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https://www.readbyqxmd.com/read/28211680/two-way-gold-nanoparticle-label-free-sensing-of-specific-sequence-and-small-molecule-targets-using-switchable-concatemers
#1
Longjiao Zhu, Xiangli Shao, Yunbo Luo, Kunlun Huang, Wentao Xu
A two-way colorimetric biosensor based on unmodified gold nanoparticles (GNPs) and a switchable double-stranded DNA (dsDNA) concatemer have been demonstrated. Two hairpin probes (H1&H2) were first designed that provided the fuels to assemble the dsDNA concatemers via hybridization chain reaction (HCR). A functional hairpin (FH) was rationally designed to recognize the target sequences. All the hairpins contained single-stranded DNA (ssDNA) loop and sticky-ends to prevent GNPs from salt-induced aggregation. In the presence of target sequence, the capture probe blocked in the FH recognizes the target to form a duplex DNA, which causes the release of the initiator probe by FH conformational change...
February 17, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28165224/programmable-dna-guided-artificial-restriction-enzymes
#2
Behnam Enghiad, Huimin Zhao
Restriction enzymes are essential tools for recombinant DNA technology that have revolutionized modern biological research. However, they have limited sequence specificity and availability. Here we report a Pyrococcus furiosus Argonaute (PfAgo) based platform for generating artificial restriction enzymes (AREs) capable of recognizing and cleaving DNA sequences at virtually any arbitrary site and generating defined sticky ends of varying length. Short DNA guides are used to direct PfAgo to target sites for cleavage at high temperatures (>87 °C) followed by reannealing of the cleaved single stranded DNAs...
February 6, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28115632/the-cctl-cpf1-assisted-cutting-and-taq-dna-ligase-assisted-ligation-method-for-efficient-editing-of-large-dna-constructs-in-vitro
#3
Chao Lei, Shi-Yuan Li, Jia-Kun Liu, Xuan Zheng, Guo-Ping Zhao, Jin Wang
As Cpf1 cleaves double-stranded DNA in a staggered way, it can be used in DNA assembly. However, the Cpf1 cleavage was found to be inaccurate, which may cause errors in DNA assembly. Here, the Cpf1 cleavage sites were precisely characterized, where the cleavage site on the target strand was around the 22nd base relative to the protospacer adjacent motif site, but the cleavage on the non-target strand was affected by the spacer length. When the spacer length was 20 nt or longer, Cpf1 mainly cleaved around the 14th and the 18th bases on the non-target strand; otherwise, with a shorter spacer (i...
January 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28107938/nucleotide-base-analog-pyrrolo-deoxycytidine-as-fluorescent-probe-signal-for-enzyme-free-and-signal-amplified-nucleic-acids-detection
#4
Zhijuan Duan, Zhuo Li, Jianyuan Dai, Hongfei He, Dan Xiao
In the present work, an enzyme-free and signal amplified nucleic acids detection method based on the fluorescent nucleotide base analog pyrrolo-deoxycytidine (P-dC) and catalyzed hairpin assembly (CHA) has been developed. In the CHA signal amplification system, two hairpin auxiliary probes, H1 and H2, which containing a fluorescent P-dC at the end of the stem, respectively, were used as the fluorescent probes. The fluorescence of P-dC in H1 and H2 was quenched owing to the stacking interaction among the bases in the stem...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28032108/faunal-distribution-and-seasonal-bio-ecology-of-naturally-infected-sand-flies-in-a-new-endemic-zoonotic-cutaneous-leishmaniasis-focus-of-southern-iran
#5
Kourosh Azizi, Hayedeh Parvinjahromi, Mohammad Djaefar Moemenbellah-Fard, Bahador Sarkari, Mohammad Reza Fakoorziba
BACKGROUND: Cutaneous leishmaniasis is a major health problem in Iran in spite of implementation of control program. This infectious disease caused morbidity in less than 27000 people in 2010. This study was set to determine some ecological aspects of sand flies in Fasa district, Fars Province, southern Iran during 2011-2012. METHODS: A total of 4792 sand flies were captured by means of sticky paper and CDC miniature light traps in 10 selected villages from the beginning to the end of the active season, from which 1115 specimens were captured for abundance study and 3677 specimens captured for monitoring monthly activities in Fasa...
