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https://www.readbyqxmd.com/read/29147695/synthesis-of-an-ethyleneimine-tetrahedral-dna-nanostructure-complex-and-its-potential-application-as-a-multi-functional-delivery-vehicle
#1
Taoran Tian, Tao Zhang, Tengfei Zhou, Shiyu Lin, Sirong Shi, Yunfeng Lin
Nowadays, DNA nanostructures are extensively researched for their biocompatibility, editable functionality, and structural stability. Tetrahedral DNA nanostructures (TDNs), widely known for their membrane permeability, are regarded as potential candidates for drug delivery. However, the stability and membrane permeability of TDNs call for further enhancement if in vivo usage is ascribed. To overcome the drawbacks of TDNs, ethylene imine (PEI, 25 kDa, branched)-a classic cationic polymer in the field of gene delivery-was applied...
November 17, 2017: Nanoscale
https://www.readbyqxmd.com/read/29147539/reversible-control-of-cell-membrane-receptor-function-using-dna-nano-spring-multivalent-ligands
#2
Kaixiang Zhang, Ruijie Deng, Yupeng Sun, Ling Zhang, Jinghong Li
Chemically functionalized and nanostructured materials, which mimic the features of the natural extracellular matrix, provide a tool to organize cell surface receptors into nanoscale clusters and manipulate cell functions. However, the existing materials are mainly based on static structures. Herein, we developed a DNA based structure-switchable and multivalent material that acts as a 'nano-spring', enabling reversible control of membrane receptor function at the cell surface. This 'nano-spring' can be easily synthesized by rolling circle amplification and finely tuned by changing the circular template design...
October 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29144399/dna-g-wire-formation-using-an-artificial-peptide-is-controlled-by-protease-activity
#3
Kenji Usui, Arisa Okada, Shungo Sakashita, Masayuki Shimooka, Takaaki Tsuruoka, Shu-Ichi Nakano, Daisuke Miyoshi, Tsukasa Mashima, Masato Katahira, Yoshio Hamada
The development of a switching system for guanine nanowire (G-wire) formation by external signals is important for nanobiotechnological applications. Here, we demonstrate a DNA nanostructural switch (G-wire <--> particles) using a designed peptide and a protease. The peptide consists of a PNA sequence for inducing DNA to form DNA-PNA hybrid G-quadruplex structures, and a protease substrate sequence acting as a switching module that is dependent on the activity of a particular protease. Micro-scale analyses via TEM and AFM showed that G-rich DNA alone forms G-wires in the presence of Ca(2+), and that the peptide disrupted this formation, resulting in the formation of particles...
November 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29141138/differential-effects-of-strand-asymmetry-on-the-energetics-and-structural-flexibility-of-dna-internal-loops
#4
Thao Tran, Brian Cannon
Internal loops within structured nucleic acids disrupt local base-stacking and destabilize neighboring helical domains; however, these structural motifs also expand the conformational and functional capabilities for structured nucleic acids. Variations in size, distribution of loop nucleotides on opposing strands (strand asymmetry), and sequence alter their biophysical properties. Here, the thermodynamics and structural flexibility of poly(T)-rich DNA internal loops were systematically investigated in terms of loop size and strand asymmetry...
November 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/29131541/rhombic-shaped-nanostructures-and-mechanical-properties-of-2d-dna-origami-constructed-with-different-crossover-nick-designs
#5
Zhipeng Ma, Yunfei Huang, Seongsu Park, Kentaro Kawai, Do-Nyun Kim, Yoshikazu Hirai, Toshiyuki Tsuchiya, Hirofumi Yamada, Osamu Tabata
DNA origami methods enable the fabrication of various nanostructures and nanodevices, but their effective use depends on an understanding of their structural and mechanical properties and the effects of basic structural features. Frequency-modulation atomic force microscopy is introduced to directly characterize, in aqueous solution, the crossover regions of sets of 2D DNA origami based on different crossover/nick designs. Rhombic-shaped nanostructures formed under the influence of flexible crossovers placed between DNA helices are observed in DNA origami incorporating crossovers every 3, 4, or 6 DNA turns...
