Sequence-based separation of single-stranded DNA using nucleotides in capillary electrophoresis: focus on phosphate.
Identifieur interne : 001D04 ( PubMed/Curation ); précédent : 001D03; suivant : 001D05Sequence-based separation of single-stranded DNA using nucleotides in capillary electrophoresis: focus on phosphate.
Auteurs : Xueru Zhang [États-Unis] ; Linda B. McgownSource :
- Electrophoresis [ 1522-2683 ] ; 2013.
Descripteurs français
- KwdFr :
- ADN simple brin (), ADN simple brin (isolement et purification), Concentration en ions d'hydrogène, Données de séquences moléculaires, Dénaturation d'acide nucléique, Glucides (), Guanosine monophosphate (), Humains, Substances tampon, Séquence nucléotidique, Température, Électrophorèse capillaire ().
- MESH :
English descriptors
- KwdEn :
- Base Sequence, Buffers, Carbohydrates (chemistry), DNA, Single-Stranded (chemistry), DNA, Single-Stranded (isolation & purification), Electrophoresis, Capillary (methods), Guanosine Monophosphate (chemistry), Humans, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Denaturation, Temperature.
- MESH :
- chemical , chemistry : Carbohydrates, DNA, Single-Stranded, Guanosine Monophosphate.
- chemical , isolation & purification : DNA, Single-Stranded.
- chemical : Buffers.
- methods : Electrophoresis, Capillary.
- Base Sequence, Humans, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Denaturation, Temperature.
Abstract
DNA analysis has widespread applicability in biology, medicine, biotechnology, and forensics. DNA separation by length is readily achieved using sieving gels in electrophoresis. Separation by sequence is less simple, generally requiring adequate differences in native or induced conformation or differences in thermal or chemical stability of the strands that are hybridized prior to measurement. We previously demonstrated separation of four single-stranded DNA 76-mers that differ by only a few A-G substitutions based solely on sequence using guanosine-5'-monophosphate (GMP) in the running buffer. We attributed separation to the unique self-assembly of GMP to form higher order structures. Here, we examine an expanded set of 76-mers designed to probe the mechanism of the separation and effects of experimental conditions. We were surprised to find that other ribonucleotides achieved the similar separation to GMP, and that some separation was achieved using sodium phosphate instead of GMP. Potassium phosphate achieved almost as good separations as the ribonucleotides. This suggests that the separation medium provides a physicochemical environment for the DNA that effects strand migration in a sequence-selective manner. Further investigation is needed to determine whether the mechanism involves specific interactions between the phosphates and the DNA strands or is a result of other properties of the separation medium. Phosphate generally has been avoided in DNA separations by capillary gel electrophoresis because its high ionic strength exacerbates Joule heating. Our results suggest that phosphate compounds should be examined for separation of DNA based on sequence.
DOI: 10.1002/elps.201200683
PubMed: 23576075
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: Pour aller vers cette notice dans l'étape Curation :001D04
Links to Exploration step
pubmed:23576075Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Sequence-based separation of single-stranded DNA using nucleotides in capillary electrophoresis: focus on phosphate.</title><author><name sortKey="Zhang, Xueru" sort="Zhang, Xueru" uniqKey="Zhang X" first="Xueru" last="Zhang">Xueru Zhang</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry and Chemical Biology, 321 Cogswell Laboratory, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry and Chemical Biology, 321 Cogswell Laboratory, Rensselaer Polytechnic Institute, Troy, NY 12180</wicri:regionArea></affiliation></author><author><name sortKey="Mcgown, Linda B" sort="Mcgown, Linda B" uniqKey="Mcgown L" first="Linda B" last="Mcgown">Linda B. Mcgown</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2013">2013</date><idno type="RBID">pubmed:23576075</idno><idno type="pmid">23576075</idno><idno type="doi">10.1002/elps.201200683</idno><idno type="wicri:Area/PubMed/Corpus">001D04</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001D04</idno><idno type="wicri:Area/PubMed/Curation">001D04</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001D04</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Sequence-based separation of single-stranded DNA using nucleotides in capillary electrophoresis: focus on phosphate.</title><author><name sortKey="Zhang, Xueru" sort="Zhang, Xueru" uniqKey="Zhang X" first="Xueru" last="Zhang">Xueru Zhang</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry and Chemical Biology, 321 Cogswell Laboratory, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry and Chemical Biology, 321 Cogswell Laboratory, Rensselaer Polytechnic Institute, Troy, NY 12180</wicri:regionArea></affiliation></author><author><name sortKey="Mcgown, Linda B" sort="Mcgown, Linda B" uniqKey="Mcgown L" first="Linda B" last="Mcgown">Linda B. Mcgown</name></author></analytic><series><title level="j">Electrophoresis</title><idno type="eISSN">1522-2683</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>Buffers</term><term>Carbohydrates (chemistry)</term><term>DNA, Single-Stranded (chemistry)</term><term>DNA, Single-Stranded (isolation & purification)</term><term>Electrophoresis, Capillary (methods)</term><term>Guanosine Monophosphate (chemistry)</term><term>Humans</term><term>Hydrogen-Ion Concentration</term><term>Molecular Sequence Data</term><term>Nucleic Acid Denaturation</term><term>Temperature</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN simple brin ()</term><term>ADN simple brin (isolement et purification)</term><term>Concentration