Read by QxMD icon Read

Sticky ends

I Caglar Tanrikulu, Audrey Forticaux, Song Jin, Ronald T Raines
Sticky-ended DNA duplexes can associate spontaneously into long double helices; however, such self-assembly is much less developed with proteins. Collagen is the most prevalent component of the extracellular matrix and a common clinical biomaterial. As for natural DNA, the ~10(3)-residue triple helices (~300 nm) of natural collagen are recalcitrant to chemical synthesis. Here we show how the self-assembly of short collagen-mimetic peptides (CMPs) can enable the fabrication of synthetic collagen triple helices that are nearly a micrometre in length...
November 2016: Nature Chemistry
Younsuk Dong, Steven I Safferman, Jeff Ostahowski, Tom Herold, Ronald Panter
When a fast-food restaurant's wastewater containing fats, oil and grease (FOG) is discharged into a collection system, it builds up over time and clogs pipes. Similarly, when such wastewater flows into a septic soil treatment system, it adheres to the surface of inlet pipes, gravel/distribution media and soil, restricting the flow and eventually clogging the septic soil treatment system. In this study, an enzymatic pretreatment system was tested on wastewater from a fast-food restaurant to determine its effectiveness in preventing septic soil treatment system clogging...
October 11, 2016: Journal of Environmental Science and Health. Part A, Toxic/hazardous Substances & Environmental Engineering
Jaimie Marie Stewart, Mathias Viard, Hari K K Subramanian, Brandon K Roark, Kirill A Afonin, Elisa Franco
RNA is a natural multifunctional polymer, and is an essential component in both complex pathways and structures within the cellular environment. For this reason, artificial self-assembling RNA nanostructures are emerging as a powerful tool with broad applications in drug delivery and metabolic pathway regulation. To date, coordinated delivery of functional molecules via programmable RNA assemblies has been primarily done using nanosize RNA scaffolds. However, larger scaffolds could expand existing capabilities for spatial arrangement of ligands, and enable the controlled delivery of highly concentrated molecular loads...
October 14, 2016: Nanoscale
Evi Stahl, Florian Praetorius, Carina C de Oliveira Mann, Karl-Peter Hopfner, Hendrik Dietz
One key goal of DNA nanotechnology is the bottom-up construction of macroscopic crystalline materials. Beyond applications in fields such as photonics or plasmonics, DNA-based crystal matrices could possibly facilitate the diffraction-based structural analysis of guest molecules. Seeman and coworkers reported in 2009 the first designed crystal matrices based on a 38 kDa DNA triangle that was composed of seven chains. The crystal lattice was stabilized, unprecedentedly, by Watson-Crick base pairing. However, 3D crystallizing larger designed DNA objects that include more chains such as DNA origami remains an unsolved problem...
September 1, 2016: ACS Nano
Yu Mi Baek, Soojin Yoon, Yeo Eun Hwang, Dong-Eun Kim
Exogenous nucleic acids induce an innate immune response in mammalian host cells through activation of the retinoic acid-inducible gene I (RIG-I). We evaluated RIG-I protein for RNA binding and ATPase stimulation with RNA ligands to investigate the correlation with the extent of immune response through RIG-I activation in cells. RIG-I protein favored blunt-ended, double-stranded RNA (dsRNA) ligands over sticky-ended dsRNA. Moreover, the presence of the 5'-triphosphate (5'-ppp) moiety in dsRNA further enhanced binding affinity to RIG-I...
August 2016: Immune Network
Shahrzad Ghasemi Monjezi, Seyedeh Elham Rezatofighi, Khalil Mirzadeh, Saadat Rastegarzadeh
A novel bovine viral diarrheal virus (BVDV)-RNA detection method was developed using a combination of the amplification capability of hybridization chain reaction (HCR) with the sensitivity of an unmodified-gold nanoparticle (AuNP) colorimetric detection assay. Two auxiliary probes were designed to target a conserved RNA sequence among the BVDV isolates. The complementary target BVDV-RNA was used as the initiator to trigger a cascade of hybridization events to yield nicked double-helix DNA analogous to the alternating copolymers...
October 2016: Applied Microbiology and Biotechnology
Hongfei He, Jianyuan Dai, Zhijuan Duan, Yan Meng, Cuisong Zhou, Yuyin Long, Baozhan Zheng, Juan Du, Yong Guo, Dan Xiao
Self-assembly of DNA nanostructures is of great importance in nanomedicine, nanotechnology and biosensing. Herein, a novel target-catalyzed autonomous assembly pathway for the formation of dendrimer-like DNA nanostructures that only employing target DNA and three hairpin DNA probes was proposed. We use the sticky-ended Y shape DNA (Y-DNA) as the assembly monomer and it was synthesized by the catalyzed hairpin assembly (CHA) instead of the DNA strand annealing method. The formed Y-DNA was equipped with three ssDNA sticky ends and two of them were predesigned to be complementary to the third one, then the dendrimer-like DNA nanostructures can be obtained via an autonomous assembly among these sticky-ended Y-DNAs...
