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DNA nanotechnology

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https://www.readbyqxmd.com/read/28521201/validation-of-the-use-of-an-artificial-mitochondrial-reporter-dna-vector-containing-a-cytomegalovirus-promoter-for-mitochondrial-transgene-expression
#1
Yuma Yamada, Takuya Ishikawa, Hideyoshi Harashima
Mitochondria have their own gene expression system that is independent of the nuclear system, and control cellular functions in cooperation with the nucleus. While a number of useful technologies for achieving nuclear transgene expression have been reported, only a few have focused on mitochondria. In this study, we validated the utility of an artificial mitochondrial DNA vector with a virus promoter on mitochondrial transgene expression. We designed and constructed pCMV-mtLuc (CGG) that contains a CMV promotor derived from Cytomegalovirus and an artificial mitochondrial genome with a NanoLuc (Nluc) luciferase gene that records adjustments to the mitochondrial codon system...
May 10, 2017: Biomaterials
https://www.readbyqxmd.com/read/28520255/core-shell-and-layer-by-layer-assembly-of-3d-dna-crystals
#2
Ronald McNeil, Paul J Paukstelis
A long-standing goal of DNA nanotechnology has been to assemble 3D crystals to be used as molecular scaffolds. The DNA 13-mer, BET66, self-assembles via Crick-Watson and noncanonical base pairs to form crystals. The crystals contain solvent channels that run through them in multiple directions, allowing them to accommodate tethered guest molecules. Here, the first example of biomacromolecular core-shell crystal growth is described, by showing that these crystals can be assembled with two or more discrete layers...
May 18, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28514955/label-free-biosensing-of-salmonella-enterica-serovars-at-single-cell-level
#3
Bin Wang, Bosoon Park, Bingqian Xu, Yongkuk Kwon
BACKGROUND: The emerging nanotechnologies have greatly facilitated the development of label-free biosensors. The atomic force microscopy (AFM) has been used to study the molecular mechanism of the reactions for protein and aptamers. The surface plasmon resonance (SPR) have been used in fast detections of various pathogens such as bacteria. This study used both AFM and SPR to investigate the complex reactions between aptamers and outer membrane proteins (OMPs) on the surface of S. typhimurium...
May 17, 2017: Journal of Nanobiotechnology
https://www.readbyqxmd.com/read/28514924/rapid-and-annealing-free-self-assembly-of-dna-building-blocks-for-3d-hydrogel-chaperoned-by-cationic-comb-type-copolymers
#4
Zheng Zhang, Yuyang Wu, Feng Yu, Chaoqun Niu, Zhi Du, Yong Chen, Jie Du
The construction and self-assembly of DNA building blocks are the foundation of bottom-up development of three-dimensional DNA nanostructures or hydrogels. However, most self-assembly from DNA components is impeded by the mishybridized intermediates or the thermodynamic instability. To enable rapid production of complicated DNA objects with high yields no need for annealing process, herein different DNA building blocks (Y-shaped, L- and L'-shaped units) were assembled in presence of a cationic comb-type copolymer, poly (L-lysine)-graft-dextran (PLL-g-Dex), under physiological conditions...
May 18, 2017: Journal of Biomaterials Science. Polymer Edition
https://www.readbyqxmd.com/read/28505598/interlocked-dna-topologies-for-nanotechnology
#5
REVIEW
Julián Valero, Finn Lohmann, Michael Famulok
Interlocked molecular architectures are well known in supramolecular chemistry and are widely used for various applications like sensors, molecular machines and logic gates. The use of DNA for constructing these interlocked structures has increased significantly within the current decade. Because of Watson-Crick base pairing rules, DNA is an excellent material for the self-assembly of well-defined interlocked nanoarchitectures. These DNA nanostructures exhibit sufficient stability, good solubility in aqueous media, biocompatibility, and can be easily combined with other biomolecules in bio-hybrid nano-assemblies...
May 12, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28504414/high-molecular-weight-polynucleotides-by-transferase-catalyzed-living-chain-growth-polycondensation
#6
Lei Tang, Luis A Navarro, Ashutosh Chilkoti, Stefan Zauscher
We present terminal deoxynucleotidyl transferase-catalyzed enzymatic polymerization (TcEP) for the template-free synthesis of high-molecular-weight, single-stranded DNA (ssDNA) and demonstrate that it proceeds by a living chain-growth polycondensation mechanism. We show that the molecular weight of the reaction products is nearly monodisperse, and can be manipulated by the feed ratio of nucleotide (monomer) to oligonucleotide (initiator), as typically observed for living polymerization reactions. Understanding the synthesis mechanism and the reaction kinetics enables the rational, template-free synthesis of ssDNA that can be used for a range of biomedical and nanotechnology applications...
May 15, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28491290/dna-nanochannels
#7
REVIEW
Dianming Wang, Yiyang Zhang, Dongsheng Liu
Transmembrane proteins are mostly nanochannels playing a highly important role in metabolism. Understanding their structures and functions is vital for revealing life processes. It is of fundamental interest to develop chemical devices to mimic biological channels. Structural DNA nanotechnology has been proven to be a promising method for the preparation of fine DNA nanochannels as a result of the excellent properties of DNA molecules. This review presents the development history and current situation of three different types of DNA nanochannel: tile-based nanotube, DNA origami nanochannel, and DNA bundle nanochannel...
2017: F1000Research
https://www.readbyqxmd.com/read/28488883/ultrasensitive-bioanalysis-current-status-and-future-trends
#8
Stéphanie Simon, Eric Ezan
Ligand-binding techniques such as immunoassays, the reference for clinical diagnosis, offer a wide range of innovative approaches based on signal DNA amplification, nanotechnologies or digital assays, which result in technologies with sensitivities more than 1000-times that of formats used 20 years ago. Providing that these technologies gain acceptance and translate into robust commercial platforms, we expect that several fields will be impacted in the near future, including the clinical diagnosis of cancer markers, the early detection of infectious diseases and the safety of biotherapeutics...
May 10, 2017: Bioanalysis
https://www.readbyqxmd.com/read/28485577/site-selective-conjugation-of-native-proteins-with-dna
#9
Julie B Trads, Thomas Tørring, Kurt V Gothelf
Conjugation of DNA to proteins is increasingly used in academia and industry to provide proteins with tags for identification or handles for hybridization to other DNA strands. Assay technologies such as immuno-PCR and proximity ligation and the imaging technology DNA-PAINT require DNA-protein conjugates. In DNA nanotechnology, the DNA handle is exploited to precisely position proteins by self-assembly. For these applications, site-selective conjugation is almost always desired because fully functional proteins are required to maintain the specificity of antibodies and the activity of enzymes...
May 9, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28474522/shear-dependent-lc-purification-of-an-engineered-dna-nanoswitch-and-implications-for-dna-origami
#10
Ken Halvorsen, Megan E Kizer, Xing Wang, Arun Richard Chandrasekaran, Maria Basanta-Sanchez
As DNA nanotechnology matures, there is increasing need for fast, reliable, and automated purification methods. Here, we develop UHPLC methods to purify self-assembled DNA nanoswitches, which are formed using DNA origami approaches and are designed to change conformations in response to a binding partner. We found that shear degradation hindered LC purification of the DNA nanoswitches, removing oligonucleotides from the scaffold strand and causing loss of function. However, proper choice of column, flow rate, and buffers enabled robust and automated purification of DNA nanoswitches without loss of function in under a half hour...
