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https://www.readbyqxmd.com/read/30637509/chronocoulometric-aptamer-based-assay-for-staphylococcal-enterotoxin-b-by-target-triggered-assembly-of-nanostructured-dendritic-nucleic-acids-on-a-gold-electrode
#1
Xiaoye Chen, Yun Liu, Yichen Lu, Xiong Xiong, Yi Li, Yuanjian Liu, Xiaohui Xiong
A rapid and ultrasensitive method is described for the detection of staphylococcal enterotoxin B (SEB). It is based on the formation of a dendritic DNA superstructure by integrating (a) target-induced triggering of DNA release with (b) signal amplification by a hybridization chain reaction. Partially complementary pairing of aptamer and trigger DNA forms a duplex structure. The capture DNA is then placed on the surface of a gold electrode through gold-thiol chemistry. In the presence of SEB, the aptamer-target conjugate is compelled to form...
January 14, 2019: Mikrochimica Acta
https://www.readbyqxmd.com/read/30633263/emerging-platinum-iv-prodrugs-to-combat-cisplatin-resistance-from-isolated-cancer-cells-to-tumor-microenvironment
#2
Zhigang Wang, Zhiqin Deng, Guangyu Zhu
Cisplatin plays a pivotal role in the treatment of various malignant tumors, but its therapeutic effects are hampered by drug resistance. Pt(iv) prodrugs represent a promising class of "non-conventional" platinum-based anticancer agents to circumvent drug resistance, which can be easily functionalized with other bioactive ligands. One strategy is to build "dual-action" and "multi-action" Pt(iv) prodrugs that not only damage DNA but also perturb other pathways related to cisplatin resistance to achieve combinatorial therapeutic effects...
January 11, 2019: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/30624036/an-electrochemical-biosensor-for-dna-methylation-detection-through-hybridization-chain-amplified-reaction-coupled-with-a-tetrahedral-dna-nanostructure
#3
Xi Chen, Jian Huang, Shu Zhang, Fei Mo, Shasha Su, Yan Li, Lichao Fang, Jun Deng, Hui Huang, Zhaoxun Luo, Junsong Zheng
DNA methylation is a key factor in the pathogenesis of gene expression disorder diseases or malignancies. So it has become a significant biomarker for the diagnosis and prognosis of these diseases. In this paper, we designed an ultrasensitive and specific electrochemical biosensor for DNA methylation detection. The platform consisted of stem-loop-tetrahedron composite DNA probes anchoring at an Au nanoparticle-coated gold electrode, a restriction enzyme digestion of Hpa II and signal amplification procedures of electrodeposition of Au nanoparticles (AuNPs), hybridization chain reaction (HCR) and horseradish peroxidase (HRP) enzymatic catalysis...
January 9, 2019: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/30620200/highly-localized-sers-measurements-using-single-silicon-nanowires-decorated-with-dna-origami-based-sers-probe
#4
Ardeshir Moeinian, Fatih Nadi Gür, Julio César González-Torres, Linsen Zhou, Vignesh Murugesan, Ashkan Djaberi Dashtestani, Hua Guo, Thorsten L Schmidt, Steffen Strehle
Surface enhanced Raman spectroscopy (SERS) measurements are conventionally performed using assemblies of metal nanostructures on a macro to micro sized substrate or by dispersing colloidal metal nanoparticles directly onto the sample of interest. Despite intense use, these methods allow neither the removal of the nanoparticles after a measurement nor a defined confinement of the SERS measurement position. So far, tip enhanced Raman spectroscopy is still the key technique in this regard but not adequate for various samples mainly due to diminished signal enhancement compared to other techniques, poor device fabrication reproducibility and cumbersome experimental setup requirements...
January 8, 2019: Nano Letters
https://www.readbyqxmd.com/read/30609150/solid-phase-synthesis-and-purification-of-protein-dna-origami-nanostructures
#5
Teresa Burgahn, Ruben Garrecht, Kersten S Rabe, Christof M Niemeyer
We present a facile method for the combined synthesis and purification of protein-decorated DNA origami nanostructures (DONs). DONs bearing reductively cleavable biotin groups in addition to ligands for ligation of recombinant proteins are bound to magnetic beads. Protein immobilization is conducted with a large protein excess to achieve high ligation yields. Subsequent to cleavage from the solid support, pure sample solutions are obtained which are suitable for direct AFM analysis of occupation patterns. We demonstrate the method's utility using three different orthogonal ligation methods, the 'halo-based oligonucleotide binder' (HOB), a variant of Halo-tag, the SpyTag/SpyCatcher (ST/SC) system, and the enzymatic 'ybbR tag' coupling...
