Read by QxMD icon Read

Dna origami

Benjamin Kick, Samantha Hensler, Florian Praetorius, Hendrik Dietz, Dirk Weuster-Botz
The bacteriophage M13 has found frequent applications in nanobiotechnology due to its chemically and genetically tunable protein surface and its ability to self-assemble into colloidal membranes. Additionally, its single-stranded (ss) genome is commonly used as scaffold for DNA origami. Despite the manifold uses of M13, upstream production methods for phage and scaffold ssDNA are underexamined with respect to future industrial usage. Here, the high-cell-density phage production with Escherichia coli as host organism was studied in respect of medium composition, infection time, multiplicity of infection and specific growth rate...
October 17, 2016: Biotechnology and Bioengineering
Amalia R Driller-Colangelo, Karen W L Chau, Jessica M Morgan, Nathan D Derr
Cytoplasmic dynein is a minus-end directed microtubule-based motor protein that drives intracellular cargo transport in eukaryotic cells. Although many intracellular cargos are propelled by small groups of dynein motors, the biophysical mechanisms governing ensemble motility remain largely unknown. To investigate the emergent motility of motor ensembles, we have designed a programmable DNA origami synthetic cargo "chassis" enabling us to control the number of dynein motors in the ensemble and vary the rigidity of the cargo chassis itself...
October 8, 2016: Cytoskeleton
Michael H Räz, Kumi Hidaka, Shana J Sturla, Hiroshi Sugiyama, Masayuki Endo
To examine the effect of the torsional constraints imposed on DNA substrates on Cas9 cleavage, we prepared con-strained DNA substrates using a DNA origami frame. By fixing the dsDNA at the connectors of the DNA frame, we created four different dsDNA substrates containing torsion-ally constrained or relaxed strands. We quantified the cleav-age of constrained and relaxed substrates by Cas9 with quantitative PCR. Moreover, we observed the Cas9/sgRNA complex bound to the DNA substrates and characterized the dissociation of the complex with high-speed AFM...
October 6, 2016: Journal of the American Chemical Society
Feng Kong, Hongbo Zhang, Xiangmeng Qu, Xu Zhang, Dong Chen, Ruihua Ding, Ermei Mäkilä, Jarno Salonen, Hélder A Santos, Mingtan Hai
Gold nanorods, DNA origami, and porous silicon nanoparticle-functionalized biocompatible double emulsion are developed for versatile molecular targeted therapeutics and antibody combination therapy. This advanced photothermal responsive all-in-one biocompatible platform can be easily formed with great therapeutics loading capacity for different cancer treatments with synergism and multidrug resistance inhibition, which has great potential in advancing biomedical applications.
September 30, 2016: Advanced Materials
Yang Du, Qiao Jiang, Nicolas Beziere, Linlin Song, Qian Zhang, Dong Peng, Chongwei Chi, Xin Yang, Hongbo Guo, Gaël Diot, Vasilis Ntziachristos, Baoquan Ding, Jie Tian
A functional cancer theranostic nanoplatform is developed, specifically tailored toward the optoacoustic modality by combining gold nanorods with DNA nanostructures (D-AuNR). DNA origami is used as an efficient delivery vehicle owing to its prominent tumor-targeting property. The D-AuNR hybrids display an enhanced tumor diagnostic sensitivity by improved optoacoustic imaging and excellent photothermal therapeutic properties in vivo.
September 28, 2016: Advanced Materials
Igor Drobnak, Ajasja Ljubetič, Helena Gradišar, Tomaž Pisanski, Roman Jerala
Proteins are highly perfected natural molecular machines, owing their properties to the complex tertiary structures with precise spatial positioning of different functional groups that have been honed through millennia of evolutionary selection. The prospects of designing new molecular machines and structural scaffolds beyond the limits of natural proteins make design of new protein folds a very attractive prospect. However, de novo design of new protein folds based on optimization of multiple cooperative interactions is very demanding...
2016: Advances in Experimental Medicine and Biology
Sabrina Simoncelli, Eva-Maria Roller, Patrick Urban, Robert Schreiber, Andrew J Turberfield, Tim Liedl, Theobald Lohmueller
DNA origami is a powerful approach for assembling plasmonic nanoparticle dimers and Raman dyes with high yields and excellent positioning control. Here we show how optothermal induced shrinking of a DNA origami template can be employed to control the gap sizes between two 40 nm gold nanoparticles in a range of 1 nm - 2 nm. The high field confinement achieved with this optothermal approach was demonstrated by detection of surface-enhanced Raman spectroscopy (SERS) signals from single molecules that are precisely placed within the DNA origami template that spans the nanoparticle gap...