December 15, 2016: Biosensors & Bioelectronics
Hongfei He, Jianyuan Dai, Zhijuan Duan, Baozhan Zheng, Yan Meng, Yong Guo, Dan Xiao
It is known that the adsorption of short single-stranded DNA (ssDNA) on unmodified gold nanoparticles (AuNPs) is much faster than that for long ssDNA, and thus leads to length-dependent AuNPs aggregation after addition of salt, the color of the solutions sequentially changed from red to blue in accordance with the increase of ssDNA length. However, we found herein that the ssDNA sticky end of hairpin DNA exhibited a completely different adsorption behavior compared to ssDNA, an inverse blue-to-red color variation was observed in the colloid solution with the increase of sticky end length when the length is within a certain range...
2016: Scientific Reports
Hua Xie, Qin Wang, Yaqin Chai, Yali Yuan, Ruo Yuan
In this work, a label-free electrochemical biosensor was developed for sensitive and selective detection of mercury (II) ions (Hg(2+)) based on in-situ deposition of silver nanoparticles (AgNPs) on terminal deoxynucleotidyl transferase (TdT) extended ssDNA for signal output and nicking endonuclease for cycling amplification. In the presence of target Hg(2+), the T-rich DNA (HP1) could partly fold into duplex-like structure (termed as output DNA) via T-Hg(2+)-T base pairs and thus exposed its sticky end. The sticky end of output DNA could then hybridize with 3'-PO4 terminated capture DNA (HP2) on electrode surface to form output DNA-HP2 hybridization complex with the sequence 5'-CCTCAGC-3'/3'-GGAGTCG-5' (the sequence could be recognized by nicking endonuclease Nt...
December 15, 2016: Biosensors & Bioelectronics
Chad R Simmons, Fei Zhang, Jens J Birktoft, Xiaodong Qi, Dongran Han, Yan Liu, Ruojie Sha, Hatem O Abdallah, Carina Hernandez, Yoel P Ohayon, Nadrian C Seeman, Hao Yan
Structural DNA nanotechnology combines branched DNA junctions with sticky-ended cohesion to create self-assembling macromolecular architectures. One of the key goals of structural DNA nanotechnology is to construct three-dimensional (3D) crystalline lattices. Here we present a new DNA motif and a strategy that has led to the assembly of a 3D lattice. We have determined the X-ray crystal structures of two related constructs to 3.1 Å resolution using bromine-derivatized crystals. The motif we used employs a five-nucleotide repeating sequence that weaves through a series of two-turn DNA duplexes...
August 10, 2016: Journal of the American Chemical Society
Christina L Duncan, Paul T Enlow, Margo M Szabo, Eric Tolchin, Robert W Kelly, Lourdes Castanon, Ariel M Aballay
OBJECTIVE: Research suggests that active Leptospermum honey (ALH) improves outcomes in patients with partial-thickness burns by enhancing healing and reepithelialization rates, as well as by protecting against antibiotic-resistant microorganisms. This study assessed the effectiveness of ALH gel on healing time, bacterial growth, patient satisfaction, and cost of treatment. DESIGN: Single-arm, prospective case series. SETTING AND PATIENTS: Seven patients (aged 7-64 years) with partial-thickness facial burns were recruited from a northeastern US burn center...
August 2016: Advances in Skin & Wound Care
K Deepika Devi, Sanjib Kr Paul, Jatindra K Sahu
In the study, the storage life of vacuum puffed honey powder at accelerated storage environment (90 % relative humidity and 36 °C) was computed by determining the sticky-point moisture content as the critical parameter of the honey powder. The value of monolayer moisture content in the GAB model was calculated to be 0.081 kg water/kg dry solids by fitting water activity and moisture sorption data. Shelf life of the honey powder was predicted to be 222 days when the powder was packaged in aluminum foil-laminated polyethylene pouches with permeability value of 5...
May 2016: Journal of Food Science and Technology
Seonghyun Lee, Kyubong Jo
Large DNA molecules tethered on the functionalized glass surface have been utilized in polymer physics and biochemistry particularly for investigating interactions between DNA and its binding proteins. Here, we report a method that uses fluorescent microscopy for visualizing large DNA molecules tethered on the surface. First, glass coverslips are biotinylated and passivated by coating with biotinylated polyethylene glycol, which specifically binds biotinylated DNA via avidin protein linkers and significantly reduces undesirable binding from non-specific interactions of proteins or DNA molecules on the surface...
2016: Journal of Visualized Experiments: JoVE
Hua Wei, Suming Tang, Tianyu Hu, Guojie Zhao, Yifu Guan
Dumbbell probe (DP) attracts increasing interests in rolling circle amplification (RCA). A universal DP production method through cleavage-ligation of hairpin was proposed and optimized. The production is characterized by restriction endonuclease (RE)-induced cleavage ends ligation. It has the advantage of phosphorylation-free, splint-free and purification-free. To optimize designing, we found that the position of RE cleavage sequence in the stem and the primer position in the loop affected the formation and amplification of DP obviously...
2016: Scientific Reports
Vera Loorents, Johan Rosell, Helen Salgado Willner, Sussanne Börjeson
BACKGROUND: Detailed symptom specific descriptions of health-related quality of life (HRQOL), using validated questionnaires in patients with head and neck cancer (HNC) are sparse. The aim of the present study was to investigate HRQOL in patients with HNC up to 1 year after radiotherapy (RT), using two standardised questionnaires. METHODS: The data for the present study was originally collected in a randomised, prospective study. Forty-seven patients from two RT clinics in Sweden were included to investigate the secondary aim: HRQOL...
2016: SpringerPlus
Cong Wang, Xiaomin Chen, Yuying Wu, Hao Li, Yu Wang, Xiaofu Pan, Tingting Tang, Ziying Liu, Xiaokun Li
OBJECTIVES: To develop a convenient and sensitive point-of-care test for detecting gene mutations based on allele-specific PCR. RESULTS: To develop a lateral flow strip for visual detection of K-ras mutations based on a modified PCR, a specific DNA tag was covalently linked to the 5'-end of each primer by a nine-carbon linker to produce a sticky end. One of the sticky ends of the PCR products bound to gold nano-particles, while the other sticky end was captured onto a nitrocellulose membrane of lateral flow strips...
October 2016: Biotechnology Letters
Domenico Gazzillo, Gianmarco Munaò, Santi Prestipino
We study a pure fluid of heteronuclear sticky Janus dumbbells, considered to be the result of complete chemical association between unlike species in an initially equimolar mixture of hard spheres (species A) and sticky hard spheres (species B) with different diameters. The B spheres are particles whose attractive surface layer is infinitely thin. Wertheim's two-density integral equations are employed to describe the mixture of AB dumbbells together with unbound A and B monomers. After Baxter factorization, these equations are solved analytically within the associative Percus-Yevick approximation...
June 21, 2016: Journal of Chemical Physics
Wen-Sheng Xu, Karl F Freed
Telechelic polymers are chain macromolecules that may self-assemble through the association of their two mono-functional end groups (called "stickers"). A deep understanding of the relation between microscopic molecular details and the macroscopic physical properties of telechelic polymers is important in guiding the rational design of telechelic polymer materials with desired properties. The lattice cluster theory (LCT) for strongly interacting, self-assembling telechelic polymers provides a theoretical tool that enables establishing the connections between important microscopic molecular details of self-assembling polymers and their bulk thermodynamics...
June 7, 2016: Journal of Chemical Physics
Chenyu Wang, Sithara S Nair, Sharon Veeravalli, Patricia Moseh, Kenneth J Wynne
In the course of studies on Sylgard 184 (S-PDMS), we discovered strong effects on receding contact angles (CAs), θrec, while cure conditions have little effect on advancing CAs. Network formation at high temperatures resulted in high θadv of 115-120° and high θrec ≥ 80°. After network formation at low temperatures (≤25 °C), θadv was still high but θrec was 30-50°. Uncertainty about compositional effects on wetting behavior resulted in similar experiments with a model D(V)D(H) silicone elastomer (Pt-PDMS) composed of a vinyl-terminated poly(dimethylsiloxane) (PDMS) base and a polymeric hydromethylsilane cross-linker...
June 8, 2016: ACS Applied Materials & Interfaces
Jace C Bradshaw, Allea Belle Gongola, Nathan S Reyna
The goal of this protocol is to allow for the rapid verification of bioinformatically identified terminators. Further, the plasmid (pGR-Blue) is designed specifically for this protocol and allows for the quantification of terminator efficiency. As a proof of concept, six terminators were bioinformatically identified in the mycobacteriophage Bernal13. Once identified, terminators were then made as oligonucleotides with the appropriate sticky ends and annealed together. Using Golden Gate Assembly (GGA), terminators were then cloned into pGR-Blue...
2016: Journal of Visualized Experiments: JoVE
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"