scholarly journals Enzyme-free synthesis of cyclic single-stranded DNA constructs containing a single triazole, amide or phosphoramidate backbone linkage and their use as templates for rolling circle amplification and nanoflower formation

2018 ◽  
Vol 9 (42) ◽  
pp. 8110-8120 ◽  
Author(s):  
Jinfeng Chen ◽  
Ysobel R. Baker ◽  
Asha Brown ◽  
Afaf H. El-Sagheer ◽  
Tom Brown
Keyword(s):  
Rolling Circle Amplification ◽  
Single Stranded Dna ◽  
Rolling Circle

Three different chemical cyclisation reactions yield biocompatible cyclic oligonucleotide templates for use in RCA and DNA nanoflower formation.

scholarly journals An improved experimental pipeline for preparing circular ssDNA viruses for next-generation sequencing

2020 ◽  
Author(s):  
Catherine D. Aimone ◽  
J. Steen Hoyer ◽  
Anna E. Dye ◽  
David O. Deppong ◽  
Siobain Duffy ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Rolling Circle Amplification ◽  
Next Generation ◽  
Viral Dna ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Short Read ◽  
Rolling Circle ◽  
Optimized Protocol ◽  
Generation Sequencing

AbstractWe present an optimized protocol for enhanced amplification and enrichment of viral DNA for Next Generation Sequencing of begomovirus genomes. The rapid ability of these viruses to evolve threatens many crops and underscores the importance of using next generation sequencing efficiently to detect and understand the diversity of these viruses. We combined enhanced rolling circle amplification (RCA) with EquiPhi29 polymerase and size selection to generate a cost-effective, short-read sequencing method. This optimized protocol produced short-read sequencing with at least 50% of the reads mapping to the viral reference genome. We provide other insights into common misconceptions about RCA and lessons we have learned from sequencing single-stranded DNA viruses. Our protocol can be used to examine viral DNA as it moves through the entire pathosystem from host to vector, providing valuable information for viral DNA population studies, and would likely work well with other CRESS DNA viruses.HighlightsProtocol for short-read, high throughput sequencing of single-stranded DNA viruses using random primersComparison of the sequencing of total DNA versus size-selected DNAComparison of phi29 and Equiphi29 DNA polymerases for rolling circle amplification of viral single-stranded DNA genomes

Real-time monitoring of rolling circle amplification using aggregation-induced emission: applications in biological detection

2015 ◽  
Vol 51 (92) ◽  
pp. 16518-16521 ◽  
Author(s):  
Hong-Xin Jiang ◽  
Meng-Yao Zhao ◽  
Chen-Di Niu ◽  
De-Ming Kong
Keyword(s):  
Real Time ◽  
Rolling Circle Amplification ◽  
Real Time Monitoring ◽  
Biological Detection ◽  
Single Stranded Dna ◽  
Rolling Circle ◽  
Aggregation Induced Emission

Real-time monitoring of rolling circle amplification (RCA) was achieved by the super-aggregation of a tetraphenylethene dye QAPTE along single-stranded DNA products and consequent enhanced aggregation-induced emission, it can work for all RCA reactions.

scholarly journals Generation of long, fully modified, and serum-resistant oligonucleotides by rolling circle amplification

2015 ◽  
Vol 13 (38) ◽  
pp. 9820-9824 ◽  
Author(s):  
Marcel Hollenstein
Keyword(s):  
Rolling Circle Amplification ◽  
Single Stranded Dna ◽  
Rolling Circle ◽  
Dna Oligonucleotides ◽  
Amplification Method ◽  
Nucleoside Triphosphates

Nucleoside triphosphates modified at any level of the scaffold were shown to be compatible with the rolling circle amplification method. The combination of modified dNTPs and RCA enables the generation of long, fully modified, single-stranded DNA oligonucleotides.

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>

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