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https://www.readbyqxmd.com/read/28448145/coarse-grained-molecular-dynamics-model-of-double-stranded-dna-for-dna-nanostructure-design
#1
Hiromasa Yagyu, Jae-Young Lee, Do-Nyun Kim, Osamu Tabata
A new coarse-grained molecular dynamics double-stranded DNA model (nCG-dsDNA model) using an improved beads-spring model was proposed. In this model, nucleotide comprising phosphate, sugar, and base group were replaced by a single bead. The double stranded model with 202 base pairs was created to tune the parameters of the bond, the non-bond, stack, angle bending, and electrostatic interaction. The average twisted angle and the persistence length of the model without electrostatic interaction were calculated at 35...
April 27, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28445644/broadband-fluorescence-enhancement-with-self-assembled-silver-nanoparticle-optical-antennas
#2
Carolin Vietz, Izabela Kaminska, Maria Sanz Paz, Philip Tinnefeld, Guillermo P Acuna
Plasmonic structures are known to affect the fluorescence properties of dyes placed in close proximity. This effect has been exploited in combination with single-molecule techniques for several applications in the field of biosensing. Among these plasmonic structures, top-down zero mode waveguides stand out due to their broadband capabilities. In contrast, optical antennas based on gold nanostructures exhibit fluorescence enhancement on a narrow fraction of the visible spectrum typically restricted to the red to near-infrared region...
April 26, 2017: ACS Nano
https://www.readbyqxmd.com/read/28444822/triplex-dna-nanostructures-from-basic-properties-to-applications
#3
Yuwei Hu, Alessandro Cecconello, Andrea Idili, Francesco Ricci, Itamar Willner
Triplex nucleic acids attract recent interest as part of the rich "tool-box" of structures used to develop DNA-based nanostructures and materials. This review addresses the use of DNA triplexes to assemble sensing platforms and molecular switches. Furthermore, the pH-induced, switchable assembly and dissociation of triplex DNA-bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles and the reversible oligomerization of "origami" tiles or DNA circles are described. Also, the use of triplex-DNA structures as functional units to assemble pH-responsive systems and materials are presented...
April 26, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28439556/selective-control-of-reconfigurable-chiral-plasmonic-metamolecules
#4
Anton Kuzyk, Maximilian J Urban, Andrea Idili, Francesco Ricci, Na Liu
Selective configuration control of plasmonic nanostructures using either top-down or bottom-up approaches has remained challenging in the field of active plasmonics. We demonstrate the realization of DNA-assembled reconfigurable plasmonic metamolecules, which can respond to a wide range of pH changes in a programmable manner. This programmability allows for selective reconfiguration of different plasmonic metamolecule species coexisting in solution through simple pH tuning. This approach enables discrimination of chiral plasmonic quasi-enantiomers and arbitrary tuning of chiroptical effects with unprecedented degrees of freedom...
April 2017: Science Advances
https://www.readbyqxmd.com/read/28435250/sl2b-aptamer-and-folic-acid-dual-targeting-dna-nanostructures-for-synergic-biological-effect-with-chemotherapy-to-combat-colorectal-cancer
#5
Pengchao Sun, Nan Zhang, Yafang Tang, Yanan Yang, Xiao Chu, Yongxing Zhao
DNA nanostructures prepared by self-assembly possess good stability, high biocompatibility, and low immunogenicity as drug delivery vehicles. In this work, DNA tetrahedron (TD) was constructed and modified with SL2B aptamer (S) and folic acid (F). TD possessed a small diameter (~6 nm) and entered into the nucleus quickly. SL2B aptamer can inhibit cancer cell growth by disturbing vascular endothelial growth factor/Notch signaling pathways. To explore the effect of SL2B number on colorectal cancer inhibition, SL2B multimers (dimer, trimer, and tetramer) were constructed by functionalization of TD with different numbers of SL2B...
