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

scholarly journals High-throughput, cost-effective verification of structural DNA assembly

2013 ◽  
Vol 42 (4) ◽  
pp. e22-e22 ◽  
Author(s):  
Yandi Dharmadi ◽  
Kedar Patel ◽  
Elaine Shapland ◽  
Daniel Hollis ◽  
Todd Slaby ◽  
...  
Keyword(s):  
High Throughput ◽  
Low Cost ◽  
Rolling Circle Amplification ◽  
Cost Effective ◽  
Building Blocks ◽  
Pathway Engineering ◽  
Dna Assembly ◽  
Rolling Circle ◽  
Enzyme Screening ◽  
First Time

Abstract DNA ‘assembly’ from ‘building blocks’ remains a cornerstone in synthetic biology, whether it be for gene synthesis (∼1 kb), pathway engineering (∼10 kb) or synthetic genomes (>100 kb). Despite numerous advances in the techniques used for DNA assembly, verification of the assembly is still a necessity, which becomes cost-prohibitive and a logistical challenge with increasing scale. Here we describe for the first time a comprehensive, high-throughput solution for structural DNA assembly verification by restriction digest using exhaustive in silico enzyme screening, rolling circle amplification of plasmid DNA, capillary electrophoresis and automated digest pattern recognition. This low-cost and robust methodology has been successfully used to screen over 31 000 clones of DNA constructs at <$1 per sample.

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

scholarly journals High-throughput genotyping of single nucleotide polymorphisms with rolling circle amplification

BMC Genomics ◽  
2001 ◽  
Vol 2 (1) ◽  
Author(s):  
A Fawad Faruqi ◽  
Seiyu Hosono ◽  
Mark D Driscoll ◽  
Frank B Dean ◽  
Osama Alsmadi ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
High Throughput ◽  
Rolling Circle Amplification ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Rolling Circle

scholarly journals ENDO-Pore: High-throughput linked-end mapping of single DNA cleavage events using nanopore sequencing

2021 ◽  
Author(s):  
Oscar E Torres Montaguth ◽  
Stephen J Cross ◽  
Kincaid W.A. Ingram ◽  
Laura Lee ◽  
Fiona M Diffin ◽  
...  
Keyword(s):  
High Throughput ◽  
Single Molecule ◽  
Dna Cleavage ◽  
Cleavage Site ◽  
Rolling Circle Amplification ◽  
Time Resolved ◽  
Rolling Circle ◽  
Precise Position ◽  
And Function

Mapping the precise position of DNA cleavage events plays a key role in determining the mechanism and function of endonucleases. ENDO-Pore is a high-throughput nanopore-based method that allows the time resolved mapping single molecule DNA cleavage events in vitro. Following linearisation of a circular DNA substrate by the endonuclease, a resistance cassette is ligated recording the position of the cleavage event. A library of single cleavage events is constructed and subjected to rolling circle amplification to generate concatemers. These are sequenced and used to produce accurate consensus sequences. To identify the cleavage site(s), we developed CSI (Cleavage Site Investigator). CSI recognizes the ends of the cassette ligated into the cleaved substrate and triangulates the position of the dsDNA break. We firstly benchmarked ENDO-Pore using Type II restriction endonucleases. Secondly, we analysed the effect of crRNA length on the cleavage pattern of CRISPR Cas12a. Finally, we mapped the time-resolved DNA cleavage by the Type ISP restriction endonuclease LlaGI that introduces random double-strand breaks into its DNA substrates.

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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