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W2040444329 abstract "Interactions between the human DNA polymerase β (pol β) and a single-stranded (ss) DNA have been studied using the quantitative fluorescence titration technique. Examination of the fluorescence increase of the poly(dA) etheno-derivative (poly(dεA)) as a function of the binding density of pol β-nucleic acid complexes reveals the existence of two binding phases. In the first high affinity phase, pol β forms a complex with a ssDNA in which 16 nucleotides are occluded by the enzyme. In the second phase, transition to a complex where the polymerase occludes only 5 nucleotides occurs. Thus, human pol β binds a ssDNA in two binding modes, which differ in the number of occluded nucleotide residues. We designate the first complex as (pol β)16 and the second as (pol β)5binding modes. The analyses of the enzyme binding to ssDNA have been performed using statistical thermodynamic models, which account for the existence of the two binding modes of the enzyme, cooperative interactions, and the overlap of potential binding sites. The importance of the discovery that human pol β binds a ssDNA, using different binding modes, for the possible mechanistic model of the functioning of human pol β, is discussed. Interactions between the human DNA polymerase β (pol β) and a single-stranded (ss) DNA have been studied using the quantitative fluorescence titration technique. Examination of the fluorescence increase of the poly(dA) etheno-derivative (poly(dεA)) as a function of the binding density of pol β-nucleic acid complexes reveals the existence of two binding phases. In the first high affinity phase, pol β forms a complex with a ssDNA in which 16 nucleotides are occluded by the enzyme. In the second phase, transition to a complex where the polymerase occludes only 5 nucleotides occurs. Thus, human pol β binds a ssDNA in two binding modes, which differ in the number of occluded nucleotide residues. We designate the first complex as (pol β)16 and the second as (pol β)5binding modes. The analyses of the enzyme binding to ssDNA have been performed using statistical thermodynamic models, which account for the existence of the two binding modes of the enzyme, cooperative interactions, and the overlap of potential binding sites. The importance of the discovery that human pol β binds a ssDNA, using different binding modes, for the possible mechanistic model of the functioning of human pol β, is discussed. polymerase β single-stranded double-stranded macromolecular competition titration. Polymerase β (pol β)1 is one of the four recognized DNA-directed polymerases of the eucaryotic nucleus: α, β, δ, and ε (1Kornberg A. Baker T.A. DNA Replication. W. H. Freeman, New York1992Google Scholar, 2Friedberg E.C. Walker G.C. Siede W. DNA Repair and Mutagenesis. ASM Press, Washington, DC1995Google Scholar, 3Budd M.E. Campbell J.L. Mutat. Res. 1997; 384: 157-167Crossref PubMed Scopus (53) Google Scholar). The enzyme is lacking intrinsic accessory activities, such as 3′ or 5′ exonuclease, endonuclease, dNMP turnover, and pyrophosphorolysis (1Kornberg A. Baker T.A. DNA Replication. W. H. Freeman, New York1992Google Scholar, 2Friedberg E.C. Walker G.C. Siede W. DNA Repair and Mutagenesis. ASM Press, Washington, DC1995Google Scholar, 3Budd M.E. Campbell J.L. Mutat. Res. 1997; 384: 157-167Crossref PubMed Scopus (53) Google Scholar, 4Prasad R. Singhal R.K. Srivastava D.K. Molina J.T. Tomkinson A.E. Wilson S.H. J. Biol. Chem. 1996; 271: 16000-16007Abstract Full Text Full Text PDF PubMed Scopus (230) Google Scholar, 5Sobol R.W. Horton J.K. Kühn R. Hua G. Singhal R.K. Prasad R. Rajewsky K. Wilson S.H. Nature. 