keyword
MENU ▼
Read by QxMD icon Read
search

Dna origami

keyword
https://www.readbyqxmd.com/read/29141133/hierarchical-assembly-of-dna-filaments-with-designer-elastic-properties
#1
Barbara Sacca, Wolfgang Pfeifer, Pascal Lill, Christos Gatsogiannis
The elastic features of protein filaments are encoded in their component units and in the way they are connected, thus defining a biunivocal relationship between the monomer and the result of its self-assembly. Using DNA origami approaches, we constructed a reconfigurable module, composed of two quasi-independent domains and four possible interfaces, capable of facial and lateral growing through specific recognition patterns. Whereas the flexibility of the intra-domains region can be regulated by switchable DNA motifs, the inter-domain interfaces feature mutually and self-complementary shapes, whose pairwise association leads to filaments of programmable periodicity and variable persistence length...
November 15, 2017: ACS Nano
https://www.readbyqxmd.com/read/29131610/real-time-imaging-of-single-molecule-enzyme-cascade-using-a-dna-origami-raft
#2
Lele Sun, Yanjing Gao, Yan Xu, Jie Chao, Huajie Liu, Lianhui Wang, Di Li, Chunhai Fan
The dynamics of enzymes are directly associated with their functions in various biological processes. Nevertheless, the ability to image motions of single enzymes in a highly parallel fashion remains a challenge. Here, we develop a DNA origami raft-based platform for in-situ real-time imaging of enzyme cascade at the single-molecule level. The motions of enzymes are rationally controlled via different tethering modes on a two-dimensional (2D) supported lipid bilayer (SLB). We construct an enzyme cascade by anchoring catalase on cholesterol-labeled double stranded (ds) DNA, and glucose oxidase on cholesterol-labeled origami rafts...
November 13, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29131541/rhombic-shaped-nanostructures-and-mechanical-properties-of-2d-dna-origami-constructed-with-different-crossover-nick-designs
#3
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/29129049/dna-origami-directed-au-nanostar-dimers-for-single-molecule-surface-enhanced-raman-scattering
#4
Swati Tanwar, Krishna Haldar, Tapasi Sen
We demonstrate the synthesis of Au nanostar dimer with tunable interparticle gap and controlled stoichiometry as-sembled on DNA origami. Au nanostars with uniform and sharp tips were immobilized on rectangular DNA origami dimerized structures to create nanoantennas containing monomeric and dimeric Au nanostars. Single Texas red dye was specifically attached in the junction of the dimerized origami which acts as a Raman reporter molecule. The SERS enhancement factors of single Texas red dye located in the conjunction region in the dimer structures having inter-particle gaps of 7 nm and 13 nm are 2 × 1010 and 8 × 109, respectively, which are strong enough for single analyte detec-tion...
November 13, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29120602/porphyrin-assisted-docking-of-a-thermophage-portal-protein-into-lipid-bilayers-nanopore-engineering-and-characterization
#5
Benjamin Cressiot, Sandra J Greive, Wei Si, Tomas C Pascoa, Mehrnaz Mojtabavi, Maria Chechik, Huw T Jenkins, Xueguang Lu, Ke Zhang, Aleksei Aksimentiev, Alfred A Antson, Meni Wanunu
Nanopore-based sensors for nucleic acid sequencing and single-molecule detection typically employ pore-forming membrane proteins with hydrophobic external surfaces, suitable for insertion into a lipid bilayer. In contrast, hydrophilic pore-containing molecules, such as DNA origami, have been shown to require chemical modification to favor insertion into a lipid environment. In this work, we describe a strategy for inserting polar proteins with an inner pore into lipid membranes, focusing here on a circular 12-subunit assembly of the thermophage G20c portal protein...
November 15, 2017: ACS Nano
https://www.readbyqxmd.com/read/29111693/electrical-actuation-of-a-dna-origami-nanolever-on-an-electrode
#6
Felix Kroener, Andreas Heerwig, Wolfgang Kaiser, Michael Mertig, Ulrich Rant
The development of electrically powered DNA origami nanomachines requires effective means to actuate moving origami parts by externally applied electric fields. Here, we demonstrate how origami nanolevers on an electrode can be manipulated (switched) at high frequency by alternating voltages. The orientation switching is long-time stable and can be induced by applying low voltages of merely 200 mV. The mechanical response time of a 100 nm long origami lever to an applied voltage step is less than 100 µs, allowing for a highly dynamic control of the induced motion...
November 7, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29097546/self-assembled-three-dimensional-chiral-colloidal-architecture
#7
Matan Yah Ben Zion, Xiaojin He, Corinna C Maass, Ruojie Sha, Nadrian C Seeman, Paul M Chaikin
Although stereochemistry has been a central focus of the molecular sciences since Pasteur, its province has previously been restricted to the nanometric scale. We have programmed the self-assembly of micron-sized colloidal clusters with structural information stemming from a nanometric arrangement. This was done by combining DNA nanotechnology with colloidal science. Using the functional flexibility of DNA origami in conjunction with the structural rigidity of colloidal particles, we demonstrate the parallel self-assembly of three-dimensional microconstructs, evincing highly specific geometry that includes control over position, dihedral angles, and cluster chirality...
