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dna nanostructure

Y Yasinskyi, Protsenko A, Maistrenko O, Rybalchenko V, Yu Prylutskyy, E Tauscher, U Ritter, I Kozeretska
Fullerenes have attracted attention since their discovery as structural units of complex carbon nanostructures capable of transporting drugs and macromolecules. As such artificial nanomaterials are applied in biology and medicine, they are routinely scrutinized for their effects on living organisms. The results of such studies range from direct destabilizing effects on DNA molecules to amelioration of the toxic effects of known genotoxic agents. We tested the effect of buckminsterfullerene (C60) on Drosophila melanogaster at DNA, tissue and organism levels...
April 15, 2019: Toxicology Letters
Tatiane R Cardozo, Raíne F De Carli, Allan Seeber, Wladimir H Flores, Jordana A N da Rosa, Queila S G Kotzal, Mauricio Lehmann, Fernanda R da Silva, Rafael R Dihl
Zinc oxide (ZnO) NPs are being used worldwide in consumer products and industrial applications. Based on predefined pathways, this study synthesized and characterized the nanostructures of ZnO NPs. The genotoxic effects of these nanomaterials were evaluated using a short-term in vivo bioassay, the somatic mutation and recombination test (SMART) in Drosophila melanogaster . In addition, a systems biology approach was used to search for known and predicted interaction networks between ZnO and proteins. The results observed in this study after in vivo exposure indicate that ZnO NPs are genotoxic and that homologous recombination (HR) was the main mechanism inducing loss of heterozygosis in the somatic cells of D...
March 1, 2019: Toxicology Research
Stefano Palazzolo, Mohamad Hadla, Concetta Russo Spena, Samer Bayda, Vinit Kumar, Francesco Lo Re, Muhammad Adeel, Isabella Caligiuri, Flavio Romano, Giuseppe Corona, Vincenzo Canzonieri, Giuseppe Toffoli, Flavio Rizzolio
One of the most promising applications of DNA origami is its use as an excellent evolution of nanostructured intelligent systems for drug delivery, but short in vivo lifetime and immune-activation are still major challenges to overcome. On the contrary, stealth liposomes have long-circulation time and are well tolerated by the immune system. To overcome DNA origami limitations, we have designed and synthesized a compact short tube DNA origami (STDO) of approximately 30 nm in length and 10 nm in width. These STDO are highly stable ≥48 h in physiological conditions without any postsynthetic modifications...
April 11, 2019: ACS Medicinal Chemistry Letters
Thorbjørn B Nielsen, Rasmus P Thomsen, Michael R Mortensen, Jørgen Kjems, Per F Nielsen, Thomas E Nielsen, Anne Louise Bank Kodal, Emiliano Clo, Kurt Vesterager Gothelf
The development of methods for conjugation of DNA to proteins is of high relevance for integration of protein function and DNA structures. Here, we demonstrate that protein binding peptides can direct a DNA-templated reaction, furnishing DNA-protein conjugates selectively with one DNA label. Quantitative conversion of oligonucleotides is achieved at low stoichiometries and the reaction can be performed in complex biological matrixes such as cell lysates. Further, we have applied a star-like pentameric DNA nanostructure to assemble five DNA-Rituximab conjugates, made by our reported method, into a pseudo-IgM antibody structure that was subsequently characterized by negative stain transmission electron microscopy (nsTEM) analysis...
April 17, 2019: Angewandte Chemie
Heini Ijäs, Iiris Hakaste, Boxuan Shen, Mauri A Kostiainen, Veikko Linko
DNA nanotechnology provides a toolbox for creating custom and precise nanostructures with nanometer-level accuracy. These nano-objects are often static by nature and serve as versatile templates for assembling various molecular components in a user-defined way. In addition to the static structures, the intrinsic programmability of DNA nanostructures allows design of dynamic devices that can perform predefined tasks when triggered with external stimuli, such as drug delivery vehicles whose cargo display or release can be triggered with a specified physical or chemical cue in the biological environment...
April 16, 2019: ACS Nano
Stefano Stassi, Monica Marini, Marco Allione, Sergei Lopatin, Domenico Marson, Erik Laurini, Sabrina Pricl, Candido Fabrizio Pirri, Carlo Ricciardi, Enzo Di Fabrizio
The effect of direct or indirect binding of intercalant molecules on DNA structure is of fundamental importance in understanding the biological functioning of DNA. Here we report on self-suspended DNA nanobundles as ultrasensitive nanomechanical resonators for structural studies of DNA-ligand complexes. Such vibrating nanostructures represent the smallest mechanical resonator entirely composed of DNA. A correlative analysis between the mechanical and structural properties is exploited to study the intrinsic changes of double strand DNA, when interacting with different intercalant molecules (YOYO-1 and GelRed) and a chemotherapeutic drug (Cisplatin), at different concentrations...