2017: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/28434989/colorimetric-detection-of-microrna-based-hybridization-chain-reaction-for-signal-amplification-and-enzyme-for-visualization
#6
Na Ying, Taifan Sun, Zhibao Chen, Guangping Song, Bingyao Qi, Shengjun Bu, Xiuwei Sun, Jiayu Wan, Zehong Li
MicroRNAs (miRNAs) have key roles in gene expression and can be employed as biomarkers for early diagnosis of various diseases, especially cancers. Detection of miRNAs remains challenging and often requires detection platforms. Here, a horseradish peroxidase (HRP)-assisted hybridization chain reaction (HCR) for colorimetric detection of miR-155 was described. In the presence of target miRNA, the capture probe immobilized on the microplate sandwiched the target miR-155 with the 3' end of the reporter probe. Another exposed part of the RP at the 5'end triggered HCR producing double-stranded DNA polymers with multiple fluorescein isothiocyanates (FITC) for signal amplification...
April 20, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28429586/bubble-mediated-ultrasensitive-multiplex-detection-of-metal-ions-in-three-dimensional-dna-nanostructure-encoded-microchannels
#7
Xiangmeng Qu, Fan Yang, Hong Chen, Jiang Li, Hongbo Zhang, Guo-Jun Zhang, Li Li, Lihua Wang, Shiping Song, Yang Tian, Hao Pei
The development of rapid and sensitive point-of-test devices for the on-site monitoring of heavy-metal contamination has great scientific and technological importance. However, developing fast, inexpensive, and sensitive microarray sensors to achieve such goal remains challenging. In this work, we present a DNA nanostructured microarray (DNM) with tubular three-dimensional (3D) sensing surface and ordered nanotopography. This microarray enables enhanced molecular interaction toward the rapid and sensitive multiplex detection of heavy-metal ions...
April 21, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28423273/conformational-dynamics-of-mechanically-compliant-dna-nanostructures-from-coarse-grained-molecular-dynamics-simulations
#8
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/28417635/crystallization-of-amphiphilic-dna-c-stars
#9
Ryan A Brady, Nicholas J Brooks, Pietro Cicuta, Lorenzo Di Michele
Many emerging technologies require materials with well-defined three-dimensional nanoscale architectures. Production of these structures is currently underpinned by self-assembling amphiphilic macromolecules or engineered all-DNA building blocks. Both of these approaches produce restricted ranges of crystal geometries due to synthetic amphiphiles' simple shape and limited specificity, or the technical difficulties in designing space-filling DNA motifs with targeted shapes. We have overcome these limitations with amphiphilic DNA nanostructures, or "C-Stars", that combine the design freedom and facile functionalization of DNA-based materials with robust hydrophobic interactions...
April 20, 2017: Nano Letters
https://www.readbyqxmd.com/read/28406032/deposition-of-dna-nanostructures-on-highly-oriented-pyrolytic-graphite
#10
Karen B Ricardo, Anqin Xu, Muhammad Salim, Feng Zhou, Haitao Liu
We report the deposition of DNA origami nanostructures on highly oriented pyrolytic graphite (HOPG). The DNA origami goes through a structural rearrangement and the DNA base is exposed to interact with the graphite surface. Exposure to ambient air, which is known to result in a hydrophilic-to-hydrophobic wetting transition of HOPG, does not significantly impact the deposition yield or the shape deformation of DNA nanostructures. The deposited DNA nanostructures maintain their morphology for at least a week and promote site-selective chemical vapor deposition of SiO2...
April 13, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28406014/sequence-modulated-interactions-between-single-multivalent-dna-conjugated-gold-nanoparticles
#11
Chunyan Qiao, Jia Wu, Zhenrong Huang, Xuan Cao, Jiayu Liu, Bin Xiong, Yan He, Edward S Yeung
DNA-conjugated gold nanoparticle (AuNP) is an attractive building block to construct elegant plasmonic nanomaterials by self-assembly but the complicated interaction between multivalent nanoconjugates governing the assembly process and the properties of assembled structures remains poorly understood. Herein, with an in-situ kinetic single-particle imaging method, we report the dy-namic interaction between single multivalent DNA-conjugated AuNPs quantitatively depends on the nucleic acid sequence in nano-conjugates...
