A method for DNA sequencing by hybridization with oligonucleotide matrix.
Identifieur interne : 000540 ( Ncbi/Curation ); précédent : 000539; suivant : 000541A method for DNA sequencing by hybridization with oligonucleotide matrix.
Auteurs : K R Khrapko [Russie] ; Lysov YuP ; A A Khorlin ; I B Ivanov ; G M Yershov ; S K Vasilenko ; V L Florentiev ; A D MirzabekovSource :
- DNA sequence : the journal of DNA sequencing and mapping [ 1042-5179 ] ; 1991.
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Abstract
A new technique of DNA sequencing by hybridization with oligonucleotide matrix (SHOM) which could also be applied for DNA mapping and fingerprinting, mutant diagnostics, etc., has been tested in model experiments. A dot matrix was prepared which contained 9 overlapping octanucleotides (8-mers) complementary to a common 17-mer. Each of the 8-mers was immobilized as individual dot in thin layer of polyacrylamide gel fixed on a glass plate. The matrix was hybridized with the 32P-labeled 17-mer and three other 17-mers differing from the first one by a single base change. The hybridization enabled us to distinguish perfect duplexes from those containing mismatches in 32 out of 35 cases. These results are discussed with respect to the applicability of the approach for sequencing. It was shown that hybridization of DNA with an immobilized 8-mer in the presence of a labeled 5-mer led to the formation of a stable duplex with the 5-mer only if the 5- and the 8-mers were in continuous stacking making a perfect nicked duplex 13 (5+8) base pairs long. These experiments and computer simulations suggest that continuous stacking hybridization may increase the efficiency of sequencing so that random or natural coding DNA fragments about 1000 bases long could be sequenced in more than 97% of cases. Miniaturized matrices or sequencing chips were designed, where oligonucleotides were immobilized within 100 x 100 micron dots disposed at 100 micron intervals. Hybridization of fluorescently labeled DNA fragments with microchips may simplify sequencing and ensure sensitivity of at least 10 attomoles per dot. The perspectives and limitations of SHOM are discussed.
DOI: 10.3109/10425179109020793
PubMed: 1768861
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Engelhardt Institute of Molecular Biology, Academy of Sciences of the USSR</wicri:orgArea></affiliation></author><author><name sortKey="Lysov Yup" sort="Lysov Yup" uniqKey="Lysov Yup" last="Lysov Yup">Lysov YuP</name></author><author><name sortKey="Khorlin, A A" sort="Khorlin, A A" uniqKey="Khorlin A" first="A A" last="Khorlin">A A Khorlin</name></author><author><name sortKey="Ivanov, I B" sort="Ivanov, I B" uniqKey="Ivanov I" first="I B" last="Ivanov">I B Ivanov</name></author><author><name sortKey="Yershov, G M" sort="Yershov, G M" uniqKey="Yershov G" first="G M" last="Yershov">G M Yershov</name></author><author><name sortKey="Vasilenko, S K" sort="Vasilenko, S K" uniqKey="Vasilenko S" first="S K" last="Vasilenko">S K Vasilenko</name></author><author><name sortKey="Florentiev, V L" sort="Florentiev, V L" uniqKey="Florentiev V" first="V L" last="Florentiev">V L Florentiev</name></author><author><name sortKey="Mirzabekov, A D" sort="Mirzabekov, A D" uniqKey="Mirzabekov A" first="A D" last="Mirzabekov">A D Mirzabekov</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="1991">1991</date><idno type="RBID">pubmed:1768861</idno><idno type="pmid">1768861</idno><idno type="doi">10.3109/10425179109020793</idno><idno type="wicri:Area/PubMed/Corpus">002A09</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002A09</idno><idno type="wicri:Area/PubMed/Curation">002A09</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002A09</idno><idno type="wicri:Area/PubMed/Checkpoint">002853</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002853</idno><idno type="wicri:Area/Ncbi/Merge">000540</idno><idno type="wicri:Area/Ncbi/Curation">000540</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">A method for DNA sequencing by hybridization with oligonucleotide matrix.</title><author><name sortKey="Khrapko, K R" sort="Khrapko, K R" uniqKey="Khrapko K" first="K R" last="Khrapko">K R Khrapko</name><affiliation wicri:level="3"><nlm:affiliation>V.A. Engelhardt Institute of Molecular Biology, Academy of Sciences of the USSR, Moscow.