Non-Natural Nucleotide Analogs as Probes of DNA Polymerase Activity

Babho      Devadoss; Anthony   J.   Berdis

doi:10.2174/2212796810701030241

Abstract

DNA polymerases catalyze the addition of mononucleotides into a growing polymer using a DNA template as a guide for directing each incorporation event. The efficiency and fidelity of this biological process have been historically attributed to the ability of the DNA polymerase to coordinate proper hydrogen-bonding interactions between the incoming nucleotide with the templating nucleobase. However, the strength of this model has been weakened since several laboratories have demonstrated that non-natural nucleotides, i.e., those devoid of typical hydrogen-bonding capabilities, can be utilized by DNA polymerases with varying degrees of efficiencies. This review provides a comprehensive summary of current research efforts leading to the development and implementation of these analogs as probes for DNA polymerase function and activity. The ability of various non-natural purines and pyrimidines to be incorporated opposite templating nucleobases suggests that polymerization efficiency is not directly influenced by hydrogen-bonding interactions but rather by the overall shape and size of the formed base-pair. Conflicting evidence is obtained when the dynamics of nucleotide incorporation is assessed using nucleic acid containing permutations in hydrogen bonding capabilities or completely devoid of these interactions. With respect to replication opposite an abasic site, it appears that the π-electron surface area and desolvation properties of the incoming nucleotide play a significant role for facilitating incorporation. This information has lead to the development of new models for DNA polymerization as well as toward strategies for novel biotechnology platforms and unique chemotherapeutic agents.

Keywords: deoxynucleoside triphosphates, hydrogen bonding, Nucleotide Insertion, DNA polymerization, HIV reverse transcriptase, Moloney-murine leukemia virus