April 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28390838/super-resolution-microscopy-approaches-to-nuclear-nanostructure-imaging
#12
Christoph Cremer, Aleksander Szczurek, Florian Schock, Amine Gourram, Udo Birk
The human genome has been decoded, but we are still far from understanding the regulation of all gene activities. A largely unexplained role in these regulatory mechanisms is played by the spatial organization of the genome in the cell nucleus which has far-reaching functional consequences for gene regulation. Until recently, it appeared to be impossible to study this problem on the nanoscale by light microscopy. However, novel developments in optical imaging technology have radically surpassed the limited resolution of conventional far-field fluorescence microscopy (ca...
April 5, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28385547/in-vitro-and-in-vivo-stimulation-of-toll-like-receptor-9-by-cpg-oligodeoxynucleotides-incorporated-into-polypod-like-dna-nanostructures
#13
Yosuke Takahashi, Tatsuoki Maezawa, Yuki Araie, Yuki Takahashi, Yoshinobu Takakura, Makiya Nishikawa
Cytosine-phosphate-guanine (CpG) DNA is known to increase the potency of vaccines. Here, in vitro and in vivo stimulation of Toll-like receptor 9 (TLR9) by CpG DNA incorporated into polypod-like DNA nanostructures was evaluated by measuring the levels of tumor necrosis factor alpha (TNF-α) released from macrophage-like RAW 264.7 cells and plasma interleukin (IL)-12p40 in vivo following intravenous injection into mice. Phosphodiester CpG1668 was selected as the CpG DNA, and tripodna and hexapodna, which were CpG1668-containing tripod and hexapod-like DNA nanostructures, respectively, were designed...
April 3, 2017: Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28383245/exploring-the-chemistry-of-genetic-information-storage-and-propagation-through-polymerase-engineering
#14
Gillian Houlihan, Sebastian Arangundy-Franklin, Philipp Holliger
Nucleic acids are a distinct form of sequence-defined biopolymer. What sets them apart from other biopolymers such as polypeptides or polysaccharides is their unique capacity to encode, store, and propagate genetic information (molecular heredity). In nature, just two closely related nucleic acids, DNA and RNA, function as repositories and carriers of genetic information. They therefore are the molecular embodiment of biological information. This naturally leads to questions regarding the degree of variation from this seemingly ideal "Goldilocks" chemistry that would still be compatible with the fundamental property of molecular heredity...
April 18, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28382928/dna-origami-based-shape-ids-for-single-molecule-nanomechanical-genotyping
#15
Honglu Zhang, Jie Chao, Dun Pan, Huajie Liu, Yu Qiang, Ke Liu, Chengjun Cui, Jianhua Chen, Qing Huang, Jun Hu, Lianhui Wang, Wei Huang, Yongyong Shi, Chunhai Fan
Variations on DNA sequences profoundly affect how we develop diseases and respond to pathogens and drugs. Atomic force microscopy (AFM) provides a nanomechanical imaging approach for genetic analysis with nanometre resolution. However, unlike fluorescence imaging that has wavelength-specific fluorophores, the lack of shape-specific labels largely hampers widespread applications of AFM imaging. Here we report the development of a set of differentially shaped, highly hybridizable self-assembled DNA origami nanostructures serving as shape IDs for magnified nanomechanical imaging of single-nucleotide polymorphisms...
April 6, 2017: Nature Communications
https://www.readbyqxmd.com/read/28374130/dna-nanopore-functionalized-with-aptamer-and-cell-penetrating-peptide-for-tumor-cell-recognition
#16
Xi-Lin Guo, Dan-Dan Yuan, Ting Song, Xue-Mei Li
In the present work, DNA nanopore was composed of a bundle of six DNA duplexes folded from six DNA strands and functionalized with Ramos cell aptamer and cell-penetrating peptide (CPP). Herein, we present a unique dually conjugated molecule with an aptamer and cell-penetrating peptide for targeting and recognition of Ramos cells. The aptamer sequence was specific bound to Ramos cell, at the meanwhile the nanopore assembly was taken onto the surface of cell membrane and then got into the cells with the help of CPP...
