B Family DNA Polymerases Asymmetrically Recognize Pyrimidines and Purines

We utilized a series of pyrimidine analogues modified at O2, N-3, and N4/O4 to determine if two B family DNA polymerases, human DNA polymerase α and herpes simplex virus I DNA polymerase, choose whether to polymerize pyrimidine dNTPs using the same mechanisms they use for purine dNTPs. Removing O2 o...

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Bibliographic Details
Published in:Biochemistry (Easton) 2011-08, Vol.50 (33), p.7243-7250
Main Authors: Lund, Travis J, Cavanaugh, Nisha A, Joubert, Nicolas, Urban, Milan, Patro, Jennifer N, Hocek, Michal, Kuchta, Robert D
Format: Article
Language:English
Subjects:
DNA Polymerase I - chemistry
DNA Polymerase I - metabolism
DNA Replication
DNA-Directed DNA Polymerase - chemistry
DNA-Directed DNA Polymerase - metabolism
Exodeoxyribonucleases - chemistry
Exodeoxyribonucleases - metabolism
Herpes simplex virus
Humans
Hydrogen Bonding
Polymerization
Purines - chemistry
Purines - metabolism
Pyrimidines - chemistry
Pyrimidines - metabolism
Viral Proteins - chemistry
Viral Proteins - metabolism
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Summary:We utilized a series of pyrimidine analogues modified at O2, N-3, and N4/O4 to determine if two B family DNA polymerases, human DNA polymerase α and herpes simplex virus I DNA polymerase, choose whether to polymerize pyrimidine dNTPs using the same mechanisms they use for purine dNTPs. Removing O2 of a pyrimidine dNTP vastly decreased the level of incorporation by these enzymes and also compromised fidelity in the case of C analogues, while removing O2 from the templating base had more modest effects. Removing the Watson–Crick hydrogen bonding groups of N-3 and N4/O4 greatly impaired polymerization, both of the resulting dNTP analogues and of natural dNTPs opposite these pyrimidine analogues when present in the template strand. Thus, the Watson–Crick hydrogen bonding groups of a pyrimidine clearly play an important role in enhancing correct dNTP polymerization but are not essential for preventing misincorporation. These studies also indicate that DNA polymerases recognize bases extremely asymmetrically, both in terms of whether they are a purine or pyrimidine and whether they are in the template or are the incoming dNTP. The mechanistic implications of these results with regard to how polymerases discriminate between right and wrong dNTPs are discussed.
ISSN:0006-2960
1520-4995
DOI:10.1021/bi2006916