Abstract
We propose a model for DNA polymerase fidelity in which free energy differences, delta delta G, between matched and mismatched nucleotides are magnified at the enzyme's active site. Both hydrogen bonding and stacking components of the interaction energy are amplified, with the most profound effect being on the magnitude of hydrogen-bonding interactions. Magnification in delta delta G values follows from the exclusion of water around base pairs in the active site cleft of the enzyme. After showing that base-pair dissociation energies calculated from hydrogen-bonding and base-stacking interactions in vacuo are greatly reduced by water, it is proposed that water removal results in a proportional restoration of these contributions to base pairing. Assuming approximately equal to 40% exclusion of surrounding water, one predicts magnified values of delta delta G sufficient to account for polymerase insertion and proofreading fidelity, thereby avoiding the need to postulate additional active site constraints in order to select or reject nucleotides.
Full text
PDF
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Brutlag D., Kornberg A. Enzymatic synthesis of deoxyribonucleic acid. 36. A proofreading function for the 3' leads to 5' exonuclease activity in deoxyribonucleic acid polymerases. J Biol Chem. 1972 Jan 10;247(1):241–248. [PubMed] [Google Scholar]
- DEVOE H., TINOCO I., Jr The stability of helical polynucleotides: base contributions. J Mol Biol. 1962 Jun;4:500–517. doi: 10.1016/s0022-2836(62)80105-3. [DOI] [PubMed] [Google Scholar]
- Dewar M. J., Storch D. M. Alternative view of enzyme reactions. Proc Natl Acad Sci U S A. 1985 Apr;82(8):2225–2229. doi: 10.1073/pnas.82.8.2225. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hopfield J. J. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc Natl Acad Sci U S A. 1974 Oct;71(10):4135–4139. doi: 10.1073/pnas.71.10.4135. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jordan F., Sostman H. D. Molecular orbital (CNDO/2 and MINDO) calculations on protonated deoxyribonucleic acid bases. The effects of base protonation on intermolecular interactions. J Am Chem Soc. 1973 Oct 3;95(20):6544–6554. doi: 10.1021/ja00801a004. [DOI] [PubMed] [Google Scholar]
- Loeb L. A., Kunkel T. A. Fidelity of DNA synthesis. Annu Rev Biochem. 1982;51:429–457. doi: 10.1146/annurev.bi.51.070182.002241. [DOI] [PubMed] [Google Scholar]
- Muzyczka N., Poland R. L., Bessman M. J. Studies on the biochemical basis of spontaneous mutation. I. A comparison of the deoxyribonucleic acid polymerases of mutator, antimutator, and wild type strains of bacteriophage T4. J Biol Chem. 1972 Nov 25;247(22):7116–7122. [PubMed] [Google Scholar]
- Ninio J. Kinetic amplification of enzyme discrimination. Biochimie. 1975;57(5):587–595. doi: 10.1016/s0300-9084(75)80139-8. [DOI] [PubMed] [Google Scholar]
- Petruska J., Goodman M. F. Influence of neighboring bases on DNA polymerase insertion and proofreading fidelity. J Biol Chem. 1985 Jun 25;260(12):7533–7539. [PubMed] [Google Scholar]
- Pless R. C., Bessman M. J. Influence of local nucleotide sequence on substitution of 2-aminopurine for adenine during deoxyribonucleic acid synthesis in vitro. Biochemistry. 1983 Oct 11;22(21):4905–4915. doi: 10.1021/bi00290a006. [DOI] [PubMed] [Google Scholar]
- Vilpo J. A., Ridell J. Uracil in deoxyribonucleotide polymers reduces their template-primer activity for E. coli DNA polymerase I. Nucleic Acids Res. 1983 Jun 11;11(11):3753–3765. doi: 10.1093/nar/11.11.3753. [DOI] [PMC free article] [PubMed] [Google Scholar]