November 3, 2017: Science
https://www.readbyqxmd.com/read/29063765/directional-photonic-wire-mediated-by-homo-f%C3%A3-rster-resonance-energy-transfer-on-a-dna-origami-platform
#8
Francesca Nicoli, Anders Barth, Wooli Bae, Fabian Neukirchinger, Alvaro H Crevenna, Don C Lamb, Tim Liedl
Elaborating efficient strategies and deepening the understanding of light transport at the nanoscale is of great importance for future designs of artificial light-harvesting assemblies and dye-based photonic circuits. In this work, we focus on studying the phenomenon of Förster resonance energy transfer (FRET) among fluorophores of the same kind (homo-FRET) and its implications for energy cascades containing two or three different dye molecules. Utilizing the spatial programmability of DNA origami, we arranged a chain of cyanine 3 (Cy3) dyes flanked at one end with a dye of lower excitation energy, cyanine 5 (Cy5), with or without an additional dye of higher excitation energy, Alexa488, at the other end...
November 1, 2017: ACS Nano
https://www.readbyqxmd.com/read/29051565/control-of-enzyme-reactions-by-a-reconfigurable-dna-nanovault
#9
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/29044955/single-molecule-observation-of-the-photoregulated-conformational-dynamics-of-dna-origami-nanoscissors
#10
Masayuki Endo, Elena M Willner, Yuu Kamada, Yuki Suzuki, Tomoko Emura, Kumi Hidaka, Hendrik Dietz, Hiroshi Sugiyama
We demonstrate direct observation of the dynamic opening and closing behavior of photo-controllable DNA origami nanoscissors (NS) using high-speed AFM. First the conformational change between the open and closed state controlled by adjustment of salt concentration could be directly observed during AFM scanning. Then light-responsive moieties were incorporated into the NS to control the structural changes by irradiation. Using photo-switchable DNA strands, we created a photoresponsive NS variant and were able to distinguish between the open and closed conformations after respective irradiation with UV and visible (Vis) light via gel electrophoresis and AFM imaging...
October 17, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29035374/design-of-coiled-coil-protein-origami-cages-that-self-assemble-in-vitro-and-in-vivo
#11
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
https://www.readbyqxmd.com/read/29027713/engineering-cell-surface-function-with-dna-origami
#12
Ehsan Akbari, Molly Y Mollica, Christopher R Lucas, Sarah M Bushman, Randy A Patton, Melika Shahhosseini, Jonathan W Song, Carlos E Castro
A specific and reversible method is reported to engineer cell-membrane function by embedding DNA-origami nanodevices onto the cell surface. Robust membrane functionalization across epithelial, mesenchymal, and nonadherent immune cells is achieved with DNA nanoplatforms that enable functions including the construction of higher-order DNA assemblies at the cell surface and programed cell-cell adhesion between homotypic and heterotypic cells via sequence-specific DNA hybridization. It is anticipated that integration of DNA-origami nanodevices can transform the cell membrane into an engineered material that can mimic, manipulate, and measure biophysical and biochemical function within the plasma membrane of living cells...
October 13, 2017: Advanced Materials
https://www.readbyqxmd.com/read/29024433/cation-induced-stabilization-and-denaturation-of-dna-origami-nanostructures-in-urea-and-guanidinium-chloride
#13
Saminathan Ramakrishnan, Georg Krainer, Guido Grundmeier, Michael Schlierf, Adrian Keller
The stability of DNA origami nanostructures under various environmental conditions constitutes an important issue in numerous applications, including drug delivery, molecular sensing, and single-molecule biophysics. Here, the effect of Na(+) and Mg(2+) concentrations on DNA origami stability is investigated in the presence of urea and guanidinium chloride (GdmCl), two strong denaturants commonly employed in protein folding studies. While increasing concentrations of both cations stabilize the DNA origami nanostructures against urea denaturation, they are found to promote DNA origami denaturation by GdmCl...
October 12, 2017: Small
https://www.readbyqxmd.com/read/28990389/stimulus-responsive-plasmonic-chiral-signals-of-gold-nanorods-organized-on-dna-origami
#14
Qiao Jiang, Qing Liu, Yuefeng Shi, Zhen-Gang Wang, Pengfei Zhan, Jianbing Liu, Chao Liu, Hui Wang, Xinghua Shi, Li Zhang, Jiashu Sun, Baoquan Ding, Minghua Liu
In response to environmental variations, living cells need to arrange the conformational changes of macromolecules to achieve the specific biofunctions. Inspired by natural molecular machines, artificial macromolecular assemblies with controllable nanostructures and environmentally responsive functions can be designed. By assembling macromolecular nanostructures with noble metal nanoparticles, environmental information could be significantly amplified and modulated. However, manufacturing dynamic plasmonic nanostructures that are efficiently responsive to different stimuli is still a challenging task...