April 12, 2019: Nature Communications
Masayuki Endo
Direct visualization of the biomolecules of interest is a straightforward way to elucidate the physical properties of individual molecules and their reaction processes. Atomic force microscopy (AFM) enables direct imaging of biomolecules in suitable solution conditions. As AFM visualizes the molecules at a nanometer-scale spatial resolution, a versatile observation platform is required for precise imaging of the molecules in action. The DNA origami technology allows precise placement of target molecules in a designed nanostructure, enabling their detection at the single-molecule level...
April 9, 2019: Methods: a Companion to Methods in Enzymology
Lan Zhou, Simone Poggesi, Giuliocesare Casari Bariani, Rakesh Mittapalli, Pierre-Michel Adam, Marisa Manzano, Rodica Elena Ionescu
In this study, stable gold nanoparticles (AuNPs) are fabricated for the first time on commercial ultrafine glass coverslips coated with gold thin layers (2 nm, 4 nm, 6 nm, and 8 nm) at 25 °C and annealed at high temperatures (350 °C, 450 °C, and 550 °C) on a hot plate for different periods of time. Such gold nanostructured coverslips were systematically tested via surface enhanced Raman spectroscopy (SERS) to identify their spectral performances in the presence of different concentrations of a model molecule, namely 1,2-bis-(4-pyridyl)-ethene (BPE)...
April 10, 2019: Biosensors
Dandan Wang, Xiaolong Xu, Ya Zhou, Haijuan Li, Guohua Qi, Ping Hu, Yongdong Jin
Glass capillary nanopore has been developed as a promising sensing platform for bioassay with single-molecule resolution. Although the diameter of glass capillary nanopore can be easily tuned, direct event-readouts of small biomacromolecules, like short-chain oligonucleotide fragments (within ∼20 nucleotides) remain great challenge, which limited by the configuration of the conical-shaped nanopore and the instrumental temporal resolution. Here, we exploit a smart strategy for glass nanopore detection of short-chain oligonucleotides by using relatively big-sized tetrahedral DNA nanostructures as a signal amplifier, which can amplify the signals and retard the translocation speed meanwhile...
July 31, 2019: Analytica Chimica Acta
Jia Kong, Yuefei Wang, Wei Qi, Rongxin Su, Zhimin He
Owing to their potential applications in biomedicine and biotechnology, peptide nanostructures that exhibit stable intrinsic fluorescence in the visible range are highly desired. This research proposes a facile strategy to construct peptidyl virus-like nanoparticles (NVPs) that show green luminescence by co-assembly of two bioactive ferrocene-diphenylalanine-based (Fc-FF) peptides. The green fluorescence of NVPs was originated from the highly ordered structures assembled by the amphiphilic Fc-FF-based peptides via strong π-π stacking interactions...
April 9, 2019: ACS Applied Materials & Interfaces
Ashok Kumar Nayak, Sakti Kanta Rath, Umakanta Subudhi
The construction of functionalizable branched DNA (bDNA) relies on the designing of oligonucleotides and exploitation of their complementary chemistries. The stability of these structures largely depend on the hybridization specificity of the contributing oligonucleotides. However, most of the bDNA structures are not found suitable for in vivo application due to poor yield owing to uncharacterized hybridization efficiency and instability in biological fluids. In this report, our group has explored a mechanistic way for studying the hybridization pathway of genomic sequence derived oligonucleotides which are self-assembled to fabricate robust bDNA structures...
April 9, 2019: Journal of Physical Chemistry. B
Megan E Kizer, Yanxiang Deng, GeoumYoung Kang, Paiyz E Mikael, Xing Wang, Aram J Chung
The successful intracellular delivery of exogenous macromolecules is crucial for a variety of applications ranging from basic biology to the clinic. However, traditional intracellular delivery methods such as those relying on viral/non-viral nanocarriers or physical membrane disruptions suffer from low throughput, toxicity, and inconsistent delivery performance and are time-consuming and/or labor-intensive. In this study, we developed a single-step hydrodynamic cell deformation-induced intracellular delivery platform named "hydroporator" without the aid of vectors or a complicated/costly external apparatus...
April 9, 2019: Lab on a Chip
Na Chen, Xinyu Meng, Pan Ding, Yuanyuan Su, Houyu Wang, Yao He
The fouling and stability are two most critical limiting factors for practical applications of surface-enhanced Raman scattering (SERS)-based microfluidic electrophoresis device. Herein, we present a novel biomimetic nanoengineering strategy to achieve a SERS substrate featuring antifouling ability, good stability and reliable quantitative capability. Typically, by employing tea polyphenol as the reducing agent, the substrate made of silver core-gold shell nanostructures in situ grown on silicon wafer surface is fabricated...