January 4, 2019: Chemistry: a European Journal
https://www.readbyqxmd.com/read/30605316/dna-quadruple-helices-in-nanotechnology
#6
Jean-Louis Mergny, Dipankar Sen
DNA has played an early and powerful role in the development of bottom-up nanotechnologies, not least because of DNA's precise, predictable, and controllable properties of assembly on the nanometer scale. Watson-Crick complementarity has been used to build complex 2D and 3D architectures and design a number of nanometer-scale systems for molecular computing, transport, motors, and biosensing applications. Most of such devices are built with classical B-DNA helices and involve classical A-T/U and G-C base pairs...
January 3, 2019: Chemical Reviews
https://www.readbyqxmd.com/read/30604811/base-excision-repair-inspired-dna-motor-powered-by-intracellular-apurinic-apyrimidinic-endonuclease
#7
Lidan Li, Na Li, Shengnan Fu, Yingnan Deng, Changyuan Yu, Xin Su
The transition of DNA nanomachines from test tubes to living cells would realize the ultimate goal of smart therapeutic dynamic DNA nanotechnology. The operation of DNA nanomachines in living cells remains challenging because it is difficult to utilize an endogenous driving force. Inspired by the base excision repair (BER) process, we demonstrate a 'burnt-bridge' DNA motor system powered by intracellular apurinic/apyrimidinic (AP) endonuclease APE1. The high specificity of APE1 to the AP site in double-stranded DNA permits directional and autonomous movement...
January 3, 2019: Nanoscale
https://www.readbyqxmd.com/read/30600876/chemical-regulation-of-dna-i-motifs-for-nanobiotechnology-and-therapeutics
#8
Jyotirmayee Dash, Manish Debnath, Khushnood Fatma
DNA sequences rich in cytosine have the propensity to fold into four-stranded intercalated DNA structures called i-motifs under acidic pH. A string of recent studies provided significant breakthroughs that demonstrate how chemists can manipulate these structures for nanobiotechnology and therapeutics. The first section of this minireview discusses the development of advanced functional nanostructures by synthetic conjugation of i-motifs with organic scaffolds and metal nanoparticles and their role in therapeutics...
January 2, 2019: Angewandte Chemie
https://www.readbyqxmd.com/read/30593871/highly-tumor-specific-dna-nanostructures-discovered-by-in-vivo-screening-of-a-nucleic-acid-cage-library-and-their-applications-in-tumor-targeted-drug-delivery
#9
Kyoung-Ran Kim, Seong Jae Kang, A-Young Lee, Dohyeon Hwang, Miri Park, Haedong Park, Sanghee Kim, Kahyun Hur, Hak Suk Chung, Chengde Mao, Dae-Ro Ahn
Enormous efforts have been made to harness nanoparticles showing extravasation around tumors for tumor-targeted drug carriers. Owing to the complexity of in vivo environments, however, it is very difficult to rationally design a nanoconstruct showing high tumor specificity. Here, we show an approach to develop tumor-specific drug carriers by screening a library of self-assembled nucleic acid cages in vivo. After preparation of a library of 16 nucleic acid cages by combining the sugar backbone and the shape of cages, we screened the biodistribution of the cages intravenously injected into tumor-bearing mice, to discover the cages with high tumor-specificity...
December 26, 2018: Biomaterials
https://www.readbyqxmd.com/read/30588806/dna-origami-nanoarrays-for-multivalent-investigations-of-cancer-cell-spreading-with-nanoscale-spatial-resolution-and-single-molecule-control
#10
Da Huang, Ketan Patel, Sandra Perez-Garrido, John F Marshall, Matteo Palma
Here we present a strategy for the fabrication of biomimetic nanoarrays, based on the use of DNA origami, that permit the multivalent investigation of ligand-receptor molecule interactions in cancer cell spreading, with nanoscale spatial resolution and single-molecule control. We employed DNA-origami to control the nanoscale spatial organization of integrin- and epidermal growth factor (EGF)- binding ligands that modulate epidermal cancer cell behaviour. By organizing these multivalent DNA nanostructures in nanoarray configurations on nanopatterned surfaces, we demonstrated the cooperative behaviour of integrin- and EGF- ligands in the spreading of human cutaneous melanoma cells: this cooperation was shown to depend on both the number and ratio of the selective ligands employed...