en ions d'hydrogène</term><term>Données de séquences moléculaires</term><term>Dénaturation d'acide nucléique</term><term>Glucides ()</term><term>Guanosine monophosphate ()</term><term>Humains</term><term>Substances tampon</term><term>Séquence nucléotidique</term><term>Température</term><term>Électrophorèse capillaire ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Carbohydrates</term><term>DNA, Single-Stranded</term><term>Guanosine Monophosphate</term></keywords><keywords scheme="MESH" type="chemical" qualifier="isolation & purification" xml:lang="en"><term>DNA, Single-Stranded</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Buffers</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>ADN simple brin</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Electrophoresis, Capillary</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Humans</term><term>Hydrogen-Ion Concentration</term><term>Molecular Sequence Data</term><term>Nucleic Acid Denaturation</term><term>Temperature</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN simple brin</term><term>Concentration en ions d'hydrogène</term><term>Données de séquences moléculaires</term><term>Dénaturation d'acide nucléique</term><term>Glucides</term><term>Guanosine monophosphate</term><term>Humains</term><term>Substances tampon</term><term>Séquence nucléotidique</term><term>Température</term><term>Électrophorèse capillaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">DNA analysis has widespread applicability in biology, medicine, biotechnology, and forensics. DNA separation by length is readily achieved using sieving gels in electrophoresis. Separation by sequence is less simple, generally requiring adequate differences in native or induced conformation or differences in thermal or chemical stability of the strands that are hybridized prior to measurement. We previously demonstrated separation of four single-stranded DNA 76-mers that differ by only a few A-G substitutions based solely on sequence using guanosine-5'-monophosphate (GMP) in the running buffer. We attributed separation to the unique self-assembly of GMP to form higher order structures. Here, we examine an expanded set of 76-mers designed to probe the mechanism of the separation and effects of experimental conditions. We were surprised to find that other ribonucleotides achieved the similar separation to GMP, and that some separation was achieved using sodium phosphate instead of GMP. Potassium phosphate achieved almost as good separations as the ribonucleotides. This suggests that the separation medium provides a physicochemical environment for the DNA that effects strand migration in a sequence-selective manner. Further investigation is needed to determine whether the mechanism involves specific interactions between the phosphates and the DNA strands or is a result of other properties of the separation medium. Phosphate generally has been avoided in DNA separations by capillary gel electrophoresis because its high ionic strength exacerbates Joule heating. Our results suggest that phosphate compounds should be examined for separation of DNA based on sequence.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23576075</PMID><DateCompleted><Year>2014</Year><Month>01</Month><Day>22</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1522-2683</ISSN><JournalIssue CitedMedium="Internet"><Volume>34</Volume><Issue>12</Issue><PubDate><Year>2013</Year><Month>Jun</Month></PubDate></JournalIssue><Title>Electrophoresis</Title><ISOAbbreviation>Electrophoresis</ISOAbbreviation></Journal><ArticleTitle>Sequence-based separation of single-stranded DNA using nucleotides in capillary electrophoresis: focus on phosphate.</ArticleTitle><Pagination><MedlinePgn>1778-86</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1002/elps.201200683</ELocationID><Abstract><AbstractText>DNA analysis has widespread applicability in biology, medicine, biotechnology, and forensics. DNA separation by length is readily achieved using sieving gels in electrophoresis. Separation by sequence is less simple, generally requiring adequate differences in native or induced conformation or differences in thermal or chemical stability of the strands that are hybridized prior to measurement. We previously demonstrated separation of four single-stranded DNA 76-mers that differ by only a few A-G substitutions based solely on sequence using guanosine-5'-monophosphate (GMP) in the running buffer. We attributed separation to the unique self-assembly of GMP to form higher order structures. Here, we examine an expanded set of 76-mers designed to probe the mechanism of the separation and effects of experimental conditions. We were surprised to find that other ribonucleotides achieved the similar separation to GMP, and that some separation was achieved using sodium phosphate instead of GMP. Potassium phosphate achieved almost as good separations as the ribonucleotides. This suggests that the separation medium provides a physicochemical environment for the DNA that effects strand migration in a sequence-selective manner. Further investigation is needed to determine whether the mechanism involves specific interactions between the phosphates and the DNA strands or is a result of other properties of the separation medium. Phosphate generally has been avoided in DNA separations by capillary gel electrophoresis because its high ionic strength exacerbates Joule heating. Our results suggest that phosphate compounds should be examined for separation of DNA based on sequence.