Normalization of genomic DNA using duplex-specific nuclease

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...
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Autor*in:	Irina Shagina [verfasserIn] Ekaterina Bogdanova [verfasserIn] Ilgar Z. Mamedov [verfasserIn] Yury Lebedev [verfasserIn] Sergey Lukyanov [verfasserIn] Dmitry Shagin [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2010

Schlagwörter:	genomic DNA DSN normalization duplex-specific nuclease

Übergeordnetes Werk:	In: BioTechniques - Future Science Ltd, 2019, 48(2010), 6, Seite 455-459
Übergeordnetes Werk:	volume:48 ; year:2010 ; number:6 ; pages:455-459

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc Journal toc

DOI / URN:	10.2144/000113422

Katalog-ID:	DOAJ016188519

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520			\|a 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 repeats and coding regions at base-line levels. Thus, DSN normalization applied to C0t analysis can be used to eliminate evolutionarily young repetitive elements from genomic DNA before sequencing, and should prove invaluable in studies of large eukaryotic genomes, such as those of higher plants.
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spelling	10.2144/000113422 doi (DE-627)DOAJ016188519 (DE-599)DOAJ4925d55ba9154d45bb2876357e38f26a DE-627 ger DE-627 rakwb eng QH301-705.5 Irina Shagina verfasserin aut Normalization of genomic DNA using duplex-specific nuclease 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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 repeats and coding regions at base-line levels. Thus, DSN normalization applied to C0t analysis can be used to eliminate evolutionarily young repetitive elements from genomic DNA before sequencing, and should prove invaluable in studies of large eukaryotic genomes, such as those of higher plants. genomic DNA DSN normalization duplex-specific nuclease Biology (General) Ekaterina Bogdanova verfasserin aut Ilgar Z. Mamedov verfasserin aut Yury Lebedev verfasserin aut Sergey Lukyanov verfasserin aut Dmitry Shagin verfasserin aut In BioTechniques Future Science Ltd, 2019 48(2010), 6, Seite 455-459 (DE-627)306320746 (DE-600)1496354-1 19409818 nnns volume:48 year:2010 number:6 pages:455-459 https://doi.org/10.2144/000113422 kostenfrei https://doaj.org/article/4925d55ba9154d45bb2876357e38f26a kostenfrei https://www.future-science.com/doi/10.2144/000113422 kostenfrei https://doaj.org/toc/0736-6205 Journal toc kostenfrei https://doaj.org/toc/1940-9818 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 48 2010 6 455-459
allfields_unstemmed	10.2144/000113422 doi (DE-627)DOAJ016188519 (DE-599)DOAJ4925d55ba9154d45bb2876357e38f26a DE-627 ger DE-627 rakwb eng QH301-705.5 Irina Shagina verfasserin aut Normalization of genomic DNA using duplex-specific nuclease 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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 repeats and coding regions at base-line levels. Thus, DSN normalization applied to C0t analysis can be used to eliminate evolutionarily young repetitive elements from genomic DNA before sequencing, and should prove invaluable in studies of large eukaryotic genomes, such as those of higher plants. genomic DNA DSN normalization duplex-specific nuclease Biology (General) Ekaterina Bogdanova verfasserin aut Ilgar Z. Mamedov verfasserin aut Yury Lebedev verfasserin aut Sergey Lukyanov verfasserin aut Dmitry Shagin verfasserin aut In BioTechniques Future Science Ltd, 2019 48(2010), 6, Seite 455-459 (DE-627)306320746 (DE-600)1496354-1 19409818 nnns volume:48 year:2010 number:6 pages:455-459 https://doi.org/10.2144/000113422 kostenfrei https://doaj.org/article/4925d55ba9154d45bb2876357e38f26a kostenfrei https://www.future-science.com/doi/10.2144/000113422 kostenfrei https://doaj.org/toc/0736-6205 Journal toc kostenfrei https://doaj.org/toc/1940-9818 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 48 2010 6 455-459
allfieldsGer	10.2144/000113422 doi (DE-627)DOAJ016188519 (DE-599)DOAJ4925d55ba9154d45bb2876357e38f26a DE-627 ger DE-627 rakwb eng QH301-705.5 Irina Shagina verfasserin aut Normalization of genomic DNA using duplex-specific nuclease 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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 repeats and coding regions at base-line levels. Thus, DSN normalization applied to C0t analysis can be used to eliminate evolutionarily young repetitive elements from genomic DNA before sequencing, and should prove invaluable in studies of large eukaryotic genomes, such as those of higher plants. genomic DNA DSN normalization duplex-specific nuclease Biology (General) Ekaterina Bogdanova verfasserin aut Ilgar Z. Mamedov verfasserin aut Yury Lebedev verfasserin aut Sergey Lukyanov verfasserin aut Dmitry Shagin verfasserin aut In BioTechniques Future Science Ltd, 2019 48(2010), 6, Seite 455-459 (DE-627)306320746 (DE-600)1496354-1 19409818 nnns volume:48 year:2010 number:6 pages:455-459 https://doi.org/10.2144/000113422 kostenfrei https://doaj.org/article/4925d55ba9154d45bb2876357e38f26a kostenfrei https://www.future-science.com/doi/10.2144/000113422 kostenfrei https://doaj.org/toc/0736-6205 Journal toc kostenfrei https://doaj.org/toc/1940-9818 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 48 2010 6 455-459
allfieldsSound	10.2144/000113422 doi (DE-627)DOAJ016188519 (DE-599)DOAJ4925d55ba9154d45bb2876357e38f26a DE-627 ger DE-627 rakwb eng QH301-705.5 Irina Shagina verfasserin aut Normalization of genomic DNA using duplex-specific nuclease 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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 repeats and coding regions at base-line levels. Thus, DSN normalization applied to C0t analysis can be used to eliminate evolutionarily young repetitive elements from genomic DNA before sequencing, and should prove invaluable in studies of large eukaryotic genomes, such as those of higher plants. genomic DNA DSN normalization duplex-specific nuclease Biology (General) Ekaterina Bogdanova verfasserin aut Ilgar Z. Mamedov verfasserin aut Yury Lebedev verfasserin aut Sergey Lukyanov verfasserin aut Dmitry Shagin verfasserin aut In BioTechniques Future Science Ltd, 2019 48(2010), 6, Seite 455-459 (DE-627)306320746 (DE-600)1496354-1 19409818 nnns volume:48 year:2010 number:6 pages:455-459 https://doi.org/10.2144/000113422 kostenfrei https://doaj.org/article/4925d55ba9154d45bb2876357e38f26a kostenfrei https://www.future-science.com/doi/10.2144/000113422 kostenfrei https://doaj.org/toc/0736-6205 Journal toc kostenfrei https://doaj.org/toc/1940-9818 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 48 2010 6 455-459
language	English
source	In BioTechniques 48(2010), 6, Seite 455-459 volume:48 year:2010 number:6 pages:455-459
sourceStr	In BioTechniques 48(2010), 6, Seite 455-459 volume:48 year:2010 number:6 pages:455-459
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topic_facet	genomic DNA DSN normalization duplex-specific nuclease Biology (General)
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authorswithroles_txt_mv	Irina Shagina @@aut@@ Ekaterina Bogdanova @@aut@@ Ilgar Z. Mamedov @@aut@@ Yury Lebedev @@aut@@ Sergey Lukyanov @@aut@@ Dmitry Shagin @@aut@@
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callnumber-first	Q - Science
author	Irina Shagina
spellingShingle	Irina Shagina misc QH301-705.5 misc genomic DNA misc DSN normalization misc duplex-specific nuclease misc Biology (General) Normalization of genomic DNA using duplex-specific nuclease
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topic_title	QH301-705.5 Normalization of genomic DNA using duplex-specific nuclease genomic DNA DSN normalization duplex-specific nuclease
topic	misc QH301-705.5 misc genomic DNA misc DSN normalization misc duplex-specific nuclease misc Biology (General)
topic_unstemmed	misc QH301-705.5 misc genomic DNA misc DSN normalization misc duplex-specific nuclease misc Biology (General)
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title	Normalization of genomic DNA using duplex-specific nuclease
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author_browse	Irina Shagina Ekaterina Bogdanova Ilgar Z. Mamedov Yury Lebedev Sergey Lukyanov Dmitry Shagin
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title_sort	normalization of genomic dna using duplex-specific nuclease
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title_auth	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 repeats and coding regions at base-line levels. Thus, DSN normalization applied to C0t analysis can be used to eliminate evolutionarily young repetitive elements from genomic DNA before sequencing, and should prove invaluable in studies of large eukaryotic genomes, such as those of higher plants.
abstractGer	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 repeats and coding regions at base-line levels. Thus, DSN normalization applied to C0t analysis can be used to eliminate evolutionarily young repetitive elements from genomic DNA before sequencing, and should prove invaluable in studies of large eukaryotic genomes, such as those of higher plants.
abstract_unstemmed	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 repeats and coding regions at base-line levels. Thus, DSN normalization applied to C0t analysis can be used to eliminate evolutionarily young repetitive elements from genomic DNA before sequencing, and should prove invaluable in studies of large eukaryotic genomes, such as those of higher plants.
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title_short	Normalization of genomic DNA using duplex-specific nuclease
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Normalization of genomic DNA using duplex-specific nuclease

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