibodies as the molecular recognition components in biosensors for high-throughput screening target molecules are highlighted. Aptamer-target pairing configurations are predominantly single- or dual-site binding; the design of recognition modes of each aptamer-target pairing configuration is described. Furthermore, signal transduction strategies including optical, electrical, mechanical, and mass-sensitive modes are clearly explained together with examples. Finally, we summarize the recent progress in the development of aptamer-based biosensors for clinical diagnosis, including detection of cancer and disease biomarkers and in vivo molecular imaging. We then conclude with a discussion on the advanced development and challenges of aptasensors.

The development of biocompatible drug delivery vehicles for cancer therapy in the brain remains a big challenge. In this study, we designed self-assembled DNA nanocages functionalized with or without blood-brain barrier (BBB)-targeting ligands, d and we investigated their penetration across the BBB. Our DNA nanocages were not cytotoxic and they were substantially taken up in brain capillary endothelial cells and Uppsala 87 malignant glioma (U-87 MG) cells. We found that ligand modification is not essential for this DNA system as the ligand-free DNA nanocages (LF-NCs) could still cross the BBB by endocytosis inin vitro and in vivo models. Our spherical DNA nanocages were more permeable across the BBB compared with tubular DNA nanotubes. Remarkably, in vivo studies revealed that DNA nanocages could carry anticancer drugs across the BBB and inhibit the tumor growth in a U-87 MG xenograft mouse model. This is the first example showing the potential of DNA nanocages as innovative delivery vehicles to the brain for cancer therapy. Unlike other delivery systems, our work suggest that a DNA nanocage-based platform provides a safe and cost-effective tool for targeted delivery to the brain and therapy for brain tumors.

G-quadruplex structures are becoming useful alternative interaction modules for the assembly of DNA nanomaterials because of their unique inducibility by cations. In this study, we demonstrated a new strategy for the assembly of polymeric DNA nanoarchitectures in the presence of cations, such as K+ and Na+, by employing G-quartet toeholds at the edges of discrete mini-square DNA building blocks as adhesive units. In comparison with the Watson-Crick base-paired duplex linkers, G-quadruplex arrays embedded in the self-assembled DNA system exhibit higher thermal stability. The morphology of these doughnut-shaped or spherical-shaped DNA nanostructures is highly regulated by the orientation of the folded G-quadruplexes either in parallel or antiparallel orientation in response to different cations. Furthermore, this G-quadruplex-mediated assembly strategy is able to manipulate the cycling of DNA assemblies between discrete and polymeric states by means of introducing cations and chelating agents sequentially. This property enables the reversible manipulation of the DNA-based nanosystems for at least 4 cycles. The G-quadruplex array embedded in this self-assembled DNA system can become a scaffold for functional molecules, as a number of organic molecules and proteins exhibit specific binding to these G-quadruplex structures. Besides, embedded G-quadruplexes are also considered as functional components of nanoscale electronic materials due to their electron transport through the stacked orientation of the G-quartet. Therefore, this work is an important step towards obtaining reversible, responsive G-quadruplex-induced DNA-based nanomaterials with versatile functionalities which will be highly useful in further electronic, biomedical and drug-delivery applications.

Ruthenium(II) tris(bipyridyl) cationic complex (Ru(bpy)32+) incorporated UiO-67 (Universitetet i Oslo) nanoscale metal–organic frameworks (NMOFs) with an average diameter of ∼92 nm were developed as theranostic nanoplatform for in vitro two-photon fluorescence imaging and photodynamic therapy. After incorporation into porous UiO-67 nanoparticles, the quantum yield, luminescence lifetime, and two-photon fluorescence intensity of Ru(bpy)32+ guest molecules were much improved owing to the steric confinement effect of MOF pores. Benefiting from these merits, the as-synthesized nanoparticles managed to be internalized by A549 cells while providing excellent red fluorescence in cytoplasm upon excitation with 880 nm irradiation. Photodynamic therapeutic application of the Ru(bpy)32+-incorporated UiO-67 NMOFs was investigated in vitro. The Ru(bpy)32+-incorporated UiO-67 NMOFs exhibited good biocompatibility without irradiation while having good cell-killing rates upon irradiation. In view of these facts, the deve...

We design and synthesize a sequence-defined α-l-threose nucleic acid (TNA) polymer, which is complementary to certain nucleotide sites of target anti-apoptotic proteins, BcL-2 involving in development and progression of tumors. Compared to scramble TNA, anti-BcL-2 TNA significantly suppresses target mRNA and protein expression in cancerous cells and shows antitumor activity in carcinoma xenografts, resulting in suppression of tumor cell growth and induction of tumor cell death. Together with good biocompatibility, very low toxicity, excellent specificity features, and strong binding affinity toward the complementary target RNAs, TNAs become new useful biomaterials and effective alternatives to traditional antisense oligonucleotides including locked nucleic acids, morpholino oligomers, and peptide nucleic acids in antisense therapy. Compared to conventional cancer therapy such as radiotherapy, surgery, and chemotherapy, we anticipate that this TNA-based polymeric system will work effectively in antisense cancer therapy and shortly start to play an important role in practical application.

Nanodiamond-gold nanoparticle (ND-AuNP) dimers constitute a potent tool for controlled thermal heating of biological systems on the nanoscale, by combining a local light-induced heat source with a sensitive local thermometer. Unfortunately, previous solution-based strategies to build ND-AuNP conjugates resulted in large nanoclusters or a broad population of multimers with limited separation efficiency. Here, we describe a new strategy to synthesize discrete ND-AuNP dimers via the synthesis of biotin-labeled DNA-AuNPs through thiol chemistry and its immobilization onto the magnetic bead (MB) surface, followed by reacting with streptavidin-labeled NDs. The dimers can be easily released from MB via a strand displacement reaction and separated magnetically. Our method is facile, convenient, and scalable, ensuring high-throughput formation of very stable dimer structures. This ligand-induced self-assembly approach enables the preparation of a wide variety of dimers of designated sizes and compositions, thus opening up the possibility that they can be deployed in many biological actuation and sensing applications.

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.

We demonstrate a nanotechnology approach for the development of cancer-cell-specific subcellular organelle-targeted drug nanocarriers based on photostable nanodiamonds (ND) functionalized with folic acid and mitochondrial localizing sequence (MLS) peptides. We showed that these multifunctional NDs not only distinguish between cancer cells and normal cells, and transport the loaded drugs across the plasma membrane of cancer cells, but also selectively deliver them to mitochondria and induce significant cytotoxicity and cell death compared with free Dox localized in lysosomes. Importantly, the cellular uptake of Dox was dramatically increased in a resistant model of MCF-7 cells, which contributed to the significant circumvention of P-glycoprotein-mediated drug resistance. Our work provides a novel method of designing nanodiamond-based carriers for targeted delivery and for circumventing drug resistance in doxorubicin-resistant human breast adenocarcinoma cancer cells.

Photoresponsive DNA nanomaterials represent a new class of remarkable functional materials. By adjusting the irradiation wavelength, light intensity, and exposure time, various photocontrolled DNA-based systems can be reversibly or irreversibly regulated in respect of their size, shape, conformation, movement, and dissociation/association. This Review introduces the most updated progress in the development of photoresponsive DNA-based system and emphasizes their advantages over other stimuli-responsive systems. Their design and mechanisms to trigger the photoresponses are shown and discussed. The potential application of these photon-responsive DNA nanomaterials in biology, biomedicine, materials science, nanophotonic and nanoelectronic are also covered and described. The challenges faced and further directions of the development of photocontrolled DNA-based systems are also highlighted.

