2010
DOI: 10.2144/000113422
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Normalization of Genomic DNA Using Duplex-Specific Nuclease

Abstract: An application of duplex-specific nuclease (DSN) normalization technology to whole-genome shotgun sequencing of genomes with a large proportion of repetitive DNA is described. The method uses a thermostable DSN from the Kamchatka crab that specifically hydrolyzes dsDNA. In model experiments on human genomic DNA, we demonstrated that DSN normalization of double-stranded DNA formed during C0t analysis is effective against abundant repetitive sequences with high sequence identity, while retaining highly divergent… Show more

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Cited by 46 publications
(40 citation statements)
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“…Additional RNA-Seq data sets were generated from these RNA samples after treatment with the DSN (Duplex-Specific Nuclease) method to deplete rRNA sequences [38]. As expected, most of the DSN-treated samples include a higher fraction of reads derived from non-rRNA sequences (Table S1) and show the strongest correlation with the corresponding RNA-Seq data sets obtained from Total RNA ( e.g ., NSM-DSN vs NSM total RNA, Fig.…”
Section: Resultsmentioning
confidence: 71%
“…Additional RNA-Seq data sets were generated from these RNA samples after treatment with the DSN (Duplex-Specific Nuclease) method to deplete rRNA sequences [38]. As expected, most of the DSN-treated samples include a higher fraction of reads derived from non-rRNA sequences (Table S1) and show the strongest correlation with the corresponding RNA-Seq data sets obtained from Total RNA ( e.g ., NSM-DSN vs NSM total RNA, Fig.…”
Section: Resultsmentioning
confidence: 71%
“…DSN, isolated from the hepatopancreas of the Kamchatka crab (Paralithodes camtschaticus), cleaves double-stranded DNA and RNA-DNA hybrid duplexes, with increased activity on perfectly matched duplexes (Shagin et al 2002). DSN has been used in the normalization of cDNA libraries prior to next generation sequencing (Shagina et al 2010) and the depletion of rRNA from RNA-seq libraries (Christodoulou et al 2011;Yi et al 2011;Matvienko et al 2013;Miller et al 2013). These experiments exploited the knowledge that the rate of DNA hybridization is proportional to the product of the concentration of the two separate DNA strands.…”
Section: Introductionmentioning
confidence: 99%
“…Email: endeldw @ uc.edu DNA has also been applied for many techniques using short RNA sequences [16,[18][19][20][21][22][23][24][25][26][27][28][29], but applications for long RNA targets have remained elusive.…”
Section: * Corresponding Authormentioning
confidence: 99%