May 8, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28468256/magnetic-hyperthermia-and-oxidative-damage-to-dna-of-human-hepatocarcinoma-cells
#11
Filippo Cellai, Armelle Munnia, Jessica Viti, Saer Doumett, Costanza Ravagli, Elisabetta Ceni, Tommaso Mello, Simone Polvani, Roger W Giese, Giovanni Baldi, Andrea Galli, Marco E M Peluso
Nanotechnology is addressing major urgent needs for cancer treatment. We conducted a study to compare the frequency of 3-(2-deoxy-β-d-erythro-pentafuranosyl)pyrimido[1,2-α]purin-10(3H)-one deoxyguanosine (M₁dG) and 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) adducts, biomarkers of oxidative stress and/or lipid peroxidation, on human hepatocarcinoma HepG2 cells exposed to increasing levels of Fe₃O₄-nanoparticles (NPs) versus untreated cells at different lengths of incubations, and in the presence of increasing exposures to an alternating magnetic field (AMF) of 186 kHz using (32)P-postlabeling...
April 29, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28461258/thiolated-aunp-probes-and-multiplex-pcr-for-molecular-detection-of-staphylococcus-epidermidis
#12
Mahsa Osmani Bojd, Hossein Kamaladini, Fatemeh Haddadi, Akbar Vaseghi
The emergence of nanotechnology in biology helps to apply the gold nanoparticle probes for fast and accurate identification of pathogens compared to the time-consuming and non-precise phenotypic methods. In this study, two molecular methods have been established for the accurate identification of staphylococcus epidermidis from other coagulase-negative staphylococci. Multiplex PCR was performed using designed primers for Gmk2 and pta housekeeping genes, and SESB specific gene of S. epidermidis. Colorimetric detection by gold nanoparticle probes was carried out using two 20-base thiolated probes designed based on the sequence of pta housekeeping gene of S...
April 28, 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/28460037/probing-the-salt-dependence-of-the-torsional-stiffness-of-dna-by-multiplexed-magnetic-torque-tweezers
#13
Franziska Kriegel, Niklas Ermann, Ruaridh Forbes, David Dulin, Nynke H Dekker, Jan Lipfert
The mechanical properties of DNA fundamentally constrain and enable the storage and transmission of genetic information and its use in DNA nanotechnology. Many properties of DNA depend on the ionic environment due to its highly charged backbone. In particular, both theoretical analyses and direct single-molecule experiments have shown its bending stiffness to depend on salt concentration. In contrast, the salt-dependence of the twist stiffness of DNA is much less explored. Here, we employ optimized multiplexed magnetic torque tweezers to study the torsional stiffness of DNA under varying salt conditions as a function of stretching force...
April 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28452950/recent-advances-in-nanomaterials-for-gene-delivery-a-review
#14
REVIEW
Michael K Riley, Wilfred Vermerris
With the rapid development of nanotechnology in the recent decade, novel DNA and RNA delivery systems for gene therapy have become available that can be used instead of viral vectors. These non-viral vectors can be made of a variety of materials, including inorganic nanoparticles, carbon nanotubes, liposomes, protein and peptide-based nanoparticles, as well as nanoscale polymeric materials. They have as advantages over viral vectors a decreased immune response, and additionally offer flexibility in design, allowing them to be functionalized and targeted to specific sites in a biological system with low cytotoxicity...
April 28, 2017: Nanomaterials
https://www.readbyqxmd.com/read/28451299/charge-transfer-dynamics-in-dna-revealed-by-time-resolved-spectroscopy
#15
Mamoru Fujitsuka, Tetsuro Majima
In the past few decades, charge transfer in DNA has attracted considerable attention from researchers in a wide variety of fields, including bioscience, physical chemistry, and nanotechnology. Charge transfer in DNA has been investigated using various techniques. Among them, time-resolved spectroscopic methods have yielded valuable information on charge transfer dynamics in DNA, providing an important basis for numerical practical applications such as development of new therapy applications and nanomaterials...
