Rolling Circle Amplification For Spatially Directed Synthesis Of A Solid Phase Anchored Single-Stranded DNA Molecule

2006 ◽  
Author(s):  
Edda Reiß ◽  
Ralph Hölzel ◽  
Markus von Nickisch-Rosenegk ◽  
Frank F. Bier
Keyword(s):  
Solid Phase ◽  
Rolling Circle Amplification ◽  
Single Stranded Dna ◽  
Rolling Circle ◽  
Dna Molecule ◽  
Directed Synthesis

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

Identification of Extrachromosomal Circular DNA in Hop via Rolling Circle Amplification

2016 ◽  
Vol 148 (2-3) ◽  
pp. 237-240 ◽  
Author(s):  
Alfredo Diaz-Lara ◽  
David H. Gent ◽  
Robert R. Martin
Keyword(s):  
Electron Microscopy ◽  
Sequence Analysis ◽  
Higher Plants ◽  
Rolling Circle Amplification ◽  
Small Region ◽  
Extrachromosomal Dna ◽  
Circular Dna ◽  
Rolling Circle ◽  
Dna Molecule ◽  
The Family

During a survey for new viruses affecting hop plants, a circular DNA molecule was identified via rolling circle amplification (RCA) and later characterized. A small region of the 5.7-kb long molecule aligned with a microsatellite region in the Humulus lupulus genome, and no coding sequence was identified. Sequence analysis and literature review suggest that the small DNA molecule is an extranuclear DNA element, specifically, an extrachromosomal circular DNA (eccDNA), and its presence was confirmed by electron microscopy. This work is the first report of eccDNAs in the family Cannabaceae. Additionally, this work highlights the advantages of using RCA to study extrachromosomal DNA in higher plants.

Carbon nanotube enhanced label-free detection of microRNAs based on hairpin probe triggered solid-phase rolling-circle amplification

Nanoscale ◽  
2015 ◽  
Vol 7 (3) ◽  
pp. 987-993 ◽  
Author(s):  
Qianqian Tian ◽  
Ying Wang ◽  
Ruijie Deng ◽  
Lei Lin ◽  
Yang Liu ◽  
...  
Keyword(s):  
Carbon Nanotube ◽  
Solid Phase ◽  
Rolling Circle Amplification ◽  
Label Free ◽  
Rolling Circle ◽  
Hairpin Probe ◽  
Label Free Detection

Bead-based padlock rolling circle amplification for single DNA molecule counting

2013 ◽  
Vol 437 (1) ◽  
pp. 43-45 ◽  
Author(s):  
Kae Sato ◽  
Reina Ishii ◽  
Naoki Sasaki ◽  
Kiichi Sato ◽  
Mats Nilsson
Keyword(s):  
Rolling Circle Amplification ◽  
Rolling Circle ◽  
Dna Molecule ◽  
Single Dna Molecule

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 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.

Methylation pattern analysis using high-throughput microarray of solid-phase hyperbranched rolling circle amplification products

2008 ◽  
Vol 29 (3) ◽  
pp. 626-633 ◽  
Author(s):  
Dongrui Zhou ◽  
Renmin Zhang ◽  
Rujing Fang ◽  
Lu Cheng ◽  
Pengfeng Xiao ◽  
...  
Keyword(s):  
High Throughput ◽  
Pattern Analysis ◽  
Solid Phase ◽  
Rolling Circle Amplification ◽  
Methylation Pattern ◽  
Rolling Circle
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