ArticleNucleic acids research2005
Exploration of factors driving incorporation of unnatural dNTPS into DNA by Klenow fragment (DNA polymerase I) and DNA polymerase alpha.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 68 citations in OpenAlex.
- Nucleobase-modified nucleosides and nucleotides: Applications in biochemistry, synthetic biology, and drug discovery.Frontiers in chemistry · 2022Review
- Protein Displacement by Herpes Helicase-Primase and the Key Role of UL42 during Helicase-Coupled DNA Synthesis by the Herpes Polymerase.Biochemistry · 2017Article
- Processive Incorporation of Deoxynucleoside Triphosphate Analogs by Single-Molecule DNA Polymerase I (Klenow Fragment) Nanocircuits.Journal of the American Chemical Society · 2015Article
- In vitro selection of DNA-cleaving deoxyribozyme with site-specific thymidine excision activity.Nucleic acids research · 2014Article
- Conformational changes of the phenyl and naphthyl isocyanate-DNA adducts during DNA replication and by minor groove binding molecules.Nucleic acids research · 2013Article
- Expanding the scope of replicable unnatural DNA: stepwise optimization of a predominantly hydrophobic base pair.Journal of the American Chemical Society · 2013Article
- Unnatural base pair systems toward the expansion of the genetic alphabet in the central dogma.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2012Review
- Antimutator variants of DNA polymerases.Critical reviews in biochemistry and molecular biology · 2011Review
- B family DNA polymerases asymmetrically recognize pyrimidines and purines.Biochemistry · 2011Article
- Substitution of Ala for Tyr567 in RB69 DNA polymerase allows dAMP and dGMP to be inserted opposite Guanidinohydantoin .Biochemistry · 2010Article
- Toward a designed genetic system with biochemical function: polymerase synthesis of single and multiple size-expanded DNA base pairs.Organic & biomolecular chemistry · 2010Article
- Non-natural nucleotides as probes for the mechanism and fidelity of DNA polymerases.Biochimica et biophysica acta · 2010Review
- Replication of a universal nucleobase provides unique insight into the role of entropy during DNA polymerization and pyrophosphorolysis.Biochemistry · 2010Article
- Selective inhibition of DNA replicase assembly by a non-natural nucleotide: exploiting the structural diversity of ATP-binding sites.ACS chemical biology · 2010Article
- Nucleotide Analogues as Probes for DNA and RNA Polymerases.Current protocols in chemical biology · 2010Article
- Herpes simplex virus-1 DNA primase: a remarkably inaccurate yet selective polymerase.Biochemistry · 2009Article
- Structure and replication of yDNA: a novel genetic set widened by benzo-homologation.Chembiochem : a European journal of chemical biology · 2009Article
- Major groove derivatization of an unnatural base pair.Chembiochem : a European journal of chemical biology · 2009Article
- Interaction of human DNA polymerase alpha and DNA polymerase I from Bacillus stearothermophilus with hypoxanthine and 8-oxoguanine nucleotides.Biochemistry · 2009Article
- Ambivalent incorporation of the fluorescent cytosine analogues tC and tCo by human DNA polymerase alpha and Klenow fragment.Biochemistry · 2009Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
In order to further understand how DNA polymerases discriminate against incorrect dNTPs, we synthesized two sets of dNTP analogues and tested them as substrates for DNA polymerase alpha (pol alpha) and Klenow fragment (exo-) of DNA polymerase I (Escherichia coli). One set of analogues was designed to test the importance of the electronic nature of the base. The bases consisted of a benzimidazole ring with one or two exocyclic substituent(s) that are either electron-donating (methyl and methoxy) or electron-withdrawing (trifluoromethyl and dinitro). Both pol alpha and Klenow fragment exhibit a remarkable inability to discriminate against these analogues as compared to their ability to discriminate against incorrect natural dNTPs. Neither polymerase shows any distinct electronic or steric preferences for analogue incorporation. The other set of analogues, designed to examine the importance of hydrophobicity in dNTP incorporation, consists of a set of four regioisomers of trifluoromethyl benzimidazole. Whereas pol alpha and Klenow fragment exhibited minimal discrimination against the 5- and 6-regioisomers, they discriminated much more effectively against the 4- and 7-regioisomers. Since all four of these analogues will have similar hydrophobicity and stacking ability, these data indicate that hydrophobicity and stacking ability alone cannot account for the inability of pol alpha and Klenow fragment to discriminate against unnatural bases. After incorporation, however, both sets of analogues were not efficiently elongated. These results suggest that factors other than hydrophobicity, sterics and electronics govern the incorporation of dNTPs into DNA by pol alpha and Klenow fragment.
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