scholarly journals Fluorinated oil-surfactant mixtures with the density of water: artificial cells for synthetic biology

2021 ◽  
Author(s):  
Steven A. Benner ◽  
Roberto Laos
Keyword(s):  
Synthetic Biology ◽  
Genetic Information ◽  
Rolling Circle Amplification ◽  
Dna Origami ◽  
Biological Processes ◽  
Surfactant Mixtures ◽  
Rolling Circle ◽  
Oil Emulsions ◽  
Air Interfaces ◽  
Density Of Water

Water-in-oil emulsions provide matrices for compartments that have many uses in diversity science. However, hydrophobic species are frequently incompatible with biological systems. For this reason, fluorinated matrices are often sought, since fluorinated species are neither hydrophilic nor hydrophobic; they therefore do not interact with most biomolecules. However, most fluorinated oils have densities much higher than the density of water (1 g/ml). Consequently, water droplets float in fluorinated oils, aggregating near their surfaces. This facilitates droplet-droplet collision and fusion, exposing droplets to air interfaces and making their manipulation difficult. Here, we report the synthesis, characterization, and use of fluorinated polysiloxane oils that have densities close to the density of water. These, with a non-ionic fluorosilicone surfactant, produce thermostable water-in-oil emulsions that neither float nor sink. We show how droplets in these emulsions can host many biological processes, including PCR, DNA origami, rolling circle amplification (RCA), and Taqman ® assays. Further, oil-diffusible reagents can initiate reactions within the droplets. The droplets can also be used with unnatural DNA emerging from synthetic biology, including DNA built from artificially expanded genetic information systems (AEGIS) with six nucleotide "letters".

Rolling Circle Amplification-Based DNA Origami Nanostructrures for Intracellular Delivery of Immunostimulatory Drugs

Small ◽  
2013 ◽  
Vol 9 (18) ◽  
pp. 3082-3087 ◽  
Author(s):  
Xiangyuan Ouyang ◽  
Jiang Li ◽  
Huajie Liu ◽  
Bin Zhao ◽  
Juan Yan ◽  
...  
Keyword(s):  
Rolling Circle Amplification ◽  
Intracellular Delivery ◽  
Dna Origami ◽  
Rolling Circle

DNA Origami Nanostructures with Scaffolds Obtained from Rolling Circle Amplification

2020 ◽  
Vol 2 (10) ◽  
pp. 1322-1327
Author(s):  
Mengyuan Xu ◽  
Chi Zhang ◽  
Cunjun Zhang ◽  
Yiling Zhao ◽  
Zhi Qi ◽  
...  
Keyword(s):  
Rolling Circle Amplification ◽  
Dna Origami ◽  
Rolling Circle

Self-assembly of DNA Origami Using Rolling Circle Amplification Based DNA Nanoribbons

2014 ◽  
Vol 32 (2) ◽  
pp. 137-141 ◽  
Author(s):  
Bing Liu ◽  
Xiangyuan Ouyang ◽  
Jie Chao ◽  
Huajie Liu ◽  
Yun Zhao ◽  
...  
Keyword(s):  
Self Assembly ◽  
Rolling Circle Amplification ◽  
Dna Origami ◽  
Rolling Circle

Ferromagnetic Resonance Biosensor for Homogeneous and Volumetric Detection of DNA

2017 ◽  
Author(s):  
Bo Tian ◽  
Peter Svedlindh ◽  
Mattias Strömberg ◽  
Erik Wetterskog
Keyword(s):  
Magnetic Nanoparticles ◽  
Ferromagnetic Resonance ◽  
Limit Of Detection ◽  
Point Of Care ◽  
Rolling Circle Amplification ◽  
Resonance Field ◽  
Isothermal Amplification ◽  
Detection Sensitivity ◽  
Serum Samples ◽  
Rolling Circle

In this work, we demonstrate for the first time, a ferromagnetic resonance (FMR) based homogeneous and volumetric biosensor for magnetic label detection. Two different isothermal amplification methods, <i>i.e.</i>, rolling circle amplification (RCA) and loop-mediated isothermal amplification (LAMP) are adopted and combined with a standard electron paramagnetic resonance (EPR) spectrometer for FMR biosensing. For RCA-based FMR biosensor, binding of RCA products of a synthetic Vibrio cholerae target DNA sequence gives rise to the formation of aggregates of magnetic nanoparticles. Immobilization of nanoparticles within the aggregates leads to a decrease of the net anisotropy of the system and a concomitant increase of the resonance field. A limit of detection of 1 pM is obtained with an average coefficient of variation of 0.16%, which is superior to the performance of other reported RCA-based magnetic biosensors. For LAMP-based sensing, a synthetic Zika virus target oligonucleotide is amplified and detected in 20% serum samples. Immobilization of magnetic nanoparticles is induced by their co-precipitation with Mg<sub>2</sub>P<sub>2</sub>O<sub>7</sub> (a by-product of LAMP) and provides a detection sensitivity of 100 aM. The fast measurement, high sensitivity and miniaturization potential of the proposed FMR biosensing technology makes it a promising candidate for designing future point-of-care devices.<br>

scholarly journals Addressing widespread misidentifications of traditional medicinal mushrooms in Sanghuangporus (Basidiomycota) through ITS barcoding and designation of reference sequences

IMA Fungus ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shan Shen ◽  
Shi-Liang Liu ◽  
Ji-Hang Jiang ◽  
Li-Wei Zhou
Keyword(s):  
Species Identification ◽  
Rolling Circle Amplification ◽  
Practical Method ◽  
Morphological Characters ◽  
Its Sequences ◽  
Commercial Development ◽  
Medicinal Mushrooms ◽  
Rolling Circle ◽  
Reference Sequences ◽  
Its Barcoding

Abstract“Sanghuang” refers to a group of important traditionally-used medicinal mushrooms belonging to the genus Sanghuangporus. In practice, species of Sanghuangporus referred to in medicinal studies and industry are now differentiated mainly by a BLAST search of GenBank with the ITS barcoding region as a query. However, inappropriately labeled ITS sequences of “Sanghuang” in GenBank restrict accurate species identification and, to some extent, the utilization of these species as medicinal resources. We examined all available 271 ITS sequences related to “Sanghuang” in GenBank including 31 newly submitted sequences from this study. Of these sequences, more than half were mislabeled so we have now corrected the corresponding species names. The mislabeled sequences mainly came from strains utilized by non-taxonomists. Based on the analyses of ITS sequences submitted by taxonomists as well as morphological characters, we separate the newly described Sanghuangporus subbaumii from S. baumii and treat S. toxicodendri as a later synonym of S. quercicola. Fourteen species of Sanghuangporus are accepted, with intraspecific distances up to 1.30% (except in S. vaninii, S. weirianus and S. zonatus) and interspecific distances above 1.30% (except between S. alpinus and S. lonicerinus, and S. baumii and S. subbaumii). To stabilize the concept of these 14 species of Sanghuangporus, their taxonomic information and reliable ITS reference sequences are provided. Moreover, ten potential diagnostic sequences are provided for Hyperbranched Rolling Circle Amplification to rapidly confirm three common commercial species, viz. S. baumii, S. sanghuang, and S. vaninii. Our results provide a practical method for ITS barcoding-based species identification of Sanghuangporus and will promote medicinal studies and commercial development from taxonomically correct material.

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