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Sticky ends

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
Catherine Sharpe, David J Thornton, Richard K Grencis
Gastrointestinal (GI) nematodes are a group of successful multi-cellular parasites that have evolved to co-exist 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...
January 22, 2018: Parasite Immunology
Mariagiovanna Scarpa, Amrit Paudel, Frank Kloprogge, Wen Kai Hsiao, Massimo Bresciani, Simon Gaisford, Mine Orlu
The features rendering ODFs as 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 human panel study. Four drug-free single-polymer films were prepared by solvent casting...
January 17, 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 (%)...
December 19, 2017: Chemosphere
Michael Grasso
A central component of percutaneous nephrostolithotomy is an endoscopic lithotrite that safely and efficiently clears stone of all compositions from the intrarenal collecting system. The current multicenter trial studied 3 lithotrite combinations employing both mechanical ballistic and ultrasonic energy to fragment and evacuate with suction stone debris. What is clear from this work is that, with regard to the timely clearance of the stone burden and peri-operative complications, there is minimal difference between the devices studied, nothing special and nothing new...
November 22, 2017: Journal of Endourology
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...
November 21, 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
Noshin Afshan, Mashooq Ali, Meng Wang, Mirza Muhammad Faran Ashraf Baig, Shou-Jun Xiao
Using small circular DNA molecules of different lengths as scaffolds, we successfully synthesised DNA nanotubes consisting of Mao's DNA tensegrity triangle tiles with four-arm junctions (Holliday junctions) at all vertices. Due to the intrinsic curvature of the triangle tile and the consecutive tile alignment, the 2D arrays are organised in the form of nanotubes. Two sized triangle tiles with equilateral side lengths of 1.5 and 2.5 full helical turns are connected by the sticky ended cohesion of a duplex with a length of 2...
November 16, 2017: Nanoscale
Dong Yu, Yanning Tan, Zhizhong Sun, Xuewu Sun, Xiabing Sheng, Tianshun Zhou, Ling Liu, Yi Mo, Beibei Jiang, Ning Ouyang, Xiaolin Yin, Meijuan Duan, Dingyang Yuan
The standard binary enzymatic assembly, which operates by inserting one DNA fragment into a plasmid, has a higher assembly success rate than the polynary enzymatic assembly, which inserts two or more fragments into the plasmid. However, it often leaves a nucleotide scar at the junction site. When a large DNA molecule is assembled stepwise into a backbone plasmid in a random piecewise manner, the scars will damage the structure of the original DNA sequence in the final assembled plasmids. Here, we propose an in vitro Seamless Stack Enzymatic Assembly (SSEA) method, a novel binary enzymatic assembly method involving a seamless strategy of splicing restriction sites via a stepwise process of multiple enzymatic reactions that does not leave nucleotide scars at the junction sites...
October 27, 2017: Scientific Reports
Yukiko Kamiya, Yoshinobu Yamada, Takahiro Muro, Kazunori Matsuura, Hiroyuki Asanuma
In this study, we constructed spherical, photo-responsive microcapsules composed of three photo-switchable DNA strands. These strands first formed a three-way junction (TWJ) motif that further self-assembled to form microsphere through hybridization of the sticky-end regions of each branch. To serve as the photo-switch, multiple unmodified azobenzene (Azo) or 2,6-dimethyl-4-(methylthio)azobenzene (SDM-Azo) were introduced into the sticky-end regions via a D-threoninol linker. The DNA-capsule structure deformed upon trans-to-cis isomerization of Azo or SDM-Azo induced by specific light-irradiation...
September 25, 2017: ChemMedChem
Helmut Griesser, Alexander Schwenger, Clemens Richert
Formulating pharmaceutically active ingredients for drug delivery is a challenge. There is a need for new drug delivery systems that take up therapeutic molecules and release them into biological systems. We propose a novel mode of encapsulation that involves matrices formed through co-assembly of drugs with adamantane hybrids that feature four CG dimers as sticky ends. Such adamantanes are accessible via inexpensive solution-phase syntheses, and the resulting materials show attractive properties for controlled release...
September 15, 2017: ChemMedChem
Xiaoyan Yu, Peiwen Bian, Yang Xue, Xueren Qian, Haipeng Yu, Wenshuai Chen, Xiaohai Hu, Peng Wang, Dong Wu, Qinghui Duan, Limei Li, Jing Shen, Yonghao Ni
The unique features of cellulosic paper including flexibility, biodegradability, and low cost enables it as a versatile, sustainable biomaterial for promising applications. In the paper industry, microsized mineral particles are widely used in the production of printing/writing paper grades, while rosin derived from trees is the earliest internal sizing agent for paper hydrophobication. On the basis of existing commercial practices associated with the use of mineral particles and rosin in paper production, we present a process concept of converting cellulosic fibers (paper-grade pulp) into "sticky" superhydrophobic paper involving the use of microsized mineral particles and rosin (a tree-derived natural product, mainly a mixture of resin acids, especially abietic acid with chemical formula of C19H29COOH)...
October 15, 2017: Carbohydrate Polymers
Ze Peng, Jeff L Froula, Jan-Fang Cheng
Fosmid end sequencing has been widely utilized in genome sequence assemblies and genome structural variation studies. We have developed a new approach to construct fosmid paired-end libraries that is suitable for Illumina sequencing platform. This approach employs a newly modified fosmid vector (pFosClip) which contains two loxP sites with identical orientation and two inverse Illumina adaptor priming sites flanking the cloning site. DNA prepared from the fosmid library constructed with pFosClip can be treated with the Cre recombinase to remove most of the vector DNA, leaving only 107 bp of the vector sequence with insert DNA...
2017: Methods in Molecular Biology
Shuoxing Jiang, Fan Hong, Huiyu Hu, Hao Yan, Yan Liu
Although many models have been developed to guide the design and implementation of DNA tile-based self-assembly systems with increasing complexity, the fundamental assumptions of the models have not been thoroughly tested. To expand the quantitative understanding of DNA tile-based self-assembly and to test the fundamental assumptions of self-assembly models, we investigated DNA tile attachment to preformed "multi-tile" arrays in real time and obtained the thermodynamic and kinetic parameters of single tile attachment in various sticky end association scenarios...
September 26, 2017: ACS Nano
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