October 11, 2017: Nano Letters
https://www.readbyqxmd.com/read/28967945/nanoscale-patterning-of-self-assembled-monolayer-sam-functionalised-substrates-with-single-molecule-contact-printing
#15
M Sajfutdinow, K Uhlig, A Prager, C Schneider, B Abel, D M Smith
Defined arrangements of individual molecules are covalenty connected ("printed") onto SAM-functionalised gold substrates with nanometer resolution. Substrates were initially pre-functionlised by coating with 3,3'-dithiodipropionic acid (DTPA) to form a self-assembled monolayer (SAM), which was characterised by atomic force microscopy (AFM), contact angle goniometry, cyclic voltammetry and surface plasmon resonance (SPR) spectroscopy. Pre-defined "ink" patterns displayed on DNA origami-based single-use carriers ("stamp") were covalently conjugated to the SAM using 1-ethyl-3-(3-dimethylamino-propyl)carbodiimide (EDC) and N-hydroxy-succinimide (NHS)...
October 12, 2017: Nanoscale
https://www.readbyqxmd.com/read/28953361/dna-nanotechnology-enabled-chiral-plasmonics-from-static-to-dynamic
#16
Chao Zhou, Xiaoyang Duan, Na Liu
The development of DNA nanotechnology, especially the advent of DNA origami, has made DNA ideally suited to construct nanostructures with unprecedented complexity and arbitrariness. As a fully addressable platform, DNA origami can be used to organize discrete entities in space through DNA hybridization with nanometer accuracy. Among a variety of functionalized particles, metal nanoparticles such as gold nanoparticles (AuNPs) feature an important pathway to endow DNA-origami-assembled nanostructures with tailored optical functionalities...
September 27, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28949522/structurally-ordered-nanowire-formation-from-co-assembly-of-dna-origami-and-collagen-mimetic-peptides
#17
Tao Jiang, Travis A Meyer, Charles Modlin, Xiaobing Zuo, Vincent P Conticello, Yonggang Ke
We describe the co-assembly of two different building units: collagen-mimetic peptides and DNA origami. Two peptides CP(++) and sCP(++) are designed with a sequence comprising a central block (Pro-Hyp-Gly) and two positively charged domains (Pro-Arg-Gly) at both N- and C-termini. Co-assembly of peptides and DNA origami two-layer (TL) nanosheets affords the formation of one-dimensional nanowires with repeating periodicity of ∼10 nm. Structural analyses suggest a face-to-face stacking of DNA nanosheets with peptides aligned perpendicularly to the sheet surfaces...
October 11, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28941223/fabrication-of-calcium-phosphate-based-nanocomposites-incorporating-dna-origami-gold-nanorods-and-anticancer-drugs-for-biomedical-applications
#18
Hongbo Zhang, Xiangmeng Qu, Hong Chen, Haixin Kong, Ruihua Ding, Dong Chen, Xu Zhang, Hao Pei, Hélder A Santos, Mingtan Hai, David A Weitz
DNA origami is designed by folding DNA strands at the nanoscale with arbitrary control. Due to its inherent biological nature, DNA origami is used in drug delivery for enhancement of synergism and multidrug resistance inhibition, cancer diagnosis, and many other biomedical applications, where it shows great potential. However, the inherent instability and low payload capacity of DNA origami restrict its biomedical applications. Here, this paper reports the fabrication of an advanced biocompatible nano-in-nanocomposite, which protects DNA origami from degradation and facilities drug loading...
September 22, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/28920942/exponential-growth-and-selection-in-self-replicating-materials-from-dna-origami-rafts
#19
Xiaojin He, Ruojie Sha, Rebecca Zhuo, Yongli Mi, Paul M Chaikin, Nadrian C Seeman
Self-replication and evolution under selective pressure are inherent phenomena in life, and but few artificial systems exhibit these phenomena. We have designed a system of DNA origami rafts that exponentially replicates a seed pattern, doubling the copies in each diurnal-like cycle of temperature and ultraviolet illumination, producing more than 7 million copies in 24 cycles. We demonstrate environmental selection in growing populations by incorporating pH-sensitive binding in two subpopulations. In one species, pH-sensitive triplex DNA bonds enable parent-daughter templating, while in the second species, triplex binding inhibits the formation of duplex DNA templating...
October 2017: Nature Materials
https://www.readbyqxmd.com/read/28912216/a-cargo-sorting-dna-robot
#20
Anupama J Thubagere, Wei Li, Robert F Johnson, Zibo Chen, Shayan Doroudi, Yae Lim Lee, Gregory Izatt, Sarah Wittman, Niranjan Srinivas, Damien Woods, Erik Winfree, Lulu Qian
Two critical challenges in the design and synthesis of molecular robots are modularity and algorithm simplicity. We demonstrate three modular building blocks for a DNA robot that performs cargo sorting at the molecular level. A simple algorithm encoding recognition between cargos and their destinations allows for a simple robot design: a single-stranded DNA with one leg and two foot domains for walking, and one arm and one hand domain for picking up and dropping off cargos. The robot explores a two-dimensional testing ground on the surface of DNA origami, picks up multiple cargos of two types that are initially at unordered locations, and delivers them to specified destinations until all molecules are sorted into two distinct piles...
September 15, 2017: Science
keyword
keyword
116895
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"