April 3, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28373128/rolling-circle-transcription-based-polymeric-sirna-nanoparticles-for-tumor-targeted-delivery
#17
Jae Hyeop Lee, Sook Hee Ku, Min Ju Kim, So Jin Lee, Hyun Cheol Kim, Kwangmeyung Kim, Sun Hwa Kim, Ick Chan Kwon
RNA, one of the major biological macromolecules, has been considered as an attractive building material for bottom-up fabrication of nanostructures in the past few decades due to advancements in RNA biology, RNA chemistry and RNA nanotechnology. Most recently, an isothermal enzymatic nucleic acid amplification method termed rolling circle transcription (RCT), which achieves a large-scale synthesis of RNA nanostructures, has emerged as one of fascinating techniques for RNAi-based therapies. Herein, we proposed a newly designed RCT method for synthesis of polymeric siRNA nanoflower, referred to 'RCT and annealing-generated polymeric siRNA (RAPSI)': (1) Amplification of the antisense strand of siRNA via RCT process and (2) annealing of chimeric sense strand containing 3'-terminal DNA nucleotides that provide enzyme cleavage sites...
March 31, 2017: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/28371752/programmable-nanoassembly-consisting-of-two-hairpin-dnas-for-p53-gene-determination
#18
Jianguo Xu, Zai-Sheng Wu, Weiyu Shen, Jingqing Le, Tingting Zheng, Hongling Li, Lee Jia
As one of the most exciting building blocks, DNA has gained increasing attention in the construction of promising nanostructures for various biological and medical purposes. In this contribution, we have developed an easily constructed DNA nanoassembly-based biosensing system that consists of one signal hairpin probe (SHP) and one label-free hairpin probe (LHP) for target p53 gene analysis. The probes of SHP and LHP were designed to be incapable of interacting with each other in the absence of the p53 gene...
March 27, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28369541/programmable-i-motif-dna-folding-topology-for-a-ph-switched-reversible-molecular-sensing-device
#19
Lili Shi, Pai Peng, Yi Du, Tao Li
Four-stranded DNAs including G-quadruplexes and i-motifs are formed from four stretches of identical bases (G or C). A challenge remains in controlling the intermolecular folding of different G-rich or C-rich strands due to the self-association of each component. Here, we introduce a well-designed bimolecular i-motif that does not allow the dimerization of the same strand, and illustrate its usefulness in a pH-switched ATP-sensing DNA molecular device. We analyze two groups of i-motif DNAs containing two stretches of different C-residues (Cn-1TmCn and CnTmCn-1; n = 3-6, m = 1, 3) and show that their bimolecular folding patterns (L- and H-form) noticeably differs in the thermal stability...
March 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28351640/polyion-oligonucleotide-decorated-gold-nanoparticles-with-tunable-surface-charge-density-for-amplified-signal-output-of-potentiometric-immunosensor
#20
Shuzhen Lv, Zhenzhen Lin, Kangyao Zhang, Minghua Lu, Dianping Tang
Methods based on nanostructures have been developed for potentiometric immunosensors, but most involve low sensitivity or weak signal output and are unsuitable for routine use in diagnosis. Herein, we devise an in-situ signal-amplification strategy for enhanced electrical readout of potentiometric immunosensor toward target prostate-specific antigen (PSA, one kind of cancer biomarkers), based on polyion oligonucleotide-labeled gold nanoparticles (AuNPs). To decrease the background signal, monoclonal anti-human PSA capture antibody was covalently conjugated onto an activated glassy carbon electrode via typical carbodiimide coupling...
April 29, 2017: Analytica Chimica Acta
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