1996; 379: 183-186Crossref PubMed Scopus (783) Google Scholar). This “simplified” activity reflects a very specialized function of the polymerase in mammalian cell repair machinery. pol β conducts “gap fillings” synthesis on gapped DNA in a processive fashion (2Friedberg E.C. Walker G.C. Siede W. DNA Repair and Mutagenesis. ASM Press, Washington, DC1995Google Scholar, 4Prasad R. Singhal R.K. Srivastava D.K. Molina J.T. Tomkinson A.E. Wilson S.H. J. Biol. Chem. 1996; 271: 16000-16007Abstract Full Text Full Text PDF PubMed Scopus (230) Google Scholar, 5Sobol R.W. Horton J.K. Kühn R. Hua G. Singhal R.K. Prasad R. Rajewsky K. Wilson S.H. Nature. 1996; 379: 183-186Crossref PubMed Scopus (783) Google Scholar, 6Mullen G.P. Wilson S.H. Biochemistry. 1997; 36: 4713-4717Crossref PubMed Scopus (37) Google Scholar). The in vitro gap filling reaction has been proposed as being consistent with the role of pol β in the gap filling synthesis involved in mismatch repair (4Prasad R. Singhal R.K. Srivastava D.K. Molina J.T. Tomkinson A.E. Wilson S.H. J. Biol. Chem. 1996; 271: 16000-16007Abstract Full Text Full Text PDF PubMed Scopus (230) Google Scholar, 5Sobol R.W. Horton J.K. Kühn R. Hua G. Singhal R.K. Prasad R. Rajewsky K. Wilson S.H. Nature. 1996; 379: 183-186Crossref PubMed Scopus (783) Google Scholar, 7Wiebauer K. Jiricny J. Proc. Natl. Acad. Sci. U. S. A. 1990; 87: 5842-5845Crossref PubMed Scopus (230) Google Scholar) and in the repair of monofunctional adducts, UV damaged DNA, and abasic lesions in DNA (8Matsumoto Y. Bogenhagen D.F. Mol. Cell. Biol. 1989; 9: 3750-3757Crossref PubMed Scopus (52) Google Scholar, 9Matsumoto Y. Kim K. Bogenhagen D.F. Mol. Cell. Biol. 1994; 14: 6187-6197Crossref PubMed Scopus (260) Google Scholar, 10Singhal R.K. Prasad R. Wilson S.H. J. Biol. Chem. 1995; 270: 949-957Abstract Full Text Full Text PDF PubMed Scopus (293) Google Scholar, 11Hammond R.A. McClung J.K. Miller M.R. Biochemistry. 1990; 29: 286-291Crossref PubMed Scopus (56) Google Scholar, 12Hoffman J.S. Pillaire M.J. Maga G. Podust V. Hubscher U. Villani G. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 5356-5360Crossref PubMed Scopus (138) Google Scholar).Human pol β is a single polypeptide of ∼39,000 kDa (13Abbotts J. SenGupta D.N. Zmudzka B. Widen S.G. Notario V. Wilson S.H. Biochemistry. 1988; 27: 901-909Crossref PubMed Scopus (119) Google Scholar, 14Liu D. Prasad R. Wilson S.H. DeRose E.F. Mullen G.P. Biochemistry. 1996; 35: 6188-6200Crossref PubMed Scopus (54) Google Scholar, 15Pelletier H. Sawaya M.R. Kumar A. Wilson S.H. Kraut J.A. Science. 1994; 264: 1891-1903Crossref PubMed Scopus (756) Google Scholar, 16Pelletier H. Sawaya M.R. Wolfle W. Wilson S.H. Kraut J.A. Biochemistry. 1996; 35: 12762-12777Crossref PubMed Scopus (176) Google Scholar). Recently, crystallographic structures of rat and human pol β have been determined at 3.6- and 2.3-Å resolutions (15Pelletier H. Sawaya M.R. Kumar A. Wilson S.H. Kraut J.A. Science. 1994; 264: 1891-1903Crossref PubMed Scopus (756) Google Scholar, 16Pelletier H. Sawaya M.R. Wolfle W. Wilson S.H. Kraut J.A. Biochemistry. 1996; 35: 12762-12777Crossref PubMed Scopus (176) Google Scholar). A characteristic feature of the pol β structure is the presence of a small 8-kDa domain, which is connected with the tip of the fingers through a tether of 14 amino acids (15Pelletier H. Sawaya M.R. Kumar A. Wilson S.H. Kraut J.A. Science. 1994; 264: 1891-1903Crossref PubMed Scopus (756) Google Scholar, 16Pelletier H. Sawaya M.R. Wolfle W. Wilson S.H. Kraut J.A. Biochemistry. 1996; 35: 12762-12777Crossref PubMed Scopus (176) Google Scholar). Solution studies showed that the 8-kDa domain has a high affinity for a ss nucleic acid, thus providing evidence that it is the template-binding domain, while the catalytic activity and dsDNA affinity reside in the large 31-kDa domain (17Kumar A. Abbotts J. Karawya E.M. Wilson S.H. Biochemistry. 