Abstract
In this chapter, we gave the detailed protocols for studies of bypassing DNA damage using a DNA polymerase. These methods include kinetic analysis, LC-MS/MS sequence analysis of full-length extension products beyond DNA damage, and X-ray crystal structure analysis of DNA polymerase containing DNA damage. Kinetic analysis contains steady-state kinetic analysis of single dNTP incorporation against DNA damage, full-length extension beyond DNA damage, pre-steady-state kinetic analysis of dNTP incorporation, and kinetic analysis of conformational change. This analysis gave details about how a DNA polymerase bypasses DNA damage.
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Further Reading
Goodman MF, Creighton S, Bloom LB, Petruska J (1993) Biochemical basis of DNA replication fidelity. Crit Rev Biochem Mol Biol 28:83–126
Zang H, Irminia A, Choi JY, Angel KC, Loukachevitch LV, Egli M, Guengerich FP (2006) Efficient and high fidelity incorporation of dCTP opposite 7,8-dihydro-8-oxo-deoxyguanosine by Sulfolobus solfataricus DNA polymerase Dpo4. J Biol Chem 281:2358–2372
Johnson KA (1995) Rapid quench kinetic analysis of polymerases, adenosinetriphosphatases, and enzyme intermediates. Method Enzymol 249:38–6
Choi YJ, Guengerich FP (2004) Analysis of the effect of bulk at N2-alkylguanine DNA adducts on catalytic efficiency and fidelity of the processive DNA polymerase T7 exonuclease¯ and HIV-1 reverse transcriptase. J Biol Chem 279:19217–19229
Zang H, Goodenough AK, Choi JY, Irminia A, Loukachevitch LV, Kozekov ID, Angel KC, Rizzo CJ, Egli M, Guengerich FP (2005) DNA adduct bypass polymerization by Sulfolobus solfataricus DNA polymerase Dpo4. Analysis and crystal structures of multiple base-pair substitution and frameshift product with the adduct 1,N2-ethenoguanine. J Biol Chem 280:29750–29764
Zang H, Harris TM, Guengerich FP (2005) Kinetics of nucleotide incorporation opposite DNA guanine-N2 adducts by the processive bacteriophage T7- polymerase DNA. J Biol Chem 280:1165–1178
Patel SS, Wong I, Johnson KA (1991) Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant. Biochemistry 30:511–525
Furge LL, Guengerich FP (1997) Analysis of nucleotide insertion and extension at 8-oxo-7,8-dihydroguanine by replicative T7 polymerase exo- and human immunodeficiency virus-1 reverse transcriptase using steady-state and pre-steady-state kinetics. Biochemistry 36:6475–6487
Zang H, Goodenough AK, Choi JY, Irminia A, Loukachevitch LV, Kozekov ID, Angel KC, Rizzo CJ, Egli M, and Guengerich FP (2005) DNA adduct bypass polymerization by Sulfolobus solfataricus DNA polymerase Dpo4 - Analysis and crystal structures of multiple base pair substitution and frameshift products with the adduct 1,N-2-ethenoguanine. J Biol Chem 280:29750–29764
Vagin A, Teplyakov A (1997) MOLREP: an Automated Program for Molecular Replacement. J Appl Crystallogr 30:1022–1025
Vellieux FMD, Dijkstra BW (1997) Computation of Bhat’s OMIT maps with different coefficients. J Appl Crystallogr 30:396–399
Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr Sect D Biol Crystallogr 54:905–921
Lavery R, Sklenar H (1989) Defining the structure of irregular nucleic acids: conventions and principles. J Biomol Struct Dynam 6:655–667
Beckman JW, Wang Q, Guengerich FP (2008) Kinetic Analysis of Correct Nucleotide Insertion by a Y-family DNA Polymerase Reveals Conformational Changes Both Prior to and following Phosphodiester Bond Formation as Detected by Tryptophan Fluorescence. J Biol Chem 283:36711–36723
Zhang H, Lee S, Richardson, Charles C (2012) The roles of tryptophans in primer synthesis by the DNA primase of bacteriophage T7. J Biol Chem 287:23644–23656
Zhang H, Eoff RL, Kozekov ID, Rizzo CJ, Egli M, Guengerich FP (2009) Versatility of Y-family Sulfolobus solfataricus DNA Polymerase Dpo4 in Translesion Synthesis Past Bulky N-2-Alkylguanine Adducts. J Biol Chem 284:3563–3576
Zhang H, Beckman JW, Guengerich FP (2009) Frameshift Deletion by Sulfolobus solfataricus P2 DNA Polymerase Dpo4 T239 W Is Selective for Purines and Involves Normal Conformational Change Followed by Slow Phosphodiester Bond Formation. J Biol Chem 284:35144–35153
Zhang H, Eoff RL, Kozekov ID, Rizzo CJ, Egli M, Guengerich FP (2009) Structure-Function Relationships in Miscoding by Sulfolobus solfataricus DNA Polymerase Dpo4 Guanine N-2,N-2-dimethyl substitution produces inactive and miscoding polymerase complexes. J Biol Chem 284:17687–17699
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Zhang, H. (2015). Protocols for Studies of Bypass of DNA Damage by DNA Polymerase. In: DNA Replication - Damage from Environmental Carcinogens. SpringerBriefs in Biochemistry and Molecular Biology, vol 17. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-7212-9_6
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DOI: https://doi.org/10.1007/978-94-017-7212-9_6
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