November 13, 2017: Small
https://www.readbyqxmd.com/read/29126166/fabrication-of-circular-assemblies-with-dna-tetrahedrons-from-static-structures-to-a-dynamic-rotary-motor
#6
Liying Wang, Zhenyu Meng, Felicia Martina, Huilin Shao, Fangwei Shao
DNA tetrahedron as the simplest 3D DNA nanostructure has been applied widely in biomedicine and biosensing. Herein, we design and fabricate a series of circular assemblies of DNA tetrahedron with high purity and decent yields. These circular nanostructures are confirmed by endonuclease digestion, gel electrophoresis and atomic force microscopy. Inspired by rotary protein motor, we demonstrate these circular architectures can serve as a stator for a rotary DNA motor to achieve the circular rotation. The DNA motor can rotate on the stators for several cycles, and the locomotion of the motor is monitored by the real-time fluorescent measurements...
November 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29122734/gene-editing-of-mps-i-human-fibroblasts-by-co-delivery-of-a-crispr-cas9-plasmid-and-a-donor-oligonucleotide-using-nanoemulsions-as-nonviral-carriers
#7
Roselena Silvestri Schuh, Talita Giacomet de Carvalho, Roberto Giugliani, Ursula Matte, Guilherme Baldo, Helder Ferreira Teixeira
Mucopolysaccharidosis type I (MPS I) is an inherited disease caused by the deficiency of alpha-L-iduronidase (IDUA). This study shows the use of nanoemulsions co-complexed with the plasmid of CRISPR/Cas9 system and a donor oligonucleotide aiming at MPS I gene editing in vitro. Nanoemulsions composed of MCT, DOPE, DOTAP, DSPE-PEG, and water were prepared by high-pressure homogenization. The DNA was complexed by adsorption or encapsulation of preformed DNA/DOTAP complexes with nanoemulsions at +4/ -1 charge ratio...
November 6, 2017: European Journal of Pharmaceutics and Biopharmaceutics
https://www.readbyqxmd.com/read/29111659/collapse-of-dna-tetrahedron-nanostructure-for-off-on-fluorescence-detection-of-dna-methyltransferase-activity
#8
Xiaoyan Zhou, Min Zhao, Xiaolei Duan, Bin Guo, Wei Cheng, Shijia Ding, Huangxian Ju
As a potential detection technique, highly rigid and versatile functionality of DNA tetrahedron nanostructures is often used in biosensing systems. In this work, a novel multifunctional nanostructure has been developed as an "off-on" fluorescent probe for detection of target methyltransferase by integrating the elements of DNA tetrahedron, target recognition, and dual-labeled reporter. This sensing system is initially in an "OFF" state owing to the close proximity of fluorophores and quenchers. After the substrate is recognized by target methyltransferase, the DNA tetrahedron can be methylated to produce methylated DNA sites...
November 13, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29109407/paper-based-sensing-device-for-electrochemical-detection-of-oxidative-stress-biomarker-8-hydroxy-2-deoxyguanosine-8-ohdg-in-point-of-care
#9
Gabriela V Martins, Ana P M Tavares, Elvira Fortunato, M Goreti F Sales
This work presents a cost-effective, label-free in point-of-care (POC) biosensor for the sensitive detection of 8-hydroxy-2'-deoxyguanosine (8-OHdG), the most abundant oxidative product of DNA, that may allow a premature assessment of cancer disease, thereby improving diagnosis, prognostics and survival rates. The device targets the direct detection of 8-OHdG by using for the first time a carbon-ink 3-electrode on a paper substrate coupled to Differential Pulse Voltammetry readings. This design was optimized by adding nanostructured carbon materials to the ink and the conducting polymer PEDOT, enhancing the electrocatalytic properties of the sensor towards 8-OHdG detection...
November 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29083876/characterizing-the-motion-of-jointed-dna-nanostructures-using-a-coarse-grained-model
#10
Rahul Sharma, John S Schreck, Flavio Romano, Ard A Louis, Jonathan P K Doye
As detailed structural characterizations of large complex DNA nanostructures are hard to obtain experimentally, particularly if they have substantial flexibility, coarse-grained modeling can potentially provide an important complementary role. Such modeling can provide a detailed view of both the average structure and the structural fluctuations, as well as providing insight into how the nanostructure's design determines its structural properties. Here, we present a case study of jointed DNA nanostructures using the oxDNA model...