1990; 29: 7156-7159Crossref PubMed Scopus (89) Google Scholar, 18Casas-Finet J.R. Kumar A. Morris G. Wilson S.H. Karpel R.L. J. Biol. Chem. 1991; 266: 19618-19625Abstract Full Text PDF PubMed Google Scholar).The quantitative analysis of the interactions of human pol β with a ssDNA has not been directly addressed before. The only information about the interactions of the enzyme with a ss nucleic acid comes from studies of the interactions of an analogous rat enzyme with the fluorescent polyribonucleotide, poly(rεA) (17Kumar A. Abbotts J. Karawya E.M. Wilson S.H. Biochemistry. 1990; 29: 7156-7159Crossref PubMed Scopus (89) Google Scholar, 18Casas-Finet J.R. Kumar A. Morris G. Wilson S.H. Karpel R.L. J. Biol. Chem. 1991; 266: 19618-19625Abstract Full Text PDF PubMed Google Scholar). These studies indicated that the enzyme forms a single type of complex with ∼11 nucleotide residues occluded by the protein (18Casas-Finet J.R. Kumar A. Morris G. Wilson S.H. Karpel R.L. J. Biol. Chem. 1991; 266: 19618-19625Abstract Full Text PDF PubMed Google Scholar). The in vivo role of pol β is related to its ability to fill short ssDNA gaps, <6 nucleotides, during nucleotide excision repair (2Friedberg E.C. Walker G.C. Siede W. DNA Repair and Mutagenesis. ASM Press, Washington, DC1995Google Scholar, 3Budd M.E. Campbell J.L. Mutat. Res. 1997; 384: 157-167Crossref PubMed Scopus (53) Google Scholar, 5Sobol R.W. Horton J.K. Kühn R. Hua G. Singhal R.K. Prasad R. Rajewsky K. Wilson S.H. Nature. 1996; 379: 183-186Crossref PubMed Scopus (783) Google Scholar, 19Prasad R. Beard W.A. Wilson S.H. J. Biol. Chem. 1994; 269: 18096-18101Abstract Full Text PDF PubMed Google Scholar,20Singhal R.K. Wilson S.H. J. Biol. Chem. 1993; 268: 15906-15911Abstract Full Text PDF PubMed Google Scholar). Fundamental questions of the pol β mechanism relate to the problem of how the enzyme, which is proposed to form a single type of complex with a ssDNA (18Casas-Finet J.R. Kumar A. Morris G. Wilson S.H. Karpel R.L. J. Biol. Chem. 1991; 266: 19618-19625Abstract Full Text PDF PubMed Google Scholar), efficiently recognizes small ssDNA gaps, much smaller than the indicated site size of the complex. Another important question is: does the enzyme have the ability to adjust to the decreasing accessibility of the ssDNA in the vanishing gap during DNA synthesis?Elucidation of the pol β-ssDNA recognition processes constitutes a first step toward understanding the molecular mechanism of the enzyme. In this article, we report the quantitative analysis of human pol β interactions with the ssDNA using the thermodynamically rigorous fluorescence titration technique (21Bujalowski W. Jezewska M.J. Biochemistry. 1995; 34: 8513-8519Crossref PubMed Scopus (121) Google Scholar, 22Jezewska M.J. Kim U.-S. Bujalowski W. Biochemistry. 1996; 36: 2129-2145Crossref Scopus (83) Google Scholar, 23Jezewska M.J. Bujalowski W. Biochemistry. 1996; 35: 2117-2128Crossref PubMed Scopus (84) Google Scholar, 24Jezewska M.J. Bujalowski W. Biophys. Chem. 1997; 64: 253-269Crossref PubMed Scopus (37) Google Scholar). We provide direct evidence that human pol β binds the ssDNA in two binding modes, (pol β)16 and (pol β)5, which differ in the number of occluded nucleotide residues in the complex. Thus, the enzyme can switch between high and low site size binding modes. This ability may be crucial for efficient recognition of the small ssDNA gaps on damaged DNA and for a processive DNA synthesis. Both binding modes differ in affinities and abilities to induce conformational changes in the ssDNA. These differences strongly suggest that, in the (pol β)16 mode, the 31-kDa catalytic domain of the enzyme is involved in interactions with the ssDNA. Polymerase β (pol β)1 is one of the