September 20, 2016: ACS Nano
Chao Zhou, Yiyang Zhang, Yuanchen Dong, Fen Wu, Dianming Wang, Ling Xin, Dongsheng Liu
2D assembly of amphiphilic molecules in aqueous solution is a challenging and intriguing topic as it is normally thermodynamically unfavorable. However, through frame-guided assembly strategy and using DNA origami as the frame, monodispersed and shape-defined nanosheets are prepared. As leading hydrophobic groups (LHGs) are anchored on the frames, amphiphilic molecules in aqueous solution are guided to assemble in the hydrophobic region. By adjusting the distribution of the LHGs, the size and shape of the assemblies can be controlled precisely...
September 16, 2016: Advanced Materials
Fan Hong, Shuoxing Jiang, Tong Wang, Yan Liu, Hao Yan
Designer DNA architectures with nanoscale geometric controls provide a programmable molecular toolbox for engineering complex nanodevices. Scaffolded DNA origami has dramatically improved our ability to design and construct DNA nanostructures with finite size and spatial addressability. Here we report a novel design strategy to engineer multilayered wireframe DNA structures by introducing crossover pairs that connect neighboring layers of DNA double helices. These layered crossovers (LX) allow the scaffold or helper strands to travel through different layers and can control the relative orientation of DNA helices in neighboring layers...
October 4, 2016: Angewandte Chemie
Bezu Teschome, Stefan Facsko, Tommy Schönherr, Jochen Kerbusch, Adrian Keller, Artur Erbe
DNA origami nanostructures have been used extensively as scaffolds for numerous applications such as for organizing both organic and inorganic nanomaterials, studying single molecule reactions, and fabricating photonic devices. Yet, little has been done toward the integration of DNA origami nanostructures into nanoelectronic devices. Among other challenges, the technical difficulties in producing well-defined electrical contacts between macroscopic electrodes and individual DNA origami-based nanodevices represent a serious bottleneck that hinders the thorough characterization of such devices...
October 11, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
Fabian Kilchherr, Christian Wachauf, Benjamin Pelz, Matthias Rief, Martin Zacharias, Hendrik Dietz
We directly measured at the single-molecule level the forces and lifetimes of DNA base-pair stacking interactions for all stack sequence combinations. Our experimental approach combined dual-beam optical tweezers with DNA origami components to allow positioning of blunt-end DNA helices so that the weak stacking force could be isolated. Base-pair stack arrays that lacked a covalent backbone connection spontaneously dissociated at average rates ranging from 0.02 to 500 per second, depending on the sequence combination and stack array size...
September 9, 2016: Science
Aradhana Chopra, Swati Krishnan, Friedrich C Simmel
DNA origami structures are artificial molecular nanostructures in which DNA double helices are forced into a closely packed configuration by a multitude of DNA strand crossovers. We show that three different types of origami structures (a flat sheet, a hollow tube, and a compact origami block) can be formed in magnesium-free buffer solutions containing low (<1 mM) concentrations of the condensing agent spermidine. Much like in DNA condensation, the amount of spermidine required for origami folding is proportional to the DNA concentration...
October 12, 2016: Nano Letters
Julia Prinz, Aleksandar Matković, Jelena Pešić, Radoš Gajić, Ilko Bald
A combination of three innovative materials within one hybrid structure to explore the synergistic interaction of their individual properties is presented. The unique electronic, mechanical, and thermal properties of graphene are combined with the plasmonic properties of gold nanoparticle (AuNP) dimers, which are assembled using DNA origami nanostructures. This novel hybrid structure is characterized by means of correlated atomic force microscopy and surface-enhanced Raman scattering (SERS). It is demonstrated that strong interactions between graphene and AuNPs result in superior SERS performance of the hybrid structure compared to their individual components...
October 2016: Small
Evi Stahl, Florian Praetorius, Carina C de Oliveira Mann, Karl-Peter Hopfner, Hendrik Dietz
One key goal of DNA nanotechnology is the bottom-up construction of macroscopic crystalline materials. Beyond applications in fields such as photonics or plasmonics, DNA-based crystal matrices could possibly facilitate the diffraction-based structural analysis of guest molecules. Seeman and coworkers reported in 2009 the first designed crystal matrices based on a 38 kDa DNA triangle that was composed of seven chains. The crystal lattice was stabilized, unprecedentedly, by Watson-Crick base pairing. However, 3D crystallizing larger designed DNA objects that include more chains such as DNA origami remains an unsolved problem...
