A unified DNA- and dNTP-binding mode for DNA polymerases
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Updated: Oct 28, 2026

Nucleoside Triphosphates - From Synthesis to Biochemical Characterization
Published on: April 3, 2014
1Dept of Biochemistry and Molecular Biology, UMD-New Jersey Medical School, Newark 07103, USA.
Abstract:
Crystal structures of various DNA polymerases show a common structural topology that resembles a right hand and has distinct finger, palm and thumb subdomains. Early models of the klenow fragment (KF) of Escherichia coli polymerase I showed DNA entering a large cleft that faces the palm subdomain where the catalytic site is situated1,2. However, subsequent resolution of the structures of HIV-1 reverse transcriptase, KF and polymerase beta (pol beta) bound to DNA3-5 yielded conflicting data that suggested a different orientation for DNA bound to pol beta compared with DNA bound to other polymerases. The debate, on the correct orientation of the template-primer DNA, that followed failed to reach a consensus. Using an alternative superposition scheme, we now provide convincing evidence for a common DNA-binding mode that is applicable to all polymerases, including pol beta.
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