Programmable one-pot multistep organic synthesis using DNA junctions

A system for multistep DNA-templated synthesis is controlled by the sequential formation of DNA junctions. Reactants are attached to DNA adapters which are brought together by hybridization to DNA template strands. This process can be repeated to allow sequence-controlled oligomer synthesis while maintaining a constant reaction environment, independent of oligomer length, at each reaction step. Synthesis can take place in a single pot containing all required reactive monomers. Different oligomers can be synthesized in parallel in the same vessel, and the products of parallel synthesis can be ligated, reducing the number of reaction steps required to produce an oligomer of a given length.     

可编程DNA胶束

正DNA胶束是一段由亲水的DNA链与一段疏水链通过自组装形成的纳米结构1。得益于DNA的可编程性及其疏水链的可调控性,DNA胶束已被广泛应用于生物医学领域,例如,细胞成像、靶向药物递送以及免疫佐剂治疗等~(2–4)。然而,DNA胶束的形成通常依赖于疏水链之间的疏水-疏水相互作用,这使得其面临临界胶束浓度(Critical Micelle Concentration,CMC)较高、胶束稳定性差     

Structural arrangement of two DNA double helices using cross-linked oligonucleotide connectors

Disulfide cross-linked oligonucleotides, which connect two different sequences of DNA strands, have been synthesized and characterized. Two double helices connected by two different cross-linked oligonucleotides can be arranged in both parallel and antiparallel orientations by addition of the specific complementary strands.     

Programmable mismatch-fueled high-efficiency DNA signal amplifier

Herein, by introducing mismatches, a high-efficiency mismatch-fueled catalytic multiple-arm DNA junction assembly (M-CMDJA) with high-reactivity and a high-threshold is developed as a programmable DNA signal amplifier for rapid detection and ultrasensitive intracellular imaging of miRNA. Compared with traditional nucleic acid signal amplification (NASA) with a perfect complement, the M-CMDJA possesses larger kinetic and thermodynamic favorability owing to the more negative reaction standard free energy (ΔG) as driving force, resulting in much higher efficiency and rates. Once traces of the input initiator react with the mismatched substrate DNA, it could be converted into amounts of output multiple-arm DNA junctions via the M-CMDJA as the functional DNA conversion nanodevice. Impressively, the mismatch-fueled catalytic four-arm DNA junction assembly (M-CFDJA) exhibits high conversion efficiency up to 1.05 × 10⁸ in 30 min, which is almost ten times more than those of conventional methods. Therefore, the M-CMDJA could easily address the challenges of traditional methods: slow rates and low efficiency. In application, the M-CFDJA as a DNA signal amplifier was successfully used to develop a biosensing platform for rapid miRNA detection with a LOD of 6.11 aM and the ultrasensitive intracellular imaging of miRNA, providing a basis for the next-generation of versatile DNA signal amplification methods for ultimate applications in DNA nanobiotechnology, biosensing assay, and clinical diagnoses.

We proposed an ingenious mismatch-enhanced catalytic multiple-arm DNA junction assembly (M-CMDJA) which possesses more negative reaction standard free energy (ΔG) as the driving force, resulting in quite high conversion efficiency and much faster reaction speed.     

Programmable oligomers for minor groove DNA recognition

The four Watson-Crick base pairs of DNA can be distinguished in the minor groove by pairing side-by-side three five-membered aromatic carboxamides, imidazole (Im), pyrrole (Py), and hydroxypyrrole (Hp), four different ways. On the basis of the paradigm of unsymmetrical paired edges of aromatic rings for minor groove recognition, a second generation set of heterocycle pairs, imidazopyridine/pyrrole (Ip/Py) and hydroxybenzimidazole/pyrrole (Hz/Py), revealed that recognition elements not based on analogues of distamycin could be realized. A new set of end-cap heterocycle dimers, oxazole-hydroxybenzimidazole (No-Hz) and chlorothiophene-hydroxybenzimidazole (Ct-Hz), paired with Py-Py are shown to bind contiguous base pairs of DNA in the minor groove, specifically 5'-GT-3' and 5'-TT-3', with high affinity and selectivity. Utilizing this technology, we have developed a new class of oligomers for sequence-specific DNA minor groove recognition no longer based on the N-methyl pyrrole carboxamides of distamycin.     

