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Sticky ends

Yuki Suzuki, Masayuki Endo, Hiroshi Sugiyama
Ordered DNA origami arrays have the potential to compartmentalize space into distinct periodic domains that can incorporate a variety of nanoscale objects. Here, we aimed to use the internal cavities of a preassembled two-dimensional (2D) DNA origami framework to incorporate supplemental square-shaped DNA origamis (SQ-origamis) with shapes that were complementary to those of the cavities. In our approach, the framework was first self-assembled on a mica-supported lipid bilayer membrane from cross-shaped DNA origamis (CR-origamis), and subsequently exposed to the SQ-origamis...
April 12, 2018: Angewandte Chemie
Sefa Pekol
Metal-cutting fluids, one of the most consumed materials in the metallurgy industry, turn into oily wastewater after being used in the metalworking processes. The amount of cutting fluids used can reach up to millions of tons. And these invaluable fluids are difficult to distil and expensive, and impossible to store. Even after it is disposed and recaptured, the end product has no commercial value. In this study, the effect of this mixture was examined on the ecosystem using the Allium cepa test system in which onion root tips were treated with three different concentrations of waste-cutting fluid, based on a 24- and 48-h cell cycle...
April 11, 2018: Environmental Science and Pollution Research International
Masanori Fukumoto, Yui Nishida, Teruyo Kida, Takaki Sato, Takatoshi Kobayashi, Tsunehiko Ikeda
BACKGROUND: Perfluorocarbon liquid (PFCL) is widely used as an intraoperative heavy tamponade to flatten the retina and is replaced with silicone oil (SO) at the end of the surgery. Due to the long tamponade period, the SO is known to remain attached to the retina at the time of removal, and is commonly termed "sticky oil". The aim of this present study was to report a case of SO stickily attached to the retina via PFCL without tamponade period. CASE PRESENTATION: A 39-year-old male was referred to our hospital due to decreased vision and visual field defect in his right eye...
March 27, 2018: BMC Ophthalmology
Mirella Harsoula, George Contopoulos
We study the global and the local transport and diffusion in the case of the standard map, by calculating the diffusion exponent μ. In the global case, we find that the mean diffusion exponent for the whole phase space is either μ=1, denoting normal diffusion, or μ=2 denoting anomalous diffusion (and ballistic motion). The mean diffusion of the whole phase space is normal when no accelerator mode exists and it is anomalous (ballistic) when accelerator mode islands exist even if their area is tiny in the phase space...
February 2018: Physical Review. E
Akram Norouzi, Hadi Ravan, Abbas Mohammadi, Elyas Hosseinzadeh, Mahdieh Norouzi, Tahereh Fozooni
The development of powerful techniques to detect cancer cells at early stages plays a notable role in diagnosing and prognosing cancer patients and reducing mortality. This paper reports on a novel functional DNA nanoassembly capable of detecting cancer cells based on structural DNA nanotechnology. DNA nanoassemblies were constructed by the self-assembly of a DNA concatemer to a plenty of sticky-ended three-way junctions. While an aptamer moiety guided the nanoassembly to the target cancer cell, the peroxidase-mimicking DNAzymes embedded in the nanoassemblies were used as the sensing element to produce colorimetric signals...
August 9, 2018: Analytica Chimica Acta
Chen Zhou, Haimin Zou, Chengjun Sun, Dongxia Ren, Wei Xiong, Yongxin Li
Based on a novel signal amplification strategy by catalytic hairpin assembly and displacement of G-quadruplex DNA, an enzyme-free, non-label fluorescent aptasensing approach was established for sensitive detection of four tetracycline veterinary drugs in milk. The network consisted of a pair of partially complementary DNA hairpins (HP1 and HP2). The DNA aptamer of four tetracycline veterinary drugs was located at the sticky end of the HP1. The ring region of HP1 rich in G and C could form a stable G-quadruplex structure, which could emit specific fluorescence signal after binding with the fluorescent dye and N-methylmesoporphyrin IX (NMM)...
March 8, 2018: Analytical and Bioanalytical Chemistry
Johanna Gorges, Beatrice Wehler, Maximilian Krüger, Susanne Singer
OBJECTIVE: To date, only a few studies have investigated oral health-related quality of life (OH-QoL) in cancer patients. The European Organisation for Research and Treatment of Cancer (EORTC) has therefore developed a questionnaire, the Quality of Life Questionnaire - Oral Health Module 15 (EORTC QLQ-OH15), to enable investigation of OH-QoL. The aim of this study was to examine OH-QoL in a real-world setting. PATIENTS AND METHODS: OH-QoL was measured using the EORTC QLQ-OH15 in cancer patients at a non-specified time during treatment (t1 ) as well as two weeks (t2 ) and three months (t3 ) after baseline...
March 1, 2018: Laryngo- Rhino- Otologie
Xia Liu, Tuoping Li, Darren J Hart, Song Gao, Hongling Wang, Herui Gao, Shumin Xu, Yifeng Zhang, Yifei Liu, Yingfeng An
Currently, the most widely used strategies for molecular cloning are sticky-end ligation-based cloning, TA cloning, blunt-end ligation-based cloning and ligase-independent cloning. In this study we have developed a novel mini-vector pANY1 which can simultaneously meet the requirements of all the cloning strategies mentioned above. In addition, the selection of appropriate restriction digestion sites is difficult in some cases because of the presence of internal sites. In this study, an annealing of PCR products (APP)-based sticky-end cloning strategy was introduced to avoid this trouble...
February 12, 2018: Biochemical and Biophysical Research Communications
Jianyuan Dai, Zhijuan Duan, Mengzhu Cao, Mengru Hao, Hongfei He, Dan Xiao
A rapid signal amplified DNA detection method based on self-replicating catalyzed hairpin assembly (SRCHA) has been proposed. In this SRCHA system, two split target DNA sequences were respectively integrated into hairpin auxiliary probes H1 and H2. H2 was used as fluorescent probe which containing a fluorescent nucleotide base analog pyrrolo-deoxycytidine (P-dC) at the end of the stem. Target DNA can be circularly used in this SRCHA system to form the helix DNA H1-H2 complex, the structure change of H2 will move P-dC from hairpin stem to flexible ssDNA sticky end, leading to fluorescence increase due to the less stacking interaction...
May 1, 2018: Talanta
Yuezhou Zhang, Jing Tu, Dongqing Wang, Haitao Zhu, Sajal Kumar Maity, Xiangmeng Qu, Bram Bogaert, Hao Pei, Hongbo Zhang
DNA encodes the genetic information; recently, it has also become a key player in material science. Given the specific Watson-Crick base-pairing interactions between only four types of nucleotides, well-designed DNA self-assembly can be programmable and predictable. Stem-loops, sticky ends, Holliday junctions, DNA tiles, and lattices are typical motifs for forming DNA-based structures. The oligonucleotides experience thermal annealing in a near-neutral buffer containing a divalent cation (usually Mg2+ ) to produce a variety of DNA nanostructures...
February 1, 2018: Advanced Materials
Fanli Zeng, Suhua Zhang, Zhimin Hao, Shixin Duan, Yanan Meng, Pan Li, Jingao Dong, Yibin Lin
While the QuikChange site-directed mutagenesis method and its later modifications are extremely useful and simple, they suffer from several drawbacks. Here, we propose a new method, named LFEAP mutagenesis (Ligation of Fragment Ends After PCR) for creating various mutations in plasmid by leveraging three existing concepts: inverse PCR, single primer PCR, and sticky-end assembly. The first inverse PCR on the target plasmid yielded linearized DNA fragments with mutagenic ends, and a second single primer PCR resulted in complementary single-stranded DNA fragments with the addition of overhangs at the 5' end of each strand...
January 29, 2018: Scientific Reports
C Sharpe, D J Thornton, R K Grencis
Gastrointestinal (GI) nematodes are a group of successful multicellular parasites that have evolved to coexist within the intestinal niche of multiple species. It is estimated that over 10% of the world's population are chronically infected by GI nematodes, making this group of parasitic nematodes a major burden to global health. Despite the large number of affected individuals, there are few effective treatments to eradicate these infections. Research into GI nematode infections has primarily focused on defining the immunological and pathological consequences on host protection...
April 2018: Parasite Immunology
Mariagiovanna Scarpa, Amrit Paudel, Frank Kloprogge, Wen Kai Hsiao, Massimo Bresciani, Simon Gaisford, Mine Orlu
The features rendering orodispersible films (ODFs) patient-centric formulations are widely discussed in the scientific literature. However there is a lack of research studies exploring ODF characteristics with a potential impact on end-user acceptability. The aim of this study was to identify the key ODF characteristics affecting end-user acceptability by developing in vitro test methods for the prediction of ODFs acceptability and correlate these formulation characteristics with the data obtained from a human panel study...
April 2018: European Journal of Pharmaceutics and Biopharmaceutics
J Fernandez-Castanon, F Bomboi, F Sciortino
The proper design of DNA sequences allows for the formation of well-defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to experimentally realize particles with well-defined valence, namely, tetravalent nanostars (A) and bivalent chains (B). We specifically focus on the case in which A particles can only bind to B particles, via appropriately designed sticky-end sequences. Hence AA and BB bonds are not allowed...
January 14, 2018: Journal of Chemical Physics
Hongfei He, Jianyuan Dai, Yan Meng, Zhijuan Duan, Cuisong Zhou, Baozhan Zheng, Juan Du, Yong Guo, Dan Xiao
It is known that DNA molecules can be used to build a various of complicated geometrical DNA nanostructures with programmable sequence design, and these DNA nanomaterials show a promising application in biotechnology and biomedicine. However, the construction of large-sized three dimensional DNA-based nanomaterials still remains a challenge. In this work, we propose a new strategy that only employs one target DNA to trigger multiple catalyzed hairpin assembly (CHA) reactions and sticky ends self-assembly to prepare hundreds of nanometer-sized DNA nanoparticles...
March 1, 2018: Talanta
Firdos Fatma, Sonam Verma, Aisha Kamal, Alka Srivastava
The present experiment was designed to monitor the morphotoxic, cytotoxic and genotoxic potential of Mancozeb (fungicide) in non-target plants using bulbs of Allium cepa. Mancozeb is classified as a contact fungicide and is registered for use on a variety of crop plants. In the present monitoring, Allium cepa bulbs were exposed to different concentrations of mancozeb viz., 10, 30, 50, 70, 90, 110, 130 and 150 ppm for 24 and 48 h. The potential morphotoxic and cytotoxic effects of mancozeb were examined by determining the average root number, average root length, mitotic index, relative abnormality rate (%) and frequency of abnormalities (%)...
March 2018: Chemosphere
Jörg Schnauß, Martin Glaser, Jessica S Lorenz, Carsten Schuldt, Christin Möser, Martin Sajfutdinow, Tina Händler, Josef A Käs, David M Smith
Mechanical properties of complex, polymer-based soft matter, such as cells or biopolymer networks, can be understood in neither the classical frame of flexible polymers nor of rigid rods. Underlying filaments remain outstretched due to their non-vanishing backbone stiffness, which is quantified via the persistence length (lp), but they are also subject to strong thermal fluctuations. Their finite bending stiffness leads to unique, non-trivial collective mechanics of bulk networks, enabling the formation of stable scaffolds at low volume fractions while providing large mesh sizes...
October 25, 2017: Journal of Visualized Experiments: JoVE
Fang He, Hui Liu, Xinggang Guo, Bin-Cheng Yin, Bang-Ce Ye
Exosomes, as an important subpopulation of extracellular vesicles (EVs), play an important role in intercellular communications in various important pathophysiological processes, especially cancer-related. However, reliable and convenient quantitative methods for their determination are still technically challenging. In this study, we developed an efficient and direct method by combining immunoaffinity and lipid membrane surface modification into a single platform for specific isolation and accurate quantification of exosomes...
December 5, 2017: Analytical Chemistry
Fanli Zeng, Jinping Zang, Suhua Zhang, Zhimin Hao, Jingao Dong, Yibin Lin
BACKGROUND: Recent development of DNA assembly technologies has spurred myriad advances in synthetic biology, but new tools are always required for complicated scenarios. Here, we have developed an alternative DNA assembly method named AFEAP cloning (Assembly of Fragment Ends After PCR), which allows scarless, modular, and reliable construction of biological pathways and circuits from basic genetic parts. METHODS: The AFEAP method requires two-round of PCRs followed by ligation of the sticky ends of DNA fragments...
November 14, 2017: BMC Biotechnology
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