Nucleotide Analogues as Probes for DNA and RNA Polymerases
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- Abstract
- Table of Contents
- Figures
- Literature Cited
Abstract
Nucleotide analogues represent a major class of anti?cancer and anti?viral drugs, and provide an extremely powerful tool for dissecting the mechanisms of DNA and RNA polymerases. While the basic assays themselves are relatively straightforward, a key issue is to appropriately design the studies to answer the mechanistic question of interest. This unit addresses the major issues involved in designing these studies, and some of the potential difficulties that arise in interpreting the data. Examples are given for the type of analogues typically used, the experimental approaches with different polymerases, and issues with data interpretation. Curr. Protoc. Chem Biol. 2:111?124. © 2010 by John Wiley & Sons, Inc.
Keywords: polymerase; nucleotide; DNA; RNA; kinetics
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PDF or HTML at Wiley Online LibraryTable of Contents
- Introduction
- Sugar Analogues
- Base Analogues
- Effects of DNA Sequence
- 3′‐5′ Exonuclease Activity
- Challenges of RNA Polymerases
- Data Interpretation
- Examples of Difficulty Interpreting how a Polymerase Interacts with a Nucleotide
- Acknowledgements
- Literature Cited
- Figures
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Figure 1. Examples of clinically useful anticancer and antiviral nucleosides that involve DNA polymerase activity. (A ) Antiviral agents. (B ) Cancer chemotherapeutics. View Image -
Figure 2. Reported modifications of the sugar of a nucleoside. View Image -
Figure 3. Examples of modified bases that have been used to probe DNA and/or RNA polymerases. R = ribose or 2′‐deoxyribose. This list is not meant to be comprehensive, and my apologies to those researchers and their compounds that were not included. View Image -
Figure 4. General methods to analyze dNTP polymerization onto a primer‐template. View Image -
Figure 5. Polymerization of two consecutive dNTPs by a DNA polymerase. View Image -
Figure 6. Structure of entecavir. View Image -
Figure 7. Inhibition of herpes DNA polymerase by acyclovir triphosphate (ACVTP). View Image -
Figure 8. Partitioning analysis of NTP polymerization by a RNA polymerase. View Image -
Figure 9. Two chemically similar interconversions that have dramatically different effects on incorporation of the resulting dNTP by Klenow fragment. View Image -
Figure 10. Unusually shaped base pairs that Klenow fragment generates with high efficiency. View Image
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