April 5, 2019: Electrophoresis
Shalin Shah, Abhishek K Dubey, John Reif
Many biochemical events of importance are complex and dynamic. Fluorescence microscopy offers a versatile solution to study the dynamics of biology at the mesoscale. An important challenge in the field is the simultaneous study of several objects of interest, referred to as optical multiplexing. For improved multiplexing, some prior techniques used repeated reporter washing or the geometry of nanostructures; however, these techniques may require complex nanostructure assembly, multiple reporters or advanced multistep drift correction...
April 5, 2019: ACS Synthetic Biology
J Bohlen, Á Cuartero-González, E Pibiri, D Ruhlandt, A I Fernández-Domínguez, P Tinnefeld, G P Acuna
Metallic nanoparticles were shown to affect Förster energy transfer between fluorophore pairs. However, to date, the net plasmonic effect on FRET is still under dispute, with experiments showing efficiency enhancement and reduction. This controversy is due to the challenges involved in the precise positioning of FRET pairs in the near field of a metallic nanostructure, as well as in the accurate characterization of the plasmonic impact on the FRET mechanism. Here, we use the DNA origami technique to place a FRET pair 10 nm away from the surface of gold nanoparticles with sizes ranging from 5 to 20 nm...
April 4, 2019: Nanoscale
Shaoli Liu, Qiao Jiang, Yuanning Wang, Baoquan Ding
Strict Watson-Crick base pairing and availability by automated synthesis have allowed deoxyribonucleic acid (DNA) molecules to be used as engineerable building blocks for constructing versatile nanostructures. In recent decades, with the development of DNA nanotechnology, a range of DNA-based dynamic molecular devices with sophisticated nanostructures have been designed and constructed. Featuring programmability and biocompatibility, the applications of DNA-based nanodevices have been extensively focused on the interfaces of biological systems...
April 2, 2019: Advanced Healthcare Materials
Anubhab Mukherjee, Ariana K Waters, Pranav Kalyan, Achal Singh Achrol, Santosh Kesari, Venkata Mahidhar Yenugonda
Lipid-polymer hybrid nanoparticles (LPHNPs) are next-generation core-shell nanostructures, conceptually derived from both liposome and polymeric nanoparticles (NPs), where a polymer core remains enveloped by a lipid layer. Although they have garnered significant interest, they remain not yet widely exploited or ubiquitous. Recently, a fundamental transformation has occurred in the preparation of LPHNPs, characterized by a transition from a two-step to a one-step strategy, involving synchronous self-assembly of polymers and lipids...
2019: International Journal of Nanomedicine
Jonathan R Burns, Stefan Howorka
DNA nanopores offer a unique nano-scale foothold at the membrane interface that can help advance the life sciences as biophysical research tools or gate-keepers for drug delivery. Biological applications require sufficient physiological stability and membrane activity for viable biological action. In this report, we determine essential parameters for efficient nanopore folding and membrane binding in biocompatible cell media. The parameters are identified for an archetypal DNA nanopore composed of six interwoven strands carrying cholesterol lipid anchors...
March 29, 2019: Nanomaterials
Yunrui Li, Yuanyuan Chang, Jing Ma, Zhongyu Wu, Ruo Yuan, Yaqin Chai
Here, a novel bifunctional DNAzyme nanodevice (BFDN) with two detection paths toward the same target was intelligently designed and applied to construct a novel ratiometric electrochemical biosensor for highly reliable and sensitive mercury ion (Hg2+) detection. In the presence of target Hg2+, T-Hg2+-T pair could actuate the preassembled DNA four-branched nanostructure (DNA-4B) without cleavage capability transform into the BFDN with strong cleavage capability for triggering two synchronous Hg2+ detection paths, including a "signal-off" path 1 that consisted of a cascade DNAzyme cleavage reaction to dramatically decrease the ferrocene (Fc) response and a "signal-on" path 2 that accomplished the capture of significant amounts of methylene blue (MB) on the electrode surface under the assistant of DNAzyme2 (D2) in BFDN...
April 1, 2019: Analytical Chemistry
Upendra Nayek, Vayakkara Kolaprath Unnikrishnan, Abdul Ajees Abdul Salam, Parinda Vasa, Santhosh Chidangil, Deepak Mathur
Low-power laser pulses of 6 ns duration (1064 nm wavelength) have been used to create plasma in an aqueous solution of plasmid DNA (pUC19). Thermal-energy electrons and .OH-radicals in the plasma induce strand breakages in DNA, including double strand breaks (DSBs) and possible base oxidation/base degradation. The time-evolution of these modifications shows that it takes barely 30 s for damage to DNA to occur. Addition of physiologically relevant concentrations of a salt (NaCl) significantly inhibits such damage...
March 28, 2019: Journal of Physical Chemistry. A
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