5'-(CGA) n sequence-assisted pH-controlled assembly of supramolecular DNA nanostructure.
Ontology highlight
ABSTRACT:
SUBMITTER: Yan Y
PROVIDER: S-EPMC6124056 | biostudies-literature | 2018 Aug
REPOSITORIES: biostudies-literature
Publications
5'-(CGA) <i><sub>n</sub></i> sequence-assisted pH-controlled assembly of supramolecular DNA nanostructure.
Yan Yuting Y Cao Yanwei Y Xiao Chunsheng C Li Yang Y Xiang Xiaoxuan X Guo Xinhua X
Royal Society open science 20180801 8
Herein, the DNA strands containing 5'-(CGA) <i><sub>n</sub></i> and consecutive guanines are used to construct supramolecular DNA nanostructures that are size-controlled by pH values. Additionally, the introduction of thymine linkers within DNA nanostructures is necessary to maintain the stability of long-sized nanostructures. This work also demonstrates a method for accurately building DNA nanostructures. ...[more]
Similar Datasets
Project description:We demonstrate a strategy to trigger and finely control the assembly of supramolecular DNA nanostructures with pH. Control is achieved via a rationally designed strand displacement circuit that responds to pH and activates a downstream DNA tile self-assembly process. We observe that the DNA structures form under neutral/basic conditions, while the self-assembly process is suppressed under acidic conditions. The strategy presented here demonstrates a modular approach toward building systems capable of processing biochemical inputs and finely controlling the assembly of DNA-based nanostructures under isothermal conditions. In particular, the presented architecture is relevant for the development of complex DNA devices able to sense and respond to molecular markers associated with abnormal metabolism.
| S-EPMC5054458 | biostudies-literature
Project description:BACKGROUND: The ability to create nanostructures with biomolecules is one of the key elements in nanobiotechnology. One of the problems is the expensive and mostly custom made equipment which is needed for their development. We intended to reduce material costs and aimed at miniaturization of the necessary tools that are essential for nanofabrication. Thus we combined the capabilities of molecular ink lithography with DNA-self-assembling capabilities to arrange DNA in an independent array which allows addressing molecules in nanoscale dimensions. RESULTS: For the construction of DNA based nanostructures a method is presented that allows an arrangement of DNA strands in such a way that they can form a grid that only depends on the spotted pattern of the anchor molecules. An atomic force microscope (AFM) has been used for molecular ink lithography to generate small spots. The sequential spotting process allows the immobilization of several different functional biomolecules with a single AFM-tip. This grid which delivers specific addresses for the prepared DNA-strand serves as a two-dimensional anchor to arrange the sequence according to the pattern. Once the DNA-nanoarray has been formed, it can be functionalized by PNA (peptide nucleic acid) to incorporate advanced structures. CONCLUSIONS: The production of DNA-nanoarrays is a promising task for nanobiotechnology. The described method allows convenient and low cost preparation of nanoarrays. PNA can be used for complex functionalization purposes as well as a structural element.
| S-EPMC3248840 | biostudies-literature
Project description:Biological membranes fulfill many important tasks within living organisms. In addition to separating cellular volumes, membranes confine the space available to membrane-associated proteins to two dimensions (2D), which greatly increases their probability to interact with each other and assemble into multiprotein complexes. We here employed two DNA origami structures functionalized with cholesterol moieties as membrane anchors--a three-layered rectangular block and a Y-shaped DNA structure--to mimic membrane-assisted assembly into hierarchical superstructures on supported lipid bilayers and small unilamellar vesicles. As designed, the DNA constructs adhered to the lipid bilayers mediated by the cholesterol anchors and diffused freely in 2D with diffusion coefficients depending on their size and number of cholesterol modifications. Different sets of multimerization oligonucleotides added to bilayer-bound origami block structures induced the growth of either linear polymers or two-dimensional lattices on the membrane. Y-shaped DNA origami structures associated into triskelion homotrimers and further assembled into weakly ordered arrays of hexagons and pentagons, which resembled the geometry of clathrin-coated pits. Our results demonstrate the potential to realize artificial self-assembling systems that mimic the hierarchical formation of polyhedral lattices on cytoplasmic membranes.
| S-EPMC4415451 | biostudies-literature
Project description:In the area of artificial genetics the development of non-enzymatic self-organization of synthetic building blocks is critical for both providing biopolymers with extended functions and understanding prebiotic processes. While reversibility is believed to have played a major role in early functional genetic materials, we previously reported an efficient DNA-templated ligation of suitably designed 5'-end boronic acid and 3'-end ribonucleosidic half-sequences. Here, we report the enzyme-free and activation-free DNA- and RNA-templated assembly of bifunctional hexamers. The reversible assembly was found to be regio- and sequence specific and the stabilities of the resulting duplexes were compared to their nicked counterparts. To go further with our understanding of this unprecedented process we also examined an auto-templated duplex self-assembly representing a key step toward the evolution of sequence-defined synthetic polymers.