November 3, 2017: ACS Nano
https://www.readbyqxmd.com/read/29082397/surface-engineered-quantum-dots-electrospun-nanofibers-as-a-networked-fluorescence-aptasensing-platform-toward-biomarkers
#11
Tong Yang, Peng Hou, Lin Ling Zheng, Lei Zhan, Peng Fei Gao, Yuan Fang Li, Cheng Zhi Huang
A membrane-based fluorescent sensing platform is a facile, point-of-care and promising technique in chemo/bio-analytical fields. However, the existing fluorescence sensing films for cancer biomarkers have several problems, with dissatisfactory sensitivity and selectivity, low utilization of probes encapsulated in films as well as the tedious design of membrane structures. In this work, a novel fluorescence sensing platform is fabricated by bio-grafting quantum dots (QDs) onto the surface of electrospun nanofibers (NFs)...
November 9, 2017: Nanoscale
https://www.readbyqxmd.com/read/29070911/a-simple-surface-plasmon-resonance-biosensor-for-detection-of-pml-rar%C3%AE-based-on-heterogeneous-fusion-gene-triggered-nonlinear-hybridization-chain-reaction
#12
Bin Guo, Wei Cheng, Yongjie Xu, Xiaoyan Zhou, Xinmin Li, Xiaojuan Ding, Shijia Ding
In this work, a simple and enzyme-free surface plasmon resonance (SPR) biosensing strategy has been developed for highly sensitive detection of two major PML/RARα (promyelocytic leukemia, retinoic acid receptor alpha) subtypes based on the heterogeneous fusion gene-triggered nonlinear hybridization chain reaction (HCR). On the gold chip surface, the cascade self-assembly process is triggered after the introduction of PML/RARα. The different fragments of PML/RARα can specifically hybridize with capture probes (Cp) immobilized on the chip and the hybridization DNA1 (H1)...
October 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29064489/engineering-nucleic-acid-structures-for-programmable-molecular-circuitry-and-intracellular-biocomputation
#13
REVIEW
Jiang Li, Alexander A Green, Hao Yan, Chunhai Fan
Nucleic acids have attracted widespread attention due to the simplicity with which they can be designed to form discrete structures and programmed to perform specific functions at the nanoscale. The advantages of DNA/RNA nanotechnology offer numerous opportunities for in-cell and in-vivo applications, and the technology holds great promise to advance the growing field of synthetic biology. Many elegant examples have revealed the potential in integrating nucleic acid nanostructures in cells and in vivo where they can perform important physiological functions...
November 2017: Nature Chemistry
https://www.readbyqxmd.com/read/29058418/allosteric-control-of-oxidative-catalysis-by-a-dna-rotaxane-nanostructure
#14
Mathias Centola, Julián Valero, Michael Famulok
DNA is a versatile construction material for the bottom-up assembly of structures and functional devices in the nanoscale. Additionally, there are specific sequences called DNAzymes that can fold into tertiary structures that display catalytic activity. Here we report the design of an interlocked DNA nanostructure that is able to fine-tune the oxidative catalytic activity of a split DNAzyme in a highly controllable manner. As scaffold, we employed a double-stranded DNA rotaxane for its ability to undergo programmable and predictable conformational changes...
November 1, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29057557/valence-engineering-of-quantum-dots-using-programmable-dna-scaffolds
#15
Jianlei Shen, Qian Tang, Li Li, Jiang Li, Xiaolei Zuo, Xiangmeng Qu, Hao Pei, Lihua Wang, Chunhai Fan
Precise control over quantum dots (QDs) valency is critical and fundamental for quantitative imaging in living cells. However, prior approaches on valence control of QDs remain restricted to single types of valences. Here we report a DNA-programmed general strategy for valence engineering of QDs with high modularity and high yield. By employing a series of programmable DNA scaffolds, we generated QDs with tunable valences in a single step with near-quantitative yield (> 95%). We further demonstrated the use of these valence-engineered QDs to develop 12 types of topologically organized QDs-QDs and QDs-AuNPs and 4 types of fluorescent resonance energy transfer (FRET) nanostructures...