December 27, 2018: ACS Nano
https://www.readbyqxmd.com/read/30588792/single-particle-tracking-and-super-resolution-imaging-of-membrane-assisted-stop-and-go-diffusion-and-lattice-assembly-of-dna-origami
#11
Susanne Kempter, Alena Khmelinskaia, Maximilian T Strauss, Petra Schwille, Ralf Jungmann, Tim Liedl, Wooli Bae
DNA nanostructures offer the possibility to mimic functional biological membrane components due to their nanometer-precise shape configurability and versatile biochemical functionality. Here we show that the diffusional behavior of DNA nanostructures and their assembly into higher order membrane-bound lattices can be controlled in a stop-and-go manner and that the process can be monitored with super-resolution imaging. The DNA structures are transiently immobilized on glass-supported lipid bilayers by changing the mono- and divalent cation concentrations of the surrounding buffer...
December 27, 2018: ACS Nano
https://www.readbyqxmd.com/read/30586988/tip-enhanced-raman-imaging-of-single-stranded-dna-with-single-base-resolution
#12
Zhe He, Zehua Han, Megan Kizer, Robert J Linhardt, Xing Wang, Alexander M Sinyukov, Jizhou Wang, Volker Deckert, Alexei V Sokolov, Jonathan Hu, Marlan O Scully
Tip-enhanced Raman scattering (TERS) is a promising optical and analytical technique for chemical imaging and sensing at single molecule resolution. In particular, TERS signals generated by a gap-mode configuration where a silver tip is coupled with a gold substrate can resolve a single-stranded DNA (ssDNA) molecule with a spatial resolution below 1 nm. To demonstrate the proof of sub-nanometer resolution, we show direct nucleic acid sequencing using TERS of a phage ssDNA (M13mp18). M13mp18 provides a known sequence and, through our deposition strategy, can be stretched (uncoiled) and attached to the substrate by its phosphate groups, while exposing its nucleobases to the tip...
December 26, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/30585490/digital-data-storage-using-dna-nanostructures-and-solid-state-nanopores
#13
Kaikai Chen, Jinglin Kong, Jinbo Zhu, Niklas Ermann, Paul Predki, Ulrich F Keyser
Solid-state nanopores are powerful tools for reading out the three-dimensional shape of molecules allowing for the translation of molecular structure into electric signals. Here, we show a high-resolution integrated nanopore system for identifying DNA nanostructures that has the capability of distinguishing attached short DNA hairpins with only a stem length difference of 8 bp along a DNA double strand named DNA carrier. Using our platform, we can read up to 112 DNA hairpins with a separating distance of 114 bp attached on a DNA carrier which carries digital information...
December 26, 2018: Nano Letters
https://www.readbyqxmd.com/read/30569246/a-silver-i-doped-bud-like-dna-nanostructure-as-a-dual-functional-nanolabel-for-voltammetric-discrimination-of-methylated-from-unmethylated-genes
#14
Samaneh Hadian-Ghazvini, Hedayatollah Ghourchian, Shahram Agah, Ebrahim Ghafar-Zadeh
A small DNA structure, referred to as DNA nanobud (NB), was used for the first time to design a dual-functional nanolabel in order to recognize a particular oligonucleotide sequence, generate and amplify the electrochemical analytical signal. NBs containing numerous repetitive desired sequences were prepared through self-assembly of 8-h rolling circle amplification. Then, redox-active silver ions were loaded onto the NBs by over-night incubation with a solution of AgNO3 . The incorporation of Ag+ into NBs was confirmed by field emission scanning electron microscopy, dynamic light scattering, UV-Vis spectroscopy, zeta potential measurements, and energy-dispersive X-ray spectroscopy...
December 19, 2018: Mikrochimica Acta
https://www.readbyqxmd.com/read/30567653/a-novel-nucleic-acid-fluorescent-sensing-platform-based-on-nanostructured-films-of-intrinsically-conducting-polymers
#15
Graciela C Pedro, Filipe D S Gorza, Romário J da Silva, Kamila T O do Nascimento, Juan C Medina-Llamas, Alicia E Chávez-Guajardo, José J Alcaraz-Espinoza, Celso P de Melo
When fluorophores attach to nanostructured films of intrinsically conducting polymers (ICPs), a quenching of their fluorescence may occur. We have exploited these characteristics for the development of polymeric films that can be used in a simple and efficient molecular diagnosis protocol based on the selective detection of nucleic acids. Our procedure rests on the fact that the fluorescence of 6-carboxyfluorescein-labeled single-stranded DNA (FAM-ssDNA) probes is quenched upon their immobilization on nanostructured ICP - polypyrrole (PPY) and polyaniline (PANI) - films deposited on polyethylene terephthalate (PET) substrates...
