Enzymatic incorporation of a third nucleobase pair
Identifieur interne : 002B99 ( Main/Exploration ); précédent : 002B98; suivant : 002C00Enzymatic incorporation of a third nucleobase pair
Auteurs : Zunyi Yang [États-Unis] ; A. Michael Sismour [États-Unis] ; Pinpin Sheng [États-Unis] ; Nyssa L. Puskar [États-Unis] ; Steven A. BennerSource :
- Nucleic Acids Research [ 0305-1048 ] ; 2007.
Abstract
DNA polymerases are identified that copy a non-standard nucleotide pair joined by a hydrogen bonding pattern different from the patterns joining the dA:T and dG:dC pairs. 6-Amino-5-nitro-3-(1′-β-d-2′-deoxyribofuranosyl)-2(1H)-pyridone (dZ) implements the non-standard ‘small’ donor–donor–acceptor (pyDDA) hydrogen bonding pattern. 2-Amino-8-(1′-β-D-2′-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (dP) implements the ‘large’ acceptor–acceptor–donor (puAAD) pattern. These nucleobases were designed to present electron density to the minor groove, density hypothesized to help determine specificity for polymerases. Consistent with this hypothesis, both dZTP and dPTP are accepted by many polymerases from both Families A and B. Further, the dZ:dP pair participates in PCR reactions catalyzed by Taq, Vent (exo−) and Deep Vent (exo−) polymerases, with 94.4%, 97.5% and 97.5%, respectively, retention per round. The dZ:dP pair appears to be lost principally via transition to a dC:dG pair. This is consistent with a mechanistic hypothesis that deprotonated dZ (presenting a pyDAA pattern) complements dG (presenting a puADD pattern), while protonated dC (presenting a pyDDA pattern) complements dP (presenting a puAAD pattern). This hypothesis, grounded in the Watson–Crick model for nucleobase pairing, was confirmed by studies of the pH-dependence of mismatching. The dZ:dP pair and these polymerases, should be useful in dynamic architectures for sequencing, molecular-, systems- and synthetic-biology.
Url:
DOI: 10.1093/nar/gkm395
Affiliations:
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Michael" last="Sismour">A. Michael Sismour</name><affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>Foundation for Applied Molecular Evolution, 1115 NW 4th Street, Gainesville</wicri:cityArea></affiliation></author><author><name sortKey="Sheng, Pinpin" sort="Sheng, Pinpin" uniqKey="Sheng P" first="Pinpin" last="Sheng">Pinpin Sheng</name><affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>Foundation for Applied Molecular Evolution, 1115 NW 4th Street, Gainesville</wicri:cityArea></affiliation></author><author><name sortKey="Puskar, Nyssa L" sort="Puskar, Nyssa L" uniqKey="Puskar N" first="Nyssa L." last="Puskar">Nyssa L. Puskar</name><affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>Foundation for Applied Molecular Evolution, 1115 NW 4th Street, Gainesville</wicri:cityArea></affiliation></author><author><name sortKey="Benner, Steven A" sort="Benner, Steven A" uniqKey="Benner S" first="Steven A." last="Benner">Steven A. Benner</name><affiliation></affiliation><affiliation><wicri:noCountry code="no comma">*To whom correspondence should be addressed. Tel: +352-271-7005; Fax: +352-271-7076; Email: sbenner@ffame.org</wicri:noCountry></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><publisher>Oxford University Press</publisher><date type="published">2007</date><date type="e-published">2007</date><biblScope unit="vol">35</biblScope><biblScope unit="issue">13</biblScope><biblScope unit="page" from="4238">4238</biblScope><biblScope unit="page" to="4249">4249</biblScope></imprint><idno type="ISSN">0305-1048</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0305-1048</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract">DNA polymerases are identified that copy a non-standard nucleotide pair joined by a hydrogen bonding pattern different from the patterns joining the dA:T and dG:dC pairs. 6-Amino-5-nitro-3-(1′-β-d-2′-deoxyribofuranosyl)-2(1H)-pyridone (dZ) implements the non-standard ‘small’ donor–donor–acceptor (pyDDA) hydrogen bonding pattern. 2-Amino-8-(1′-β-D-2′-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (dP) implements the ‘large’ acceptor–acceptor–donor (puAAD) pattern. These nucleobases were designed to present electron density to the minor groove, density hypothesized to help determine specificity for polymerases. Consistent with this hypothesis, both dZTP and dPTP are accepted by many polymerases from both Families A and B. Further, the dZ:dP pair participates in PCR reactions catalyzed by Taq, Vent (exo−) and Deep Vent (exo−) polymerases, with 94.4%, 97.5% and 97.5%, respectively, retention per round. The dZ:dP pair appears to be lost principally via transition to a dC:dG pair. This is consistent with a mechanistic hypothesis that deprotonated dZ (presenting a pyDAA pattern) complements dG (presenting a puADD pattern), while protonated dC (presenting a pyDDA pattern) complements dP (presenting a puAAD pattern). This hypothesis, grounded in the Watson–Crick model for nucleobase pairing, was confirmed by studies of the pH-dependence of mismatching. The dZ:dP pair and these polymerases, should be useful in dynamic architectures for sequencing, molecular-, systems- and synthetic-biology.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Floride</li></region></list><tree><noCountry><name sortKey="Benner, Steven A" sort="Benner, Steven A" uniqKey="Benner S" first="Steven A." last="Benner">Steven A. Benner</name></noCountry><country name="États-Unis"><region name="Floride"><name sortKey="Yang, Zunyi" sort="Yang, Zunyi" uniqKey="Yang Z" first="Zunyi" last="Yang">Zunyi Yang</name></region><name sortKey="Puskar, Nyssa L" sort="Puskar, Nyssa L" uniqKey="Puskar N" first="Nyssa L." last="Puskar">Nyssa L. Puskar</name><name sortKey="Sheng, Pinpin" sort="Sheng, Pinpin" uniqKey="Sheng P" first="Pinpin" last="Sheng">Pinpin Sheng</name><name sortKey="Sismour, A Michael" sort="Sismour, A Michael" uniqKey="Sismour A" first="A. Michael" last="Sismour">A. 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