Tissue engineering combines biological cells and synthetic materials containing chemical signaling molecules to form scaffolds for tissue regeneration. Mesenchymal stem cells (MSCs) provide an attractive source for tissue engineering due to their versatility of multipotent differentiation. Recently, it has been recognized that both chemical and mechanical stimulations are essential mediators of adhesion and differentiation of MSCs. While significant progress has been made on the understanding of chemical regulatory factors within the extracellular matrix, the effects of mechanical stimulation exerted by nanomaterials on MSCs and the underlying mechanisms are less well-known. The present study showed that the adhesion, proliferation, and differentiation of MSCs cultured on vertically aligned silicon nanowire (SiNW) arrays were significantly different from those on flat silicon wafer and control substrates. The interactions between MSCs and the SiNW arrays caused the stem cells to preferentially differentiate toward osteocytes and chondrocytes but not adipocytes in the absence of supplementary growth factors. Our study demonstrated that Ca(2+) ion channels were transiently activated in MSCs upon mechanical stimulation, which eventually led to activation of Ras/Raf/MEK/ERK signaling cascades to regulate adhesion, proliferation, and differentiation of MSCs. The stretch-mediated transient Ca(2+) ion channel activation and cytoskeleton reorganization during stem cell-nanowire interaction may be early events of lineage-specific potentiation of MSCs in determining the fates of mesenchymal stem cells cultured on microenvironments with specific mechanical properties.

Stimuli-responsive DNA-based materials represent a major class of remarkable functional nanomaterials for nano-biotechnological applications. In this review, recent progress in the development of stimuli-responsive systems based on self-assembled DNA nanostructures is introduced and classified. Representative examples are presented in terms of their design, working principles and mechanisms to trigger the response of the stimuli-responsive DNA system upon expose to a large variety of stimuli including pH, metal ions, oligonucleotides, small molecules, enzymes, heat, and light. Substantial in vitro studies have clearly revealed the advantages of the use of stimuli-responsive DNA nanomaterials in different biomedical applications, particularly for biosensing, drug delivery, therapy and diagnostic purposes in addition to bio-computing. Some of the challenges faced and suggestions for further development are also highlighted.

Soluble, thermally stable, and easily processable platinum(II) polyyne polymers of the form trans-[–Pt(PBu3)2C≡CRC≡C–]n (R = 2,8-disubstituted dibenzothiophene, 2,8-disubstituted and 3,7-disubstituted dibenzothiophene-S,S-dioxide units) have been prepared in good yields by CuI-catalyzed polymerization involving the dehydrohalogenating coupling of trans-[PtCl2(PBu3)2] and HC≡CRC≡CH. We report their optical absorption and photoluminescence spectra and compare the results with the monomeric model complexes trans-[Pt(Ph)(PEt3)2C≡CRC≡CPt(Ph)(PEt3)2]. The different electronic properties and linkage geometry of the central R group lead to new organometallic materials with distinct photophysical traits. The polymer with more conjugated 3,7-disubstituted dibenzothiophene-S,S-dioxide mainly displays fluorescence band, while its isomer with less conjugated 2,8-disubstituted spacer effectively enhances the intersystem crossing rate and strong phosphorescence emission can be detected even at room temperature.

A current challenge in nanoscience is to achieve controlled organization in three-dimensions, to provide tools for biophysics, molecular sensors, enzymatic cascades, drug delivery, tissue engineering, and device fabrication. DNA displays some of the most predictable and programmable interactions of any molecule, natural or synthetic. As a result, 3D-DNA nanostructures have emerged as promising tools for biology and materials science. In this review, strategies for 3D-DNA assembly are discussed. DNA cages, nanotubes, dendritic networks, and crystals are formed, with deliberate variation of their size, shape, persistence length, and porosities. They can exhibit dynamic character, allowing their selective switching with external stimuli. They can encapsulate and position materials into arbitrarily designed patterns, and show promise for numerous biological and materials applications.

Two novel p-phenylenediamine-substituted fluorenes have been designed and synthesized. Their applications as hole injection materials in organic electroluminescent devices were investigated. These materials show a high glass transition temperature and a good hole-transporting ability. It has been demonstrated that the 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4-TCNQ) doped p-phenylene-diamine-substituted fluorenes, in which F4-TCNQ acts as p-type dopant, are highly conducting with a good hole-transporting property. The organic light emitting devices (OLEDs) utilizing these F4-TCNQ-doped materials as a hole injection layer were fabricated and investigated. The pure Alq3-based OLED device shows a current efficiency of 5.2 cd/A at the current density of 20 mA/cm2 and the operation lifetime is 1500 h with driving voltage increasing only about 0.7 mV/h. The device performance and stability of this hole injection material meet the benchmarks for the commercial requirements for OLED materials.

