Efficient Genomic DNA Extraction from Low Target Concentration Bacterial Cultures Using SCODA DNA Extraction Technology

Abstract

Methods for the extraction of nucleic acids are straightforward in instances where there is ample nucleic acid mass in the sample and contamination is minimal. However, applications in areas such as metagenomics, life science research, clinical research, and forensics, that are limited by smaller amounts of starting materials or more dilute samples, require sample preparation methods that are more efficient at extracting nucleic acids. Synchronous coefficient of drag alteration (SCODA) is a novel electrophoretic nucleic acid purification technology that has been tested successfully with both highly contaminated and dilute samples and is a promising candidate for new sample preparation challenges. In this article, as an example of SCODA's performance with limited sample material, we outline a genomic DNA (gDNA) extraction protocol from low abundance cultures of Escherichia coli DH10B. This method is equally well suited to high biomass samples.

Methods for biogeochemical studies of sea ice: The state of the art, caveats, and recommendations

“…The available extraction methods fall into three broad categories: phenol chloroform (PC), kit-based, and electrophoretic methods. Although electrophoretic extraction is a promising new technology that may overcome some of the challenges regarding biomass and interfering compounds (e.g., So et al, 2010), to date, only PC and kit-based methods have been applied to sea-ice samples. Cowie (2011) evaluated PC and kit-based methods in Antarctic sea ice and found that PC (using the methods of Moeseneder et al, 2001) is suitable for sea-ice samples.…”

Single-locus enrichment without amplification for sequencing and direct detection of epigenetic modifications

“…Electrophoretic techniques, such as synchronous coefficient of drag alteration (SCODA) that are suitable for processing large amounts of input material are being adapted to the task of target enrichment (So, Pel et al 2010), but these methods are so far limited to short fragments and have the disadvantage of unlinking the sense and antisense strands of duplex DNA, confounding the analysis of hemi-methylation (Murray, Clark et al 2012).…”

Macrofluidic Device for Preparative Concentration Based on Epitachophoresis

“…The presented results show very good DNA extraction yields compared to standard techniques; however, it seems that the concentration of large volumes of salt containing DNA fragments below 20 kbp is challenging. 25 ■ MATERIALS AND METHODS List of Chemicals and Material. Buffer components Lhistidine monohydrochloride monohydrate (99%), L-histidine (99%), N-tris(hydroxymethyl)methyl-3-aminopropanesulfonic acid (TAPS; 99.5%), and tris(hydroxymethyl)aminomethane (TRIS; 99.8%) are purchased from Sigma-Aldrich (U.S.A.).…”

“…Similarly to the present report, the DNA fragments also migrate from the edge toward the center of a multiple electrode agarose filled device. The presented results show very good DNA extraction yields compared to standard techniques; however, it seems that the concentration of large volumes of salt containing DNA fragments below 20 kbp is challenging …”