September 1, 2016: ACS Nano
Hui San Ong, Mohd Syafiq-Rahim, Noor Hayaty Abu Kasim, Mohd Firdaus-Raih, Effirul Ikhwan Ramlan
Fabrication of functional DNA nanostructures operating at a cellular level has been accomplished through molecular programming techniques such as DNA origami and single-stranded tiles (SST). During implementation, restrictive and constraint dependent designs are enforced to ensure conformity is attainable. We propose a concept of DNA polyominoes that promotes flexibility in molecular programming. The fabrication of complex structures is achieved through self-assembly of distinct heterogeneous shapes (i.e., self-organised optimisation among competing DNA basic shapes) with total flexibility during the design and assembly phases...
October 20, 2016: Journal of Biotechnology
Wenyan Liu, Jonathan Halverson, Ye Tian, Alexei V Tkachenko, Oleg Gang
The science of self-assembly has undergone a radical shift from asking questions about why individual components self-organize into ordered structures, to manipulating the resultant order. However, the quest for far-reaching nanomanufacturing requires addressing an even more challenging question: how to form nanoparticle (NP) structures with designed architectures without explicitly prescribing particle positions. Here we report an assembly concept in which building instructions are embedded into NPs via DNA frames...
September 2016: Nature Chemistry
Gaolian Xu, Debbie Nolder, Julien Reboud, Mary C Oguike, Donelly A van Schalkwyk, Colin J Sutherland, Jonathan M Cooper
We demonstrate, for the first time, the multiplexed determination of microbial species from whole blood using the paper-folding technique of origami to enable the sequential steps of DNA extraction, loop-mediated isothermal amplification (LAMP), and array-based fluorescence detection. A low-cost handheld flashlight reveals the presence of the final DNA amplicon to the naked eye, providing a "sample-to-answer" diagnosis from a finger-prick volume of human blood, within 45 min, with minimal user intervention...
August 24, 2016: Angewandte Chemie
Anja Henning-Knechtel, Matthew Wiens, Mathias Lakatos, Andreas Heerwig, Frieder Ostermaier, Nora Haufe, Michael Mertig
DNA nanostructures are promising construction materials to bridge the gap between self-assembly of functional molecules and conventional top-down fabrication methods in nanotechnology. Their positioning onto specific locations of a microstructured substrate is an important task towards this aim. Here we study manipulation and positioning of pristine and of gold nanoparticle-conjugated tubular DNA origami structures using ac dielectrophoresis. The dielectrophoretic behavior was investigated employing fluorescence microscopy...
2016: Beilstein Journal of Nanotechnology
Liulin Yang, Aijie Liu, Shuqin Cao, Rindia M Putri, Pascal Jonkheijm, Jeroen J L M Cornelissen
The study of protein self-assembly has attracted great interest over the decades, due to the important role that proteins play in life. In contrast to the major achievements that have been made in the fields of DNA origami, RNA, and synthetic peptides, methods for the design of self-assembling proteins have progressed more slowly. This Concept article provides a brief overview of studies on native protein and artificial scaffold assemblies and highlights advances in designing self-assembling proteins. The discussions are focused on design strategies for self-assembling proteins, including protein fusion, chemical conjugation, supramolecular, and computational-aided de novo design...
August 18, 2016: Chemistry: a European Journal
Eva-Maria Roller, Christos Argyropoulos, Alexander Högele, Tim Liedl, Mauricio Pilo-Pais
Coherent energy exchange between plasmons and excitons is a phenomenon that arises in the strong coupling regime resulting in distinct hybrid states. The DNA-origami technique provides an ideal framework to custom-tune plasmon-exciton nanostructures. By employing this well controlled self-assembly process, we realized hybrid states by precisely positioning metallic nanoparticles in a defined spatial arrangement with fixed nanometer-sized interparticle spacing. Varying the nanoparticle diameter between 30 nm and 60 nm while keeping their separation distance constant allowed us to precisely adjust the plasmon resonance of the structure to accurately match the energy frequency of a J-aggregate exciton...
September 14, 2016: Nano Letters
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"