When DNA Polymerases Multitask: Functions Beyond Nucleotidyl Transfer

Abstract

DNA polymerases catalyze nucleotidyl transfer, the central reaction in synthesis of DNA polynucleotide chains. They function not only in DNA replication, but also in diverse aspects of DNA repair and recombination. Some DNA polymerases can perform translesion DNA synthesis, facilitating damage tolerance and leading to mutagenesis. In addition to these functions, many DNA polymerases conduct biochemically distinct reactions. This review presents examples of DNA polymerases that carry out nuclease (3ʹ—5′ exonuclease, 5′ nuclease, or end-trimming nuclease) or lyase (5′ dRP lyase) extracurricular activities. The discussion underscores how DNA polymerases have a remarkable ability to manipulate DNA strands, sometimes involving relatively large intramolecular movement.

Interfering with nucleotide excision by the coronavirus 3’-to-5’ exoribonuclease

“…For proofreading exonucleases of DNA polymerases, it is not that the exonuclease exhibits a preference for a mispaired end relative to a properly paired end (26,27). Rather, a mispaired end is unstable in the polymerase active site, providing the opportunity for the mispaired end to partition to the exonuclease active site (26,27). To assess the impact of the terminal basepair on the kinetics of excision by ExoN, we designed two additional RNA substrates for ExoN.…”

“…ExoN prefers a primed-template-like dsRNA substrate over a ssRNA substrate and cannot access the 3’-terminus at a nick. ExoN only cleaves one or two nucleotides in a single binding event, as expected for a proofreading enzyme (26,27). Cleavage can be completely inhibited by the presence of the phosphorothioate Rp isomer at the scissile phosphodiester bond.…”

“…Proofreading DNA exonucleases are generally a subunit of the DNA polymerase holoenzyme and exhibit a preference for mispaired ends (26). This circumstance appears to reflect the preferential partitioning of the mispaired end to the active site of the exonuclease instead of the active site of the polymerase (26,27). How proofreading by ExoN is initiated is not known.…”

Editorial: Nucleic Acid Polymerases: The Two-Metal-Ion Mechanism and Beyond

“…Carvajal-Maldonado provide a comprehensive review of the other catalytic activities that are frequently associated with DNA polymerases: 3′-5′ exonuclease proofreading that increases replication fidelity, structure-specific 5′-nuclease activity required for Okazaki fragment maturation during lagging strand synthesis, 5′dRP lyase activity required in the base excision repair pathway, and 3′-end-trimming and single-strand extension involved in double-strand break repair ( Carvajal-Maldonado et al, 2021 ).…”

“…maturation during lagging strand synthesis, 5′dRP lyase activity required in the base excision repair pathway, and 3′-endtrimming and single-strand extension involved in doublestrand break repair (Carvajal-Maldonado et al, 2021).…”