</nlm:affiliation><country>Russie</country><placeName><settlement type="city">Moscou</settlement><region>District fédéral central</region></placeName><wicri:orgArea>V.A. Engelhardt Institute of Molecular Biology, Academy of Sciences of the USSR</wicri:orgArea></affiliation></author><author><name sortKey="Lysov Yup" sort="Lysov Yup" uniqKey="Lysov Yup" last="Lysov Yup">Lysov YuP</name></author><author><name sortKey="Khorlin, A A" sort="Khorlin, A A" uniqKey="Khorlin A" first="A A" last="Khorlin">A A Khorlin</name></author><author><name sortKey="Ivanov, I B" sort="Ivanov, I B" uniqKey="Ivanov I" first="I B" last="Ivanov">I B Ivanov</name></author><author><name sortKey="Yershov, G M" sort="Yershov, G M" uniqKey="Yershov G" first="G M" last="Yershov">G M Yershov</name></author><author><name sortKey="Vasilenko, S K" sort="Vasilenko, S K" uniqKey="Vasilenko S" first="S K" last="Vasilenko">S K Vasilenko</name></author><author><name sortKey="Florentiev, V L" sort="Florentiev, V L" uniqKey="Florentiev V" first="V L" last="Florentiev">V L Florentiev</name></author><author><name sortKey="Mirzabekov, A D" sort="Mirzabekov, A D" uniqKey="Mirzabekov A" first="A D" last="Mirzabekov">A D Mirzabekov</name></author></analytic><series><title level="j">DNA sequence : the journal of DNA sequencing and mapping</title><idno type="ISSN">1042-5179</idno><imprint><date when="1991" type="published">1991</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>DNA</term><term>Fluorescence</term><term>Genetic Techniques</term><term>Molecular Sequence Data</term><term>Nucleic Acid Hybridization</term><term>Oligonucleotides</term><term>Temperature</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN</term><term>Données de séquences moléculaires</term><term>Fluorescence</term><term>Hybridation d'acides nucléiques</term><term>Oligonucléotides</term><term>Séquence nucléotidique</term><term>Techniques génétiques</term><term>Température</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>DNA</term><term>Oligonucleotides</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Fluorescence</term><term>Genetic Techniques</term><term>Molecular Sequence Data</term><term>Nucleic Acid Hybridization</term><term>Temperature</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>Données de séquences moléculaires</term><term>Fluorescence</term><term>Hybridation d'acides nucléiques</term><term>Oligonucléotides</term><term>Séquence nucléotidique</term><term>Techniques génétiques</term><term>Température</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">A new technique of DNA sequencing by hybridization with oligonucleotide matrix (SHOM) which could also be applied for DNA mapping and fingerprinting, mutant diagnostics, etc., has been tested in model experiments. A dot matrix was prepared which contained 9 overlapping octanucleotides (8-mers) complementary to a common 17-mer. Each of the 8-mers was immobilized as individual dot in thin layer of polyacrylamide gel fixed on a glass plate. The matrix was hybridized with the 32P-labeled 17-mer and three other 17-mers differing from the first one by a single base change. The hybridization enabled us to distinguish perfect duplexes from those containing mismatches in 32 out of 35 cases. These results are discussed with respect to the applicability of the approach for sequencing. It was shown that hybridization of DNA with an immobilized 8-mer in the presence of a labeled 5-mer led to the formation of a stable duplex with the 5-mer only if the 5- and the 8-mers were in continuous stacking making a perfect nicked duplex 13 (5+8) base pairs long. These experiments and computer simulations suggest that continuous stacking hybridization may increase the efficiency of sequencing so that random or natural coding DNA fragments about 1000 bases long could be sequenced in more than 97% of cases. Miniaturized matrices or sequencing chips were designed, where oligonucleotides were immobilized within 100 x 100 micron dots disposed at 100 micron intervals. Hybridization of fluorescently labeled DNA fragments with microchips may simplify sequencing and ensure sensitivity of at least 10 attomoles per dot. The perspectives and limitations of SHOM are discussed.</div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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