%0 Journal Article
%T Synthetic Nucleotides as Probes of DNA Polymerase Specificity
%A Jason M. Walsh
%A Penny J. Beuning
%J Journal of Nucleic Acids
%D 2012
%I Hindawi Publishing Corporation
%R 10.1155/2012/530963
%X The genetic code is continuously expanding with new nucleobases designed to suit specific research needs. These synthetic nucleotides are used to study DNA polymerase dynamics and specificity and may even inhibit DNA polymerase activity. The availability of an increasing chemical diversity of nucleotides allows questions of utilization by different DNA polymerases to be addressed. Much of the work in this area deals with the A family DNA polymerases, for example, Escherichia coli DNA polymerase I, which are DNA polymerases involved in replication and whose fidelity is relatively high, but more recent work includes other families of polymerases, including the Y family, whose members are known to be error prone. This paper focuses on the ability of DNA polymerases to utilize nonnatural nucleotides in DNA templates or as the incoming nucleoside triphosphates. Beyond the utility of nonnatural nucleotides as probes of DNA polymerase specificity, such entities can also provide insight into the functions of DNA polymerases when encountering DNA that is damaged by natural agents. Thus, synthetic nucleotides provide insight into how polymerases deal with nonnatural nucleotides as well as into the mutagenic potential of nonnatural nucleotides. 1. Introduction Since the structure of DNA was determined [1, 2], biochemists have sought more detailed ways to study DNA and the proteins that interact with it [3, 4]. Solid phase nucleic acid synthesis of DNA molecules facilitates the site-specific incorporation of a wide range of chemically modified bases and sugar-phosphate backbones, allowing the roles of specific atoms in DNA function and recognition to be probed. Synthetic nonnatural nucleobases are useful for a variety of studies of DNA polymerase function, such as studies of DNA polymerase specificity, mutagenesis, and dynamics, as well as fluorescence resonance energy transfer (FRET) analysis of DNA polymerase interactions with DNA. The study of mutagenesis facilitated by DNA polymerases has attracted increasing interest because replication defects can lead to certain human diseases like the cancer-prone syndrome xeroderma pigmentosum variant (XPV) [5, 6] and other diseases [7¨C9], as well as potentially contribute to antibiotic resistance [10, 11]. Moreover, specialized damage-bypass DNA polymerases are implicated in conferring cellular tolerance to cancer chemotherapy agents that act via DNA damage, thereby decreasing their effectiveness [12¨C16]. This paper will focus on the ability of DNA polymerases to recognize and accept nonnatural bases either on the
%U http://www.hindawi.com/journals/jna/2012/530963/