January 24, 2019: Analytica Chimica Acta
https://www.readbyqxmd.com/read/30562007/the-clearance-effect-of-tetrahedral-dna-nanostructures-on-senescent-human-dermal-fibroblasts
#16
Chenchen Mao, Weiyi Pan, Xiao-Ru Shao, Wenjuan Ma, Yuxin Zhang, Yuxi Zhan, Yang Gao, Yun-Feng Lin
Senescent cells are characterized by their resistance to apoptosis, and upon their long-term survival, senescent cells affect tissue function and eventually become deleterious to the organism. Thus far, it has been gradually accepted that clearance these senescent cells could reduce tissue dysfunction. This study aimed to investigate biological effects of tetrahedral DNA nanostructures (TDNs) on senescent cells. And the results revealed a different biological effect of TDNs, their clearance effect, on senescent cells...
December 18, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/30561987/designed-and-evolved-nucleic-acid-nanotechnology-contrast-and-complementarity
#17
Tulsi Ram Damase, Peter B Allen
In this review, we explore progress on DNA aptamers (evolved DNA), DNA circuits (designed DNA), and the newest projects that integrate both. Designed DNA nanotechnology includes static nanostructures, dynamic nanodevices, and reaction networks (sometimes called DNA circuits). DNA circuits are dynamic DNA reactions that perform computations and sequence-specific amplification. Directed evolution can be used to produce DNA that can recognize specific targets. Aptamers are evolved nucleic acids; they are produced artificially with an in vitro selection process...
December 18, 2018: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/30560865/information-based-autonomous-reconfiguration-in-systems-of-interacting-dna-nanostructures
#18
Philip Petersen, Grigory Tikhomirov, Lulu Qian
The dynamic interactions between complex molecular structures underlie a wide range of sophisticated behaviors in biological systems. In building artificial molecular machines out of DNA, an outstanding challenge is to develop mechanisms that can control the kinetics of interacting DNA nanostructures and that can compose the interactions together to carry out system-level functions. Here we show a mechanism of DNA tile displacement that follows the principles of toehold binding and branch migration similar to DNA strand displacement, but occurs at a larger scale between interacting DNA origami structures...
December 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/30557499/spatial-presentation-of-cholesterol-units-on-a-dna-cube-as-a-determinant-of-membrane-protein-mimicking-functions
#19
Pongphak Chidchob, Daniel Offenbartl-Stiegert, Dillon McCarthy, Xin Luo, Jianing Li, Stefan Howorka, Hanadi F Sleiman
Cells use membrane proteins as gatekeepers to transport ions and molecules, catalyze reactions, relay signals, and interact with other cells. DNA nanostructures with lipidic anchors are promising as membrane protein mimics because of their high tuneability. However, the design features specifying DNA nanostructure's functions in lipid membranes are yet to be fully understood. Here, we show that altering patterns of cholesterol units on a cubic DNA scaffold dramatically changes its interaction mode with lipid membranes...
December 17, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/30551295/nanoencapsulation-of-the-flavonoid-dihydromyricetin-protects-against-the-genotoxicity-and-cytotoxicity-induced-by-cationic-nanocapsules
#20
Ana Julia F Dalcin, Bruno S Vizzotto, Guilherme V Bochi, Naiara S Guarda, Kátia Nascimento, Michele R Sagrillo, Rafael N Moresco, André P Schuch, Aline F Ourique, Patrícia Gomes
We evaluated the influence of nanoencapsulation of the flavonoid Dihydromyricetin (DMY) in reducing the genotoxicity and cytotoxicity induced by cationic nanocapsules. Assays were conducted in order to evaluate the potential of protein corona formation, cytotoxicity, genotoxicity and the antioxidant capacity. Nanocapsules containing DMY (NC-DMY) and free DMY (DMY-F) did not demonstrate cytotoxicity and genotoxicity. However, Eudragit RS100® nanocapsules (NC-E) increased cytotoxicity and DNA damage formation...
January 1, 2019: Colloids and Surfaces. B, Biointerfaces
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