Unrestricted hybridization of oligonucleotides to structure-free DNA.
Identifieur interne : 002C83 ( Main/Exploration ); précédent : 002C82; suivant : 002C84Unrestricted hybridization of oligonucleotides to structure-free DNA.
Auteurs : Howard B. Gamper [États-Unis] ; Khalil Arar ; Alan Gewirtz ; Ya-Ming HouSource :
- Biochemistry [ 0006-2960 ] ; 2006.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA, DNA Probes, Nucleotides, Oligodeoxyribonucleotides.
- Base Sequence, DNA Replication, Molecular Sequence Data, Nucleic Acid Conformation, Nucleic Acid Hybridization.
Abstract
The existence of secondary structure in long single-stranded DNA and RNA is a serious obstacle to the practical use of short oligonucleotide probes (<20-mers). Here, we show that replication of a highly structured DNA in the presence of a unique set of dNTP analogues leads to synthesis of daughter DNA with a significantly reduced level of secondary structure. This replicated DNA, composed of 2-aminoadenine, 2-thiothymine, 7-deazaguanine, and cytosine bases, was readily accessible to tiled 8-mer LNA and 15-mer DNA probes, whereas an unmodified version of the same DNA was inaccessible. Importantly, while the base analogues enhanced probe-target stability, they did not significantly reduce the specificity of base pairing. The availability of structure-free DNA targets should facilitate the use of short oligonucleotide probes and promote development of generic oligonucleotide microarrays.
DOI: 10.1021/bi0600392
PubMed: 16734433
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 002252
- to stream PubMed, to step Curation: 002252
- to stream PubMed, to step Checkpoint: 002084
- to stream Ncbi, to step Merge: 000437
- to stream Ncbi, to step Curation: 000437
- to stream Ncbi, to step Checkpoint: 000437
- to stream Main, to step Merge: 002D09
- to stream Main, to step Curation: 002C83
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Unrestricted hybridization of oligonucleotides to structure-free DNA.</title><author><name sortKey="Gamper, Howard B" sort="Gamper, Howard B" uniqKey="Gamper H" first="Howard B" last="Gamper">Howard B. Gamper</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA. howard.gamper@jefferson.edu</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107</wicri:regionArea><wicri:noRegion>Pennsylvania 19107</wicri:noRegion></affiliation></author><author><name sortKey="Arar, Khalil" sort="Arar, Khalil" uniqKey="Arar K" first="Khalil" last="Arar">Khalil Arar</name></author><author><name sortKey="Gewirtz, Alan" sort="Gewirtz, Alan" uniqKey="Gewirtz A" first="Alan" last="Gewirtz">Alan Gewirtz</name></author><author><name sortKey="Hou, Ya Ming" sort="Hou, Ya Ming" uniqKey="Hou Y" first="Ya-Ming" last="Hou">Ya-Ming Hou</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2006">2006</date><idno type="RBID">pubmed:16734433</idno><idno type="pmid">16734433</idno><idno type="doi">10.1021/bi0600392</idno><idno type="wicri:Area/PubMed/Corpus">002252</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002252</idno><idno type="wicri:Area/PubMed/Curation">002252</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002252</idno><idno type="wicri:Area/PubMed/Checkpoint">002084</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002084</idno><idno type="wicri:Area/Ncbi/Merge">000437</idno><idno type="wicri:Area/Ncbi/Curation">000437</idno><idno type="wicri:Area/Ncbi/Checkpoint">000437</idno><idno type="wicri:doubleKey">0006-2960:2006:Gamper H:unrestricted:hybridization:of</idno><idno type="wicri:Area/Main/Merge">002D09</idno><idno type="wicri:Area/Main/Curation">002C83</idno><idno type="wicri:Area/Main/Exploration">002C83</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Unrestricted hybridization of oligonucleotides to structure-free DNA.</title><author><name sortKey="Gamper, Howard B" sort="Gamper, Howard B" uniqKey="Gamper H" first="Howard B" last="Gamper">Howard B. Gamper</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA. howard.gamper@jefferson.edu</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107</wicri:regionArea><wicri:noRegion>Pennsylvania 19107</wicri:noRegion></affiliation></author><author><name sortKey="Arar, Khalil" sort="Arar, Khalil" uniqKey="Arar K" first="Khalil" last="Arar">Khalil Arar</name></author><author><name sortKey="Gewirtz, Alan" sort="Gewirtz, Alan" uniqKey="Gewirtz A" first="Alan" last="Gewirtz">Alan Gewirtz</name></author><author><name sortKey="Hou, Ya Ming" sort="Hou, Ya Ming" uniqKey="Hou Y" first="Ya-Ming" last="Hou">Ya-Ming Hou</name></author></analytic><series><title level="j">Biochemistry</title><idno type="ISSN">0006-2960</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>DNA (chemistry)</term><term>DNA Probes (chemistry)</term><term>DNA Replication</term><term>Molecular Sequence Data</term><term>Nucleic Acid Conformation</term><term>Nucleic Acid Hybridization</term><term>Nucleotides (chemistry)</term><term>Oligodeoxyribonucleotides (chemistry)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term><term>Conformation d'acide nucléique</term><term>Données de séquences moléculaires</term><term>Hybridation d'acides nucléiques</term><term>Nucléotides ()</term><term>Oligodésoxyribonucléotides ()</term><term>Réplication de l'ADN</term><term>Sondes d'ADN ()</term><term>Séquence nucléotidique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term><term>DNA Probes</term><term>Nucleotides</term><term>Oligodeoxyribonucleotides</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>DNA Replication</term><term>Molecular Sequence Data</term><term>Nucleic Acid Conformation</term><term>Nucleic Acid Hybridization</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>Conformation d'acide nucléique</term><term>Données de séquences moléculaires</term><term>Hybridation d'acides nucléiques</term><term>Nucléotides</term><term>Oligodésoxyribonucléotides</term><term>Réplication de l'ADN</term><term>Sondes d'ADN</term><term>Séquence nucléotidique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The existence of secondary structure in long single-stranded DNA and RNA is a serious obstacle to the practical use of short oligonucleotide probes (<20-mers). Here, we show that replication of a highly structured DNA in the presence of a unique set of dNTP analogues leads to synthesis of daughter DNA with a significantly reduced level of secondary structure. This replicated DNA, composed of 2-aminoadenine, 2-thiothymine, 7-deazaguanine, and cytosine bases, was readily accessible to tiled 8-mer LNA and 15-mer DNA probes, whereas an unmodified version of the same DNA was inaccessible. Importantly, while the base analogues enhanced probe-target stability, they did not significantly reduce the specificity of base pairing. The availability of structure-free DNA targets should facilitate the use of short oligonucleotide probes and promote development of generic oligonucleotide microarrays.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country></list><tree><noCountry><name sortKey="Arar, Khalil" sort="Arar, Khalil" uniqKey="Arar K" first="Khalil" last="Arar">Khalil Arar</name><name sortKey="Gewirtz, Alan" sort="Gewirtz, Alan" uniqKey="Gewirtz A" first="Alan" last="Gewirtz">Alan Gewirtz</name><name sortKey="Hou, Ya Ming" sort="Hou, Ya Ming" uniqKey="Hou Y" first="Ya-Ming" last="Hou">Ya-Ming Hou</name></noCountry><country name="États-Unis"><noRegion><name sortKey="Gamper, Howard B" sort="Gamper, Howard B" uniqKey="Gamper H" first="Howard B" last="Gamper">Howard B. Gamper</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002C83 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 002C83 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:16734433
|texte= Unrestricted hybridization of oligonucleotides to structure-free DNA.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:16734433" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |