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Sticky ends

Alexander Schwenger, Tomasz P Jurkowski, Clemens Richert
The encapsulation of folded proteins in stabilizing matrices is one of the challenges of soft-matter materials science. Capturing such fragile bio-macromolecules from aqueous solution, and embedding them in a lattice that stabilizes them against denaturation and decomposition is difficult. Here, we report that tetrahedral oligonucleotide hybrids as branching elements, and connecting DNA duplexes with sticky ends can assemble into materials. The material-forming property was used to capture DNA-binding proteins selectively from aqueous protein mixtures...
June 10, 2018: Chembiochem: a European Journal of Chemical Biology
Fabio Solis-Jimenez, Hector Hinojosa-Heredia, Luis García-Covarrubias, Virgilia Soto-Abraham, Rafael Valdez-Ortiz
Introduction: Sticky platelet syndrome (SPS) is a prothrombotic disease that is not well recognized and difficult to diagnose. Case Report: We present a case of a 49-year-old diabetic woman on ambulatory peritoneal dialysis therapy who underwent a kidney transplant from living-related donor. The donor was her sister with whom she shared one haplotype and absence of donor specific antibodies. The posttransplant evolution was torpid, developing progressive deterioration, which made us suspect a failure in the graft...
2018: Case Reports in Nephrology
Eric F LoPresti, Moria Robinson, Billy A Krimmel, Grace K Charles
In the coast range of California, the fruit of several manzanita (Arctostaphylos) species, including A. viscida, A. glandulosa, and A. hooveri, are covered in glandular-sticky hairs. The blueberry-sized fruit remain viscid after ripening, and if you walk through dense manzanita patches during the late spring and summer you are bound to end up with globs of fruit hanging loosely from your shirt and pants. While picking the fruit off your clothes, you may also notice that many of the fruit have dead insects firmly stuck in the glue-like exudates secreted by their dense glandular trichomes (Figure 1)...
May 30, 2018: Ecology
Mohammad Moradi, Yavar Rassi, Mohammad Reza Abai, Alireza Zahraei Ramazani, Mehdi Mohebali, Sayena Rafizadeh
Cutaneous leishmaniasis (CL) is endemic and a major health problem in 17 provinces out of 31 in Iran. This study aimed to determine vectors and reservoirs of the disease using molecular techniques in the borderline of Iran and Iraq. Sand flies and rodents were sampled using sticky paper traps and metal wire live traps, respectively, in the selected villages. About 10% of archived confirmed human positive slides was randomly checked for Leishmania by PCR-RFLP assay. The female sand flies were dissected in alcohol 96% in a sterile condition, the head and two segments of the abdomen end permanently mounted for identification and the remaining of body used for DNA extraction...
June 2018: Journal of Parasitic Diseases: Official Organ of the Indian Society for Parasitology
David Richard, James Hallett, Thomas Speck, C Patrick Royall
We combine experiments and simulations to study the link between criticality and gelation in sticky spheres. We employ confocal microscopy to image colloid-polymer mixtures and Monte Carlo simulations of the square-well (SW) potential as a reference model. To this end, we map our experimental samples onto the SW model. We find an excellent structural agreement between experiments and simulations, both for locally favored structures at the single particle level and large-scale fluctuations at criticality. We follow in detail the rapid structural change in the critical fluid when approaching the gas-liquid binodal and highlight the role of critical density fluctuations for this structural crossover...
May 29, 2018: Soft Matter
Marija Miljkovic, Milka Malesevic, Brankica Filipic, Goran Vukotic, Milan Kojic
Restriction enzymes are the main defence system against foreign DNA, in charge of preserving genome integrity. Lactococcus raffinolactis BGTRK10-1 expresses Lra I Type II restriction-modification enzyme, whose activity is similar to that shown for Eco RI; Lra I methyltransferase protects DNA from Eco RI cleavage. The gene encoding Lra I endonuclease was cloned and overexpressed in E. coli . Purified enzyme showed the highest specific activity at lower temperatures (between 13°C and 37°C) and was stable after storage at -20°C in 50% glycerol...
2018: BioMed Research International
Miran Liber, Toma E Tomov, Roman Tsukanov, Yaron Berger, Mary Popov, Dinesh C Khara, Eyal Nir
Organizing DNA origami building blocks into higher order structures is essential for fabrication of large structurally and functionally diverse devices and molecular machines. Unfortunately, the yields of origami building block attachment reactions are typically not sufficient to allow programed assembly of DNA devices made from more than a few origami building blocks. To investigate possible reasons for these low yields, a detailed single-molecule fluorescence study of the dynamics of rectangular origami dimerization and origami dimer dissociation reactions is conducted...
May 4, 2018: Small
Caroline D Bösch, Jovana Jevric, Nutcha Bürki, Markus Probst, Simon M Langenegger, Robert Häner
Vesicle-shaped supramolecular polymers are formed by self-assembly of a DNA duplex containing phenanthrene overhangs at both ends. In the presence of spermine, the phenanthrene overhangs act as sticky ends linking the DNA duplexes together. In aqueous solution, the assembly leads to vesicles with a diameter in the range of 50-200 nm. Fluorescence measurements show that the assembled phenanthrene units act as light-harvesting complexes and transfer absorbed energy to an acceptor, such as pyrene or Cy3, which can either be directly added to the polymer or attached via a complementary DNA strand...
May 16, 2018: Bioconjugate Chemistry
Yuki Suzuki, Hiroshi Sugiyama, Masayuki Endo
Ordered DNA origami arrays have the potential to compartmentalize space into distinct periodic domains that can incorporate a variety of nanoscale objects. Herein, we used the cavities of a preassembled 2D DNA origami framework to incorporate square-shaped DNA origami structures (SQ-origamis). The framework was self-assembled on a lipid bilayer membrane from cross-shaped DNA origami structures (CR-origamis) and subsequently exposed to the SQ-origamis. High-speed AFM revealed the dynamic adsorption/desorption behavior of the SQ-origamis, which resulted in continuous changing of their arrangements in the framework...
June 11, 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)...
May 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...
May 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 these cloning strategies. 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 issue...
March 18, 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
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