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.

In this paper, we report on the synthesis and properties of a novel series of multi-triarylamine-substituted carbazole-based dendrimers G2-OTP(n)-G2 (n = 2−5) with an oligothiophene core. The length of the oligothiophene core varied from 2 to 5 thiophene units. It was found that both the absorption and fluorescence emission peaks red-shifted with increasing oligothiophene core length. As a result, the power conversion efficiencies of the as-fabricated solar cells using the composite of these dendrimers and PCBM as the photoactive layer increased with increasing oligothiophene core length, from 0.04% for G2-DTP-G2 to 0.13% for G2-PTP-G2 under AM 1.5 simulated solar illumination at an irradiation intensity of 100 mW/cm2. After a thermal annealing at 150 °C for 15 min under nitrogen, however, the devices based on the G2-DTP-G2:PCBM blend exhibited the most dramatic improvement and almost best performance, although other devices also showed some improvement. Since only G2-DTP-G2 is the a crystalline material ...

A novel series of highly luminescent end-functionalized tetra-oligophenylene substituted calix[4]-arenes have been synthesized by palladium-catalyzed Suzuki cross-coupling of arylboronic acid and tetraiodocalix[4]arene as a key step. It is important to find that liquid crystallinity can easy be induced by introducing the polarity or enhancing the polarizability of the three-dimensional phenylene-substituted calix[4]arene rigid segment. In contrast to the classical one-dimensional 4-cyano-4‘-alkoxybiphenyl mesogens, which exhibit nematic and/or smectic A phases, cyano-phenyl-calix[4]arene and methyl-biphenyl-calix[4]arene derivatives exhibit highly ordered smectic supramolecular organization as evidenced by the polarized optical microscopy and X-ray diffraction studies. On the basis of the results of X-ray diffraction, an interdigitated antiparallel packing mode is proposed for the ordered smectic mesophase. The presence of the strong dipoles in the rigid calixarene segments not only facilitates and stabil...

This study reports biosensing using graphene field-effect transistors with the aid of pyrene-tagged DNA aptamers, which exhibit excellent selectivity, affinity, and stability for Escherichia coli (E. coli) detection. The aptamer is employed as the sensing probe due to its advantages such as high stability and high affinity toward small molecules and even whole cells. The change of the carrier density in the probe-modified graphene due to the attachment of E. coli is discussed theoretically for the first time and also verified experimentally. The conformational change of the aptamer due to the binding of E. coli brings the negatively charged E. coli close to the graphene surface, increasing the hole carrier density efficiently in graphene and achieving electrical detection. The binding of negatively charged E. coli induces holes in graphene, which are pumped into the graphene channel from the contact electrodes. The carrier mobility, which correlates the gate voltage to the electrical signal of the APG-FETs, is analyzed and optimized here. The excellent sensing performance such as low detection limit, high sensitivity, outstanding selectivity and stability of the graphene biosensor for E. coli detection paves the way to develop graphene biosensors for bacterial detection.

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.

One of the most important criteria for the successful DNA-templated polymerization to generate fully synthetic biomimetic polymers is to design the complementary structural monomers, which assemble to the templates strongly and precisely before carrying polymerization. In this study, water-soluble, laterally thymine-substituted donor-acceptor π-conjugated molecules were designed and synthesized to self-assemble with complementary oligoadenines templates, dA(20) and dA(40), into stable and tubular assemblies through noncovalent interactions including π-π stacking, dipole-dipole interactions, and the complementary adenine-thymine (A-T) hydrogen-bonding. UV-vis, fluorescence, circular dichroism (CD), atomic force microscopy (AFM), and transmission electron microscopy (TEM) techniques were used to investigate the formation of highly robust nanofibrous structures. Our results have demonstrated for the first time that the dipole-dipole interactions are stronger and useful to reinforce the assembly of donor-acceptor π-conjugated molecules to DNA templates and the formation of the stable and robust supramolecular nanofibrous complexes together with the complementary hydrogen bonding interactions. This provides an initial step toward DNA-templated polymerization to create fully synthetic DNA-mimetic polymers for biotechnological applications. This study also presents an opportunity to precisely position donor-acceptor type molecules in a controlled manner and tailor-make advanced materials for various biotechnological applications.

