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Systematic analysis of enzymatic DNA polymerization using oligo-DNA templates and triphosphate analogs involving 2′,4′-bridged nucleosides

In order to systematically analyze the effects of nucleoside modification of sugar moieties in DNA polymerase reactions, we synthesized 16 modified templates containing 2′,4′-bridged nucleotides and three types of 2′,4′-bridged nucleoside-5′-triphospates with different bridging structures. Among the...

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Autores principales: Kuwahara, Masayasu, Obika, Satoshi, Nagashima, Jun-ichi, Ohta, Yuki, Suto, Yoshiyuki, Ozaki, Hiroaki, Sawai, Hiroaki, Imanishi, Takeshi
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2490744/
https://www.ncbi.nlm.nih.gov/pubmed/18583360
http://dx.doi.org/10.1093/nar/gkn404
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author Kuwahara, Masayasu
Obika, Satoshi
Nagashima, Jun-ichi
Ohta, Yuki
Suto, Yoshiyuki
Ozaki, Hiroaki
Sawai, Hiroaki
Imanishi, Takeshi
author_facet Kuwahara, Masayasu
Obika, Satoshi
Nagashima, Jun-ichi
Ohta, Yuki
Suto, Yoshiyuki
Ozaki, Hiroaki
Sawai, Hiroaki
Imanishi, Takeshi
author_sort Kuwahara, Masayasu
collection PubMed
description In order to systematically analyze the effects of nucleoside modification of sugar moieties in DNA polymerase reactions, we synthesized 16 modified templates containing 2′,4′-bridged nucleotides and three types of 2′,4′-bridged nucleoside-5′-triphospates with different bridging structures. Among the five types of thermostable DNA polymerases used, Taq, Phusion HF, Vent(exo-), KOD Dash and KOD(exo-), the KOD Dash and KOD(exo-) DNA polymerases could smoothly read through the modified templates containing 2′-O,4′-C-methylene-linked nucleotides at intervals of a few nucleotides, even at standard enzyme concentrations for 5 min. Although the Vent(exo-) DNA polymerase also read through these modified templates, kinetic study indicates that the KOD(exo-) DNA polymerase was found to be far superior to the Vent(exo-) DNA polymerase in accurate incorporation of nucleotides. When either of the DNA polymerase was used, the presence of 2′,4′-bridged nucleotides on a template strand substantially decreased the reaction rates of nucleotide incorporations. The modified templates containing sequences of seven successive 2′,4′-bridged nucleotides could not be completely transcribed by any of the DNA polymerases used; yields of longer elongated products decreased in the order of steric bulkiness of the modified sugars. Successive incorporation of 2′,4′-bridged nucleotides into extending strands using 2′,4′-bridged nucleoside-5′-triphospates was much more difficult. These data indicate that the sugar modification would have a greater effect on the polymerase reaction when it is adjacent to the elongation terminus than when it is on the template as well, as in base modification.
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spelling pubmed-24907442008-08-01 Systematic analysis of enzymatic DNA polymerization using oligo-DNA templates and triphosphate analogs involving 2′,4′-bridged nucleosides Kuwahara, Masayasu Obika, Satoshi Nagashima, Jun-ichi Ohta, Yuki Suto, Yoshiyuki Ozaki, Hiroaki Sawai, Hiroaki Imanishi, Takeshi Nucleic Acids Res Chemistry and Synthetic Biology In order to systematically analyze the effects of nucleoside modification of sugar moieties in DNA polymerase reactions, we synthesized 16 modified templates containing 2′,4′-bridged nucleotides and three types of 2′,4′-bridged nucleoside-5′-triphospates with different bridging structures. Among the five types of thermostable DNA polymerases used, Taq, Phusion HF, Vent(exo-), KOD Dash and KOD(exo-), the KOD Dash and KOD(exo-) DNA polymerases could smoothly read through the modified templates containing 2′-O,4′-C-methylene-linked nucleotides at intervals of a few nucleotides, even at standard enzyme concentrations for 5 min. Although the Vent(exo-) DNA polymerase also read through these modified templates, kinetic study indicates that the KOD(exo-) DNA polymerase was found to be far superior to the Vent(exo-) DNA polymerase in accurate incorporation of nucleotides. When either of the DNA polymerase was used, the presence of 2′,4′-bridged nucleotides on a template strand substantially decreased the reaction rates of nucleotide incorporations. The modified templates containing sequences of seven successive 2′,4′-bridged nucleotides could not be completely transcribed by any of the DNA polymerases used; yields of longer elongated products decreased in the order of steric bulkiness of the modified sugars. Successive incorporation of 2′,4′-bridged nucleotides into extending strands using 2′,4′-bridged nucleoside-5′-triphospates was much more difficult. These data indicate that the sugar modification would have a greater effect on the polymerase reaction when it is adjacent to the elongation terminus than when it is on the template as well, as in base modification. Oxford University Press 2008-08 2008-06-26 /pmc/articles/PMC2490744/ /pubmed/18583360 http://dx.doi.org/10.1093/nar/gkn404 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Chemistry and Synthetic Biology
Kuwahara, Masayasu
Obika, Satoshi
Nagashima, Jun-ichi
Ohta, Yuki
Suto, Yoshiyuki
Ozaki, Hiroaki
Sawai, Hiroaki
Imanishi, Takeshi
Systematic analysis of enzymatic DNA polymerization using oligo-DNA templates and triphosphate analogs involving 2′,4′-bridged nucleosides
title Systematic analysis of enzymatic DNA polymerization using oligo-DNA templates and triphosphate analogs involving 2′,4′-bridged nucleosides
title_full Systematic analysis of enzymatic DNA polymerization using oligo-DNA templates and triphosphate analogs involving 2′,4′-bridged nucleosides
title_fullStr Systematic analysis of enzymatic DNA polymerization using oligo-DNA templates and triphosphate analogs involving 2′,4′-bridged nucleosides
title_full_unstemmed Systematic analysis of enzymatic DNA polymerization using oligo-DNA templates and triphosphate analogs involving 2′,4′-bridged nucleosides
title_short Systematic analysis of enzymatic DNA polymerization using oligo-DNA templates and triphosphate analogs involving 2′,4′-bridged nucleosides
title_sort systematic analysis of enzymatic dna polymerization using oligo-dna templates and triphosphate analogs involving 2′,4′-bridged nucleosides
topic Chemistry and Synthetic Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2490744/
https://www.ncbi.nlm.nih.gov/pubmed/18583360
http://dx.doi.org/10.1093/nar/gkn404
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