| S-EPMC5588539 | biostudies-literature
Project description:Summary The precise sequence control of polymer chain is an important research topic of polymer chemistry. Although some methods such as iterative synthesis and supramolecular polymerization have been developed to fabricate sequence-controllable polymer, it is still a great challenge to consecutively prepare multiple supramolecular polymers with different sequence structures. In this work, through the reasonable utilization of assembly motifs, we integrated multiple host-guest recognitions and metal coordination interactions to prepare different sequence-controlled supramolecular polymers by a multistep assembly strategy. This research provides inspiration for the design and preparation of supramolecular polymers with different sequence structures. Graphical abstract Highlights • Multiple supramolecular polymers were prepared by a multistep assembly strategy• Supramolecular polymers with different structures show different stimuli responsiveness• Different supramolecular polymer materials show different fluorescence emission Polymer chemistry; Supramolecular chemistry; Molecular self-assembly
| S-EPMC9932128 | biostudies-literature
Project description:DNA origami is a robust method for the fabrication of nanoscale 2D and 3D objects with complex features and geometries. The process of DNA origami folding has been recently studied, however quantitative understanding of it is still elusive. Here, we describe a systematic quantification of the assembly process of DNA nanostructures, focusing on the heterotypic DNA junction-in which arms are unequal-as their basic building block. Using bulk fluorescence studies we tracked this process and identified multiple levels of cooperativity from the arms in a single junction to neighboring junctions in a large DNA origami object, demonstrating that cooperativity is a central underlying mechanism in the process of DNA nanostructure assembly. We show that the assembly of junctions in which the arms are consecutively ordered is more efficient than junctions with randomly-ordered components, with the latter showing assembly through several alternative trajectories as a potential mechanism explaining the lower efficiency. This highlights consecutiveness as a new design consideration that could be implemented in DNA nanotechnology CAD tools to produce more efficient and high-yield designs. Altogether, our experimental findings allowed us to devise a quantitative, cooperativity-based heuristic model for the assembly of DNA nanostructures, which is highly consistent with experimental observations.
| S-EPMC4513873 | biostudies-literature
Project description:A multifunctional supramolecular assembly was successfully constructed by the host-guest complexation of doubly positively charged adamantane (ADA) with β-CD-modified hexabenzocoronene and the π-stacking of coronene with mitoxantrone, which was characterized by transmission electron microscopy, scanning electron microscopy, dynamic light-scattering, and zeta potential experiments. Possessing a small size and rigid backbone coronene center, the water-soluble biocompatible supramolecular assembly has intracellular imaging abilities. Moreover, after the ester group of ADA was hydrolyzed into a carboxyl group, the positively charged quaternary amine strand converted into a zwitterion structure, which realized the controlled plasmid DNA binding and release. Besides, the cytotoxicity experiments showed that the supramolecular assembly possesses slightly lower toxicity and a slightly higher anticancer activity than free drug. We believe that this work might present a convenient method for synergetic cancer treatment.
| S-EPMC6682016 | biostudies-literature
Project description:Supramolecular self-assembly offers a powerful strategy to produce high-performance, stimuli-responsive nanomaterials. However, lack of molecular understanding of stimulated responses frequently hampers our ability to rationally design nanomaterials with sharp responses. Here we elucidated the molecular pathway of pH-triggered supramolecular self-assembly of a series of ultra-pH sensitive (UPS) block copolymers. Hydrophobic micellization drove divergent proton distribution in either highly protonated unimer or neutral micelle states along the majority of the titration coordinate unlike conventional small molecular or polymeric bases. This all-or-nothing two-state solution is a hallmark of positive cooperativity. Integrated modelling and experimental validation yielded a Hill coefficient of 51 in pH cooperativity for a representative UPS block copolymer, by far the largest reported in the literature. These data suggest hydrophobic micellization and resulting positive cooperativity offer a versatile strategy to convert responsive nanomaterials into binary on/off switchable systems for chemical and biological sensing, as demonstrated in an additional anion sensing model.
| S-EPMC5095283 | biostudies-literature
Project description:We construct a fluorescent supramolecular system (TPE-Q4 ⊂ DSP5) of excellent tolerance to a wide range of pH by the facile self-assembly of a new pillar[5]arene bearing disulfonated arms (DSP5) with an AIE-active tetraphenylethene-based tetratopic guest bearing four quaternary ammonium binding sites (TPE-Q4), which exhibits strong blue emission even in dilute aqueous solutions along with much higher quantum yield and longer fluorescence lifetime than TPE-Q4 itself. This appreciable property can be attributed to the supramolecular assembly-induced emission (SAIE) mechanism endowed by the host-guest inclusion complexation based on synthetic macrocycles. Remarkably, the enhanced fluorescence of the supramolecular assembly is quenched efficiently and exclusively by ferric ions in water with a high Stern-Volmer formula constant of 1.3 × 105 mol-1, demonstrating the excellent cation selectivity and visualized responsiveness in ion sensing and detection.
| S-EPMC6750118 | biostudies-literature
Project description:Peptide amphiphiles are molecules containing a peptide segment covalently bonded to a hydrophobic tail and are known to self-assemble in water into supramolecular nanostructures with shape diversity ranging from spheres to cylinders, twisted ribbons, belts, and tubes. Understanding the self-assembly mechanisms to control dimensions and shapes of the nanostructures remains a grand challenge. We report here on a systematic study of peptide amphiphiles containing valine-glutamic acid dimeric repeats known to promote self-assembly into belt-like flat assemblies. We find that the lateral growth of the assemblies can be controlled in the range of 100 nm down to 10 nm as the number of dimeric repeats is increased from two to six. Using circular dichroism, the degree of ?-sheet twisting within the supramolecular assemblies was found to be directly proportional to the number of dimeric repeats in the PA molecule. Interestingly, as twisting increased, a threshold is reached where cylinders rather than flat assemblies become the dominant morphology. We also show that in the belt regime, the width of the nanostructures can be decreased by raising the pH to increase charge density and therefore electrostatic repulsion among glutamic acid residues. The control of size and shape of these nanostructures should affect their functions in biological signaling and drug delivery.
| S-EPMC3586767 | biostudies-literature