December 2016: Journal of Arthropod-borne Diseases
https://www.readbyqxmd.com/read/27987754/incorporation-of-biguanide-compounds-into-poly-gl-b-poly-gl-co-tmc-co-cl-b-poly-gl-monofilament-surgical-sutures
#6
Yolanda Márquez, Tània Cabral, Alice Lorenzetti, Lourdes Franco, Pau Turon, Luís J Del Valle, Jordi Puiggalí
A new biodegradable coating was developed for bioabsorbable monofilament sutures. Specifically, a random copolymer having 35wt-% and 65wt-% of lactide and trimethylene carbonate units showed appropriate flexibility, stickiness and degradation rate, as well as capability to produce a complete and uniform coating. Monofilament sutures of polyglycolide-b-poly(glycolide-co-trimethylene carbonate-co-ε-caprolactone)-b-polyglycolide were loaded with chlorhexidine (CHX) and poly(hexamethylene biguanide) (PHMB) to explore the possibility to achieve antimicrobial activity without adverse cytotoxic effects...
February 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/27937049/agglomeration-of-celecoxib-by-quasi-emulsion-solvent-diffusion-method-without-stabilizer-effect-of-good-solvent
#7
Maryam Maghsoodi, Ali Nokhodchi
AIM: The aim of the present research is to investigate the feasibility of agglomeration of crystals by the quasi emulsion solvent diffusion method without using a stabilizer. METHOD: Two solvent systems comprising a solvent and an antisolvent (water) were used to prepare celecoxib agglomerates. To this end, seven solvents including propanol, methyl acetate, methyl ethyl ketone, butanol, ethyl acetate, isopropyl acetate and pentanol were examined. The agglomerates were evaluated by micromeritic properties (e...
December 12, 2016: Pharmaceutical Development and Technology
https://www.readbyqxmd.com/read/27929588/use-of-%C3%AE-cyclodextrin-tethered-cationic-polymer-based-fluorescence-enhancement-of-pyrene-and-hybridization-chain-reaction-for-the-enzyme-free-amplified-detection-of-dna
#8
Chunxia Song, Bingjie Li, Xiaohai Yang, Kemin Wang, Qing Wang, Jianbo Liu, Jin Huang
Herein, we proposed an enzyme-free strategy for the amplified detection of DNA by combining the efficient fluorescence enhancement capability of a β-cyclodextrin-tethered cationic polymer (cationic polyβ-CD) to pyrene with the amplification capability of target DNA triggered hybridization chain reaction (HCR). Cationic polyβ-CD with positive charge was synthesized. Two hairpin probes, H1 and H2, were employed in the system and the pyrene-labelled H2 was chosen as the signal unit. The pyrene attached on the sticky end of H2 was flexible and there was strong electrostatic interaction between cationic polyβ-CD and negatively-charged H2, so pyrene could easily enter the cavity of CD that is tethered on the cationic polymer, accompanied by significant fluorescence enhancement...
December 19, 2016: Analyst
https://www.readbyqxmd.com/read/27905529/efficient-targeted-mutagenesis-of-rice-and-tobacco-genomes-using-cpf1-from-francisella-novicida
#9
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
https://www.readbyqxmd.com/read/27825528/hybridization-chain-reaction-based-colorimetric-aptasensor-of-adenosine-5-triphosphate-on-unmodified-gold-nanoparticles-and-two-label-free-hairpin-probes
#10
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...
March 15, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27813264/protein-charge-determination-and-implications-for-interactions-in-cell-extracts
#11
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...
February 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/27812997/designed-3d-dna-crystals
#12
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
https://www.readbyqxmd.com/read/27768103/peptide-tessellation-yields-micrometre-scale-collagen-triple-helices
#13
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
https://www.readbyqxmd.com/read/27726482/enzyme-pretreatment-of-fats-oil-and-grease-from-restaurant-waste-to-prolong-septic-soil-treatment-system-effectiveness
#14
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...
January 2, 2017: Journal of Environmental Science and Health. Part A, Toxic/hazardous Substances & Environmental Engineering
https://www.readbyqxmd.com/read/27714127/programmable-rna-microstructures-for-coordinated-delivery-of-sirnas
#15
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
https://www.readbyqxmd.com/read/27583560/impact-of-heterogeneity-and-lattice-bond-strength-on-dna-triangle-crystal-growth
#16
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
https://www.readbyqxmd.com/read/27574504/dependence-of-rig-i-nucleic-acid-binding-and-atp-hydrolysis-on-activation-of-type-i-interferon-response
#17
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
https://www.readbyqxmd.com/read/27535242/enzyme-free-amplification-and-detection-of-bovine-viral-diarrhea-virus-rna-using-hybridization-chain-reaction-and-gold-nanoparticles
#18
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
https://www.readbyqxmd.com/read/27498325/target-catalyzed-autonomous-assembly-of-dendrimer-like-dna-nanostructures-for-enzyme-free-and-signal-amplified-colorimetric-nucleic-acids-detection
#19
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
https://www.readbyqxmd.com/read/27477392/unusual-sequence-length-dependent-gold-nanoparticles-aggregation-of-the-ssdna-sticky-end-and-its-application-for-enzyme-free-and-signal-amplified-colorimetric-dna-detection
#20
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
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