March 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28436649/multi-arm-junctions-for-dynamic-dna-nanotechnology
#16
Shohei Kotani, William L Hughes
Nonenzymatic catalytic substrates have been engineered using toehold-mediated DNA strand displacement, and their programmable applications range from medical diagnosis to molecular computation. However, the complexity, stability, scalability, and sensitivity of those systems are plagued by network leakage. A novel way to suppress leakage is to increase its energy barrier through four-way branch migration. Presented here, we designed multi-arm junction substrates that simultaneously exploit four-way branch migration, with a high-energy barrier to minimize leakage, and three-way branch migration, with a low-energy barrier to maximize catalysis...
May 2, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28423273/conformational-dynamics-of-mechanically-compliant-dna-nanostructures-from-coarse-grained-molecular-dynamics-simulations
#17
Ze Shi, Carlos E Castro, Gaurav Arya
Structural DNA nanotechnology, the assembly of rigid 3D structures of complex yet precise geometries, has recently been used to design dynamic, mechanically compliant nanostructures with tunable equilibrium conformations and conformational distributions. Here we use coarse-grained molecular dynamics simulations to provide insights into the conformational dynamics of a set of mechanically compliant DNA nanostructures-DNA hinges that use single-stranded DNA "springs" to tune the equilibrium conformation of a layered double-stranded DNA "joint" connecting two stiff "arms" constructed from DNA helix bundles...
April 24, 2017: ACS Nano
https://www.readbyqxmd.com/read/28416486/a-squalene-based-nanomedicine-for-oral-treatment-of-colon-cancer
#18
Larissa Kotelevets, Eric Chastre, Joachim Caron, Julie Mougin, Gerard Bastian, Alain Pineau, Francine Walker, Therese Lehy, Didier Desmaele, Patrick Couvreur
Nanotechnology offers many possibilities to improve drug treatments, including with regard to drug pharmacology. The current study reports a simple approach to improve cisplatin efficacy in the treatment of colon cancer through the creation of orally administered squalenoylated nanoparticles loaded with cisplatin (SQ-CDDP NP). Cytotoxic effects of SQ-CDDP NP were assessed in human colonic cells and in mouse models of intestinal cancer. In cell culture, SQ-CDDP NP exhibited at least 10-fold greater cytotoxic potency compared to uncomplexed cisplatin, reflecting an enhancement in intracellular accumulation and DNA platination...
April 17, 2017: Cancer Research
https://www.readbyqxmd.com/read/28414914/designing-uniquely-addressable-bio-orthogonal-synthetic-scaffolds-for-dna-and-rna-origami
#19
Jerzy Kozyra, Alessandro Ceccarelli, Emanuela Torelli, Annunziata Lopiccolo, Jing-Ying Gu, Harold Fellermann, Ulrich Stimming, Natalio Krasnogor
Nanotechnology and synthetic biology are rapidly converging, with DNA origami being one of the leading bridging technologies. DNA origami was shown to work well in a wide array of biotic environments. However, the large majority of extant DNA origami scaffolds utilize bacteriophages or plasmid sequences thus severely limiting its future applicability as a bio-orthogonal nanotechnology platform. In this paper we present the design of biologically inert (i.e., "bio-orthogonal") origami scaffolds. The synthetic scaffolds have the additional advantage of being uniquely addressable (unlike biologically derived ones) and hence are better optimized for high-yield folding...
April 25, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28402651/dna-bipedal-motor-achieves-a-large-number-of-steps-due-to-operation-using-microfluidics-based-interface
#20
Toma E Tomov, Roman Tsukanov, Yair Glick, Yaron Berger, Miran Liber, Dorit Avrahami, Doron Gerber, Eyal Nir
Realization of bioinspired molecular machines that can perform many and diverse operations in response to external chemical commands is a major goal in nanotechnology, but current molecular machines respond to only a few sequential commands. Lack of effective methods for introduction and removal of command compounds and low efficiencies of the reactions involved are major reasons for the limited performance. We introduce here a user interface based on a microfluidics device and single-molecule fluorescence spectroscopy that allows efficient introduction and removal of chemical commands and enables detailed study of the reaction mechanisms involved in the operation of synthetic molecular machines...
April 25, 2017: ACS Nano
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