Sparsely cross-linked "nanogels" for microchannel DNA sequencing

We have developed sparsely cross-linked "nanogels", sub-colloidal polymer structures composed of covalently linked, linear polyacrylamide chains, as novel DNA sequencing matrices for capillary electrophoresis. The presence of covalent cross-links affords nanogel matrices with enhanced network stability relative to standard, linear polyacrylamide (LPA), improving the separation of large DNA fragments. Nanogels were synthesized via inverse emulsion (water-in-oil) copolymerization of acrylamide and N,N-methylenebisacrylamide (Bis). In order to retain the fluidity necessary in a replaceable polymer matrix for capillary array electrophoresis (CAE), a low percentage of the Bis cross-linker (< 10(-4) mol%) was used. Nanogels were characterized by multiangle laser light scattering and rheometry, and were tested for DNA sequencing by CAE with four-color laser-induced fluorescence (LIF) detection. The properties and performance of nanogel matrices were compared to those of a commercially available LPA network, which was matched for both weight-average molar mass (Mw) and extent of interchain entanglements (c/c*). Nanogels presented in this work have an average radius of gyration of 226 nm and a weight-average molar mass of 8.8 x 10(6) g/mol. At concentrations above the overlap threshold, nanogels form a clear, viscous solution, similar to the LPA matrix (Mw approximately 8.9 x 10(6) g/mol). The two matrices have similar flow and viscosity characteristics. However, because of the physical network stability provided by the internally cross-linked structure of the nanogels, a substantially longer read length ( approximately 63 bases, a 10.4% improvement) is obtained with the nanogel matrix at 98.5% accuracy of base-calling. The nanogel network provides higher-selectivity separation of ssDNA sequencing fragments longer than 375 bases. Moreover, nanogel matrices require 30% less polymer per unit volume than LPA. This is the first report of a sequencing matrix that provides better performance than LPA, in a side-by-side comparison of polymer matrices matched for Mw and extent of interchain entanglements.     

Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles

Non-canonical interactions in DNA remain under-explored in DNA nanotechnology. Recently, many structures with non-canonical motifs have been discovered, notably a hexagonal arrangement of typically rhombohedral DNA tensegrity triangles that forms through non-canonical sticky end interactions. Here, we find a series of mechanisms to program a hexagonal arrangement using: the sticky end sequence; triangle edge torsional stress; and crystallization condition. We showcase cross-talking between Watson–Crick and non-canonical sticky ends in which the ratio between the two dictates segregation by crystal forms or combination into composite crystals. Finally, we develop a method for reconfiguring the long-range geometry of formed crystals from rhombohedral to hexagonal and vice versa. These data demonstrate fine control over non-canonical motifs and their topological self-assembly. This will vastly increase the programmability, functionality, and versatility of rationally designed DNA constructs.     

二维DNA晶体的程序化设计与自组装的研究进展

按照Watson-Crick的碱基配对原则，在理论上能够人工设计与合成DNA碱基序列并自组装成任何一维和二维结构的DNA晶体。DNA分子这种底端向上(bottom-up)的自组装模式为我们提供了一种精确合成纳米材料的方法。本文将从程序化设计、合成刚性的DNA分子瓦(DNA tile)、分子瓦自组装成二维DNA晶体以及二维DNA晶体作为模板在纳米技术中的应用等方面展开，简述这一新奇的并且有着潜在应用前景的研究领域的最新进展。     

Crossed aldol reaction using cross-linked polymer-bound lithium dialkylamide

Cross-linked polymer-bound lithium dialkylamides were employed in crossed aldol reaction of various carbonyl compounds with aldehydes to afford the corresponding β-hydroxycarbonyl compounds. The introduction of spacer chains to the polymer-bound lithium dialkylamide between the base moiety and the polystyrene backbone effectively enhanced yields of the desired aldol adducts. Sometimes better yields were obtained by using the polymer-bound reagent having an appropriate spacer-chain with those obtained using lithium diisopropylamide under homogeneous conditions. Repeated use of these polymeric reagents was demonstrated with no loss of efficiency.     

Programmable pyrrole-imidazole polyamides: A potent tool for DNA targeting

Pyrrole-imidazole (Py-Im) polyamides are a class of programmable minor-groove binders that recognize pre-determined DNA double helixes with high affinity and specificity. This review summarized the recent advances of Py-Im polyamides from their synthesis to applications via various modifications at the molecular level.     

Programmable Assembly of Nano-architectures through Designing Anisotropic DNA Origami Patches

Programmable assembly of nanoparticles (NPs) into well-defined architectures has attracted attention because of tailored properties resulting from coupling effects. However, general and precise approaches to control binding modes between NPs remain a challenge owing to the difficulty in manipulating the accurate positions of the functional patches on the surface of NPs. Here, a strategy is developed to encage spherical NPs into pre-designed octahedral DNA origami frames (DOFs) through DNA base-pairings. The DOFs logically define the arrangements of functional patches in three dimensions, owing to the programmability of DNA hybridization, and thus control the binding modes of the caged nanoparticle with designed anisotropy. Applying the node-and-spacer approach that was widely used in crystal engineering to design coordination polymers, patchy NPs could be rationally designed with lower symmetry encoded to assemble a series of nano-architectures with high-order geometries.     