</AbstractText><CopyrightInformation>© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Xueru</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Department of Chemistry and Chemical Biology, 321 Cogswell Laboratory, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>McGown</LastName><ForeName>Linda B</ForeName><Initials>LB</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R21 GM104693</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>1R21GM104693-01</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Electrophoresis</MedlineTA><NlmUniqueID>8204476</NlmUniqueID><ISSNLinking>0173-0835</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D002021">Buffers</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D002241">Carbohydrates</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004277">DNA, Single-Stranded</NameOfSubstance></Chemical><Chemical><RegistryNumber>85-32-5</RegistryNumber><NameOfSubstance UI="D006157">Guanosine Monophosphate</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002021" MajorTopicYN="N">Buffers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002241" MajorTopicYN="N">Carbohydrates</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004277" MajorTopicYN="N">DNA, Single-Stranded</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000302" MajorTopicYN="Y">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019075" MajorTopicYN="N">Electrophoresis, Capillary</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006157" MajorTopicYN="N">Guanosine Monophosphate</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006863" MajorTopicYN="N">Hydrogen-Ion Concentration</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009691" MajorTopicYN="N">Nucleic Acid Denaturation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013696" MajorTopicYN="N">Temperature</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2012</Year><Month>12</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2013</Year><Month>03</Month><Day>03</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2013</Year><Month>03</Month><Day>07</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2013</Year><Month>4</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2013</Year><Month>4</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>1</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">23576075</ArticleId><ArticleId IdType="doi">10.1002/elps.201200683</ArticleId><ArticleId IdType="pmc">PMC3906628</ArticleId><ArticleId IdType="mid">NIHMS508875</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Biopolymers. 2000 Aug;54(2):137-42</Citation><ArticleIdList><ArticleId IdType="pubmed">10861374</ArticleId></ArticleIdList></Reference><Reference><Citation>Biochemistry. 2011 Oct 25;50(42):9148-57</Citation><ArticleIdList><ArticleId IdType="pubmed">21942650</ArticleId></ArticleIdList></Reference><Reference><Citation>Methods Mol Biol. 2001;162:259-77</Citation><ArticleIdList><ArticleId IdType="pubmed">11217337</ArticleId></ArticleIdList></Reference><Reference><Citation>Eur Phys J E Soft Matter. 2004 Jan;13(1):27-33</Citation><ArticleIdList><ArticleId IdType="pubmed">15024613</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell. 1979 Jan;16(1):191-200</Citation><ArticleIdList><ArticleId IdType="pubmed">369706</ArticleId></ArticleIdList></Reference><Reference><Citation>J Chromatogr. 1988 Dec 23;458:323-33</Citation><ArticleIdList><ArticleId IdType="pubmed">2853173</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 1989 Apr;86(8):2766-70</Citation><ArticleIdList><ArticleId IdType="pubmed">2565038</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biomol Struct Dyn. 1990 Dec;8(3):491-511</Citation><ArticleIdList><ArticleId IdType="pubmed">2100515</ArticleId></ArticleIdList></Reference><Reference><Citation>Int J Legal Med. 1994;106(6):319-23</Citation><ArticleIdList><ArticleId IdType="pubmed">7947340</ArticleId></ArticleIdList></Reference><Reference><Citation>J Chromatogr A. 1995 May 12;700(1-2):137-49</Citation><ArticleIdList><ArticleId IdType="pubmed">7767460</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 1996 Jun 1;24(11):2095-103</Citation><ArticleIdList><ArticleId IdType="pubmed">8668541</ArticleId></ArticleIdList></Reference><Reference><Citation>Electrophoresis. 1996 Sep;17(9):1476-84</Citation><ArticleIdList><ArticleId IdType="pubmed">8905264</ArticleId></ArticleIdList></Reference><Reference><Citation>Antonie Van Leeuwenhoek. 1998 Jan;73(1):127-41</Citation><ArticleIdList><ArticleId IdType="pubmed">9602286</ArticleId></ArticleIdList></Reference><Reference><Citation>Hum Genet. 1999 Jan;104(1):29-35</Citation><ArticleIdList><ArticleId IdType="pubmed">10071189</ArticleId></ArticleIdList></Reference><Reference><Citation>Biochemistry. 1963 Jan-Feb;2:168-75</Citation><ArticleIdList><ArticleId IdType="pubmed">13930149</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 1962 Dec 15;48:2013-8</Citation><ArticleIdList><ArticleId IdType="pubmed">13947099</ArticleId></ArticleIdList></Reference><Reference><Citation>Electrophoresis. 2007 Aug;28(17):3008-16</Citation><ArticleIdList><ArticleId IdType="pubmed">17661319</ArticleId></ArticleIdList></Reference><Reference><Citation>Biochemistry. 2011 Apr 19;50(15):3084-94</Citation><ArticleIdList><ArticleId IdType="pubmed">21410141</ArticleId></ArticleIdList></Reference><Reference><Citation>Electrophoresis. 2011 May;32(10):1209-16</Citation><ArticleIdList><ArticleId IdType="pubmed">21544840</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2000 Sep;10(9):1403-13</Citation><ArticleIdList><ArticleId IdType="pubmed">10984458</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001D04 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Curation/biblio.hfd -nk 001D04 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= PubMed
|étape= Curation
|type= RBID
|clé= pubmed:23576075
|texte= Sequence-based separation of single-stranded DNA using nucleotides in capillary electrophoresis: focus on phosphate.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Curation/RBID.i -Sk "pubmed:23576075" \
| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Curation/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |