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Sticky ends

Akira Endo, Mikami Masafumi, Hidetaka Kaya, Seiichi Toki
CRISPR/Cas9 systems are nowadays applied extensively to effect genome editing in various organisms including plants. CRISPR from Prevotella and Francisella 1 (Cpf1) is a newly characterized RNA-guided endonuclease that has two distinct features as compared to Cas9. First, Cpf1 utilizes a thymidine-rich protospacer adjacent motif (PAM) while Cas9 prefers a guanidine-rich PAM. Cpf1 could be used as a sequence-specific nuclease to target AT-rich regions of a genome that Cas9 had difficulty accessing. Second, Cpf1 generates DNA ends with a 5' overhang, whereas Cas9 creates blunt DNA ends after cleavage...
December 1, 2016: Scientific Reports
Zhuangqiang Gao, Zhenli Qiu, Minghua Lu, Jian Shu, Dianping Tang
This work designs a new label-free aptasensor for the colorimetric determination of small molecules (adenosine 5'-triphosphate, ATP) by using visible gold nanoparticles as the signal-generation tags, based on target-triggered hybridization chain reaction (HCR) between two hairpin DNA probes. The assay is carried out referring to the change in the color/absorbance by salt-induced aggregation of gold nanoparticles after the interaction with hairpins, gold nanoparticles and ATP. To construct such an assay system, two hairpin DNA probes with a short single-stranded DNA at the sticky end are utilized for interaction with gold nanoparticles...
October 20, 2016: Biosensors & Bioelectronics
Ciara Kyne, Kiara Jordon, Dana I Filoti, Thomas M Laue, Peter B Crowley
Decades of dilute-solution studies have revealed the influence of charged residues on protein stability, solubility and stickiness. Similar characterizations are now required in physiological solutions to understand the effect of charge on protein behavior under native conditions. Toward this end, we used free boundary and native gel electrophoresis to explore the charge of cytochrome c in buffer and in Escherichia coli extracts. We find that the charge of cytochrome c was ∼2-fold lower than predicted from primary structure analysis...
November 4, 2016: Protein Science: a Publication of the Protein Society
Nadrian C Seeman, Ruojie Sha, Jens Birktoft, Jianping Zheng, Wenyan Liu, Tong Wang, Chengde Mao
The simplest practical route to producing precisely designed 3D macroscopic objects is to form a crystalline arrangement by self-assembly, because such a periodic array has only conceptually simple requirements: a motif that has a robust 3D structure, dominant affinity interactions between parts of the motif when it self-associates, and predictable structures for these affinity interactions. Fulfilling these three criteria to produce a 3D periodic system is not easy, but should readily be achieved with well-structured branched DNA motifs tailed by sticky ends (Zheng et al...
2017: Methods in Molecular Biology
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
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