October 23, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29051565/control-of-enzyme-reactions-by-a-reconfigurable-dna-nanovault
#16
Guido Grossi, Mette Dalgaard Ebbesen Jepsen, Jørgen Kjems, Ebbe Sloth Andersen
Biological systems use compartmentalisation as a general strategy to control enzymatic reactions by precisely regulating enzyme-substrate interactions. With the advent of DNA nanotechnology, it has become possible to rationally design DNA-based nano-containers with programmable structural and dynamic properties. These DNA nanostructures have been used to cage enzymes, but control over enzyme-substrate interactions using a dynamic DNA nanostructure has not been achieved yet. Here we introduce a DNA origami device that functions as a nanoscale vault: an enzyme is loaded in an isolated cavity and the access to free substrate molecules is controlled by a multi-lock mechanism...
October 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/29044199/fluorescence-coded-dna-nanostructure-probe-system-to-enable-discrimination-of-tumor-heterogeneity-via-a-screening-of-dual-intracellular-microrna-signatures-in-situ
#17
Seung Won Shin, Byoung Sang Lee, Kisuk Yang, Lunjakorn Amornkitbamrung, Min Su Jang, Bo Mi Ku, Seung-Woo Cho, Jung Heon Lee, Hojae Bae, Byung-Keun Oh, Myung-Ju Ahn, Yong Taik Lim, Soong Ho Um
Since the delivery kinetics of different cell types are different, the signal from the target cell is greatly affected by the noise signal of the diagnostic system. This is a major obstacle hindering the practical application of intracellular diagnostic systems, such as tumor heterogeneity. To address these issues, here we present a microRNA detection platform using fluorescence-encoded nanostructured DNA-based probes. The nanostructured DNA was designed to include molecular beacons for detecting cytosolic microRNA as well as additional fluorophores...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29043366/distance-dependent-photoacoustics-revealed-through-dna-nanostructures
#18
James Joseph, Kevin N Baumann, Philipp Koehler, Tim J Zuehlsdorff, Daniel J Cole, Judith Weber, Sarah E Bohndiek, Silvia Hernández-Ainsa
Molecular rulers that rely on the Förster resonance energy transfer (FRET) mechanism are widely used to investigate dynamic molecular processes that occur on the nanometer scale. However, the capabilities of these fluorescence molecular rulers are fundamentally limited to shallow imaging depths by light scattering in biological samples. Photoacoustic tomography (PAT) has recently emerged as a high resolution modality for in vivo imaging, coupling optical excitation with ultrasound detection. In this paper, we report the capability of PAT to probe distance-dependent FRET at centimeter depths...
November 2, 2017: Nanoscale
https://www.readbyqxmd.com/read/29038818/a-c-hcr-assembly-of-branched-dna-nanostructures-for-amplified-uracil-dna-glycosylase-assays
#19
Jing Wang, Min Pan, Jie Wei, Xiaoqing Liu, Fuan Wang
An autonomous nonenzymatic DNA machine has been successfully engineered based on a two-layered cascaded hybridization chain reaction (C-HCR) circuit, in which the tandem outputs of the upstream HCR-1 unit activate the downstream HCR-2 unit to induce successive repeated hybridizations, generating branched DNA structures and enabling sensitive and selective detection of uracil-DNA glycosylase and its inhibitors.
October 17, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29035374/design-of-coiled-coil-protein-origami-cages-that-self-assemble-in-vitro-and-in-vivo
#20
Ajasja Ljubetič, Fabio Lapenta, Helena Gradišar, Igor Drobnak, Jana Aupič, Žiga Strmšek, Duško Lainšček, Iva Hafner-Bratkovič, Andreja Majerle, Nuša Krivec, Mojca Benčina, Tomaž Pisanski, Tanja Ćirković Veličković, Adam Round, José María Carazo, Roberto Melero, Roman Jerala
Polypeptides and polynucleotides are natural programmable biopolymers that can self-assemble into complex tertiary structures. We describe a system analogous to designed DNA nanostructures in which protein coiled-coil (CC) dimers serve as building blocks for modular de novo design of polyhedral protein cages that efficiently self-assemble in vitro and in vivo. We produced and characterized >20 single-chain protein cages in three shapes-tetrahedron, four-sided pyramid, and triangular prism-with the largest containing >700 amino-acid residues and measuring 11 nm in diameter...
November 2017: Nature Biotechnology
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