Programmable DNA Nanoflowers for Biosensing,Bioimaging, and Therapeutics

DNA nanostructures have shown excellent prospects in biomedical applications owing to their unique sequence programmability, function designability, and biocompatibility. As a type of unique DNA–inorganic hybrid nanostructures, DNA nanoflowers (DNFs) have attracted considerable attention in the past few years. Precise design of the DNA sequence enables the functions of DNFs to be customized. Specifically, DNFs exhibit high physiological stability and more diverse properties by virtue of the incorporation of inorganic materials, which in turn have been applied in an assortment of biomedical fields. In this review, the design, synthesis, and biomedical applications of programmable DNFs are discussed. First, the background of DNA-based materials and the fundamentals of DNFs are briefly introduced. In the second part, two synthetic methods of DNFs are categorized as the rolling circle amplification and salt aging method, focusing on the formation mechanism of DNFs and differences between the synthetic methods. In the third part, the biomedical applications of DNFs functional materials are summarized, including biosensing, bioimaging, and therapeutics. Finally, the challenges and future opportunities of DNFs are discussed toward more widespread applications.     

Programmable Engineering of a Biosensing Interface with Tetrahedral DNA Nanostructures for Ultrasensitive DNA Detection

Self‐assembled DNA nanostructures with precise sizes allow a programmable “soft lithography” approach to engineer the interface of electrochemical DNA sensors. By using millimeter‐sized gold electrodes modified with several types of tetrahedral DNA nanostructures (TDNs) of different sizes, both the kinetics and thermodynamics of DNA hybridization were profoundly affected. Because each DNA probe is anchored on an individual TDN, its lateral spacing and interactions are finely tuned by the TDN size. By simply varying the size of the TDNs, the hybridization time was decreased and the hybridization efficiency was increased. More significantly, the detection limit for DNA detection was tuned over four orders of magnitude with differentially nanostructured electrodes, and achieved attomolar sensitivity with polymeric enzyme amplification.     

Sequence-Dependent DNA Functionalization of Upconversion Nanoparticles and Their Programmable Assemblies

DNA-modified lanthanide-doped upconversion nanoparticles (DNA-UCNPs) that combine the functions of DNA and the optical features of UCNPs have shown great promise in a wide range of fields. However, challenges remain in precisely tethering and orienting the DNA strands on the UCNP surface. Herein, we systematically investigate the sequence dependence of DNAs in their interactions with UCNPs, and reveal that poly-cytosine (poly-C) has high affinity for the UCNP surface. A general approach to synthesize monodispersed DNA-UCNP conjugates is developed using poly-C-containing diblock DNA strands. The poly-C segment of the DNA strand binds to the surfaces of UCNPs and the second segment is oriented perpendicularly on the UCNP surface, making the DNA-UCNPs highly stable and monodispersed in aqueous solution. The dense layer of DNA on the UCNP surface enables the programmable assembly of UCNPs with other DNA-functionalized nanoparticles or DNA origamis through hybridization, resulting in the formation of well-organized complex structures.     

NIR-light-induced deformation of cross-linked liquid-crystal polymers using upconversion nanophosphors

When upconversion nanophosphors were incorporated into an azotolane-containing cross-linked liquid-crystal polymer film, the resulting composite film generated fast bending upon exposure to continuous-wave near-IR light at 980 nm. This occurs because the upconversion luminescence of the nanophosphors leads to trans-cis photoisomerization of the azotolane units and an alignment change of the mesogens. The bent film completely reverted to the initial flat state after the light source was removed.     

Secondary structure of DNA is recognized by slightly cross-linked cationic hydrogel

Interaction of salmon sperm DNA (300-500 bp) and ultrahigh molecular mass DNA (166 kbp) from bacteriophage T4dC with linear poly(N-diallyl-N-dimethylammonium chloride) (PDADMAC) and slightly cross-linked (#) PDADMAC (#PDADMAC) hydrogel in water has been studied by means of UV-spectroscopy, ultracentrifugation, atomic force, and fluorescence microscopy (FM). It is found that the linear polycation induced compaction of either native (double-stranded) or denatured (single-stranded) DNA by forming PDADMAC-DNA interpolyelectrolyte complexes (IPEC)s. At the same time, #PDADMAC hydrogel is able to distinguish between native and denatured DNA. Native DNA is adsorbed and captured in the hydrogel surface layer, while denatured DNA diffuses to the hydrogel interior until the whole hydrogel sample is transformed into the cross-linked IPEC. Both native and denatured DNA can be completely released from the hydrogel in appropriate conditions with no degradation by adding a low molecular salt. The data observed using conventional physicochemical methods with respect to DNA of a moderate molecular mass remarkably correlate with the pictures directly observed for ultrahigh molecular mass DNA in dynamics by using FM.     

Electrochemical activation of freons using electron transfer mediators

This overview discusses the electrochemical activation of freons CF₂ClCFCl₂ (CFC113), CF₃Br (FC13B1), and CF₂Cl₂ (CFC12) using various electron transfer mediators: complex nickel(ii) compounds with nitrogen-containing tetradentate ligands and bipyridyl, aromatic derivatives (perylene, p-dicyanobenzene, Å-azobenzene, and others), and sulfur dioxide. A possibility was shown of the homogeneous catalytic activation of freons by two mutually supplementing electron transfer mediators: methylviologen—SO₂ and I₂—SO₂. The involvement of freons by the electron transfer mediators into the syntheses of valuable organic products under mild conditions was demonstrated for several examples.