DNA has emerged as a powerful building block for the construction of supramolecular materials, because of its molecular recognition specificity, programmability through sequence selection, ease of functionalization, an array of enzyme-assisted modifications, and automated synthesis. This molecule has been used to create a variety of constructs, ranging from extended materials, such as two-dimensional (2D) lattices and networks and one-dimensional (1D) fibers and nanotubes, to controlled and discrete three-dimensional (3D) nanostructures, such as polygons and cages, and it has also been used to compose bulk materials such as hydrogels and crystals. This review focuses on the different approaches in DNA nanotechnology, the resulting 2D- and 3D-DNA nanostructures, and their emerging applications in biology and materials science. Keywords: DNA; nanotechnology; self-assembly; programmable structures; two-dimensional networks; three-dimensional cages; nanotubes; nanoparticles; transition metals

The site-specific insertion of organic and inorganic molecules into DNA nanostructures can provide unique structural and functional capabilities. We have demonstrated the inclusion of two types of molecules. The first is a diphenylphenanthroline (dpp, 1) molecule that is site specifically inserted into DNA strands and which can be used as a template to create metal-coordinating pockets. These building blocks can then be used to assemble metal-DNA 2D and 3D structures, including metal-DNA triangles, described here. The second insertion is a triaryl molecule that provides geometric control in the preparation of 2D single-stranded DNA templates. These can be designed to further assemble into geometrically well-defined nanotubes. Here, we detail the steps involved in the construction of metal-DNA triangles and DNA nanotubes using these methods.

DNA nanotubes can template the growth of nanowires, orient transmembrane proteins for nuclear magnetic resonance determination, and can potentially act as stiff interconnects, tracks for molecular motors and nanoscale drug carriers. Current methods for the construction of DNA nanotubes result in symmetrical and cylindrical assemblies that are entirely double-stranded. Here, we report a modular approach to DNA nanotube synthesis that provides access to geometrically well-defined triangular and square-shaped DNA nanotubes. We also construct the first nanotube assemblies that can exist in double- and single-stranded forms with significantly different stiffness. This approach allows for parameters such as geometry, stiffness, and single- or double-stranded character to be fine-tuned, and could enable the creation of designer nanotubes for a range of applications, including the growth of nanowires of controlled shape, the loading and release of cargo, and the real-time modulation of stiffness and persistence length within DNA interconnects.

Because of the chemical simplicity of α-l-threose nucleic acid (TNA) and its ability to exchange genetic information between itself and RNA, it has attracted significant interest as the RNA ancestor. We herein explore the biological properties and evaluate the potency of sequence-designed TNA polymers to suppress the gene expression in living environments. We found that sequence-specific TNA macromolecules exhibit strong affinity and specificity toward the complementary RNA targets, are highly biocompatible and nontoxic in a living cell system, and readily enter a number of cell lines without using transfecting agents. Particularly, TNA exhibited much stronger enzymatic resistance toward fetal bovine serum or human serum as compared to traditional antisense oligonucleotides, which means that the intrinsic structure of TNA is thoroughly resistant to biological degradation. Importantly, the efficacy of the TNA molecule with green fluorescent protein (GFP) target sequence (anti-GFP TNAs) as antisense agents was first demonstrated in living cells in which these polymers revealed high antisense activity in terms of the degree of inhibition of GFP gene expression. The GFP gene inhibition studies in HeLa and HEK293 cells characterize sequence-controlled TNA as a functional biomaterial and a valuable alternative to traditional antisense oligonucleotides such as peptide nucleic acids, phosphorodiamidate morpholino oligomers, and locked nucleic acids for a wide range of applications in drug discovery and life science research. Additionally, we also first reported the cost-efficient approach to synthesize the four TNA phosphoramidite monomers using 2-cyanoethyl N, N, N', N'-tetraisopropylphosphoramidite as a key reagent. Furthermore, by increasing the frequency of the deblocking and coupling reactions together with extending their reaction time in each synthesis cycle, sequence-controlled TNAs can be easily synthesized in a quantitative yield and high purity.