four recognized DNA-directed polymerases of the eucaryotic nucleus: α, β, δ, and ε (1Kornberg A. Baker T.A. DNA Replication. W. H. Freeman, New York1992Google Scholar, 2Friedberg E.C. Walker G.C. Siede W. DNA Repair and Mutagenesis. ASM Press, Washington, DC1995Google Scholar, 3Budd M.E. Campbell J.L. Mutat. Res. 1997; 384: 157-167Crossref PubMed Scopus (53) Google Scholar). The enzyme is lacking intrinsic accessory activities, such as 3′ or 5′ exonuclease, endonuclease, dNMP turnover, and pyrophosphorolysis (1Kornberg A. Baker T.A. DNA Replication. W. H. Freeman, New York1992Google Scholar, 2Friedberg E.C. Walker G.C. Siede W. DNA Repair and Mutagenesis. ASM Press, Washington, DC1995Google Scholar, 3Budd M.E. Campbell J.L. Mutat. Res. 1997; 384: 157-167Crossref PubMed Scopus (53) Google Scholar, 4Prasad R. Singhal R.K. Srivastava D.K. Molina J.T. Tomkinson A.E. Wilson S.H. J. Biol. Chem. 1996; 271: 16000-16007Abstract Full Text Full Text PDF PubMed Scopus (230) Google Scholar, 5Sobol R.W. Horton J.K. Kühn R. Hua G. Singhal R.K. Prasad R. Rajewsky K. Wilson S.H. Nature. 1996; 379: 183-186Crossref PubMed Scopus (783) Google Scholar). This “simplified” activity reflects a very specialized function of the polymerase in mammalian cell repair machinery. pol β conducts “gap fillings” synthesis on gapped DNA in a processive fashion (2Friedberg E.C. Walker G.C. Siede W. DNA Repair and Mutagenesis. ASM Press, Washington, DC1995Google Scholar, 4Prasad R. Singhal R.K. Srivastava D.K. Molina J.T. Tomkinson A.E. Wilson S.H. J. Biol. Chem. 1996; 271: 16000-16007Abstract Full Text Full Text PDF PubMed Scopus (230) Google Scholar, 5Sobol R.W. Horton J.K. Kühn R. Hua G. Singhal R.K. Prasad R. Rajewsky K. Wilson S.H. Nature. 1996; 379: 183-186Crossref PubMed Scopus (783) Google Scholar, 6Mullen G.P. Wilson S.H. Biochemistry. 1997; 36: 4713-4717Crossref PubMed Scopus (37) Google Scholar). The in vitro gap filling reaction has been proposed as being consistent with the role of pol β in the gap filling synthesis involved in mismatch repair (4Prasad R. Singhal R.K. Srivastava D.K. Molina J.T. Tomkinson A.E. Wilson S.H. J. Biol. Chem. 1996; 271: 16000-16007Abstract Full Text Full Text PDF PubMed Scopus (230) Google Scholar, 5Sobol R.W. Horton J.K. Kühn R. Hua G. Singhal R.K. Prasad R. Rajewsky K. Wilson S.H. Nature. 1996; 379: 183-186Crossref PubMed Scopus (783) Google Scholar, 7Wiebauer K. Jiricny J. Proc. Natl. Acad. Sci. U. S. A. 1990; 87: 5842-5845Crossref PubMed Scopus (230) Google Scholar) and in the repair of monofunctional adducts, UV damaged DNA, and abasic lesions in DNA (8Matsumoto Y. Bogenhagen D.F. Mol. Cell. Biol. 1989; 9: 3750-3757Crossref PubMed Scopus (52) Google Scholar, 9Matsumoto Y. Kim K. Bogenhagen D.F. Mol. Cell. Biol. 1994; 14: 6187-6197Crossref PubMed Scopus (260) Google Scholar, 10Singhal R.K. Prasad R. Wilson S.H. J. Biol. Chem. 1995; 270: 949-957Abstract Full Text Full Text PDF PubMed Scopus (293) Google Scholar, 11Hammond R.A. McClung J.K. Miller M.R. Biochemistry. 1990; 29: 286-291Crossref PubMed Scopus (56) Google Scholar, 12Hoffman J.S. Pillaire M.J. Maga G. Podust V. Hubscher U. Villani G. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 5356-5360Crossref PubMed Scopus (138) Google Scholar). Human pol β is a single polypeptide of ∼39,000 kDa (13Abbotts J. SenGupta D.N. Zmudzka B. Widen S.G. Notario V. Wilson S.H. Biochemistry. 1988; 27: 901-909Crossref PubMed Scopus (119) Google Scholar, 14Liu D. Prasad R. Wilson S.H. DeRose E.F. Mullen G.P. Biochemistry. 1996; 35: 6188-6200Crossref PubMed Scopus (54) Google Scholar, 15Pelletier H. Sawaya M.R. Kumar A. Wilson S.H. Kraut J.A. Science. 1994; 264: 1891-1903Crossref PubMed Scopus (756) Google Scholar, 16Pelletier H. Sawaya M.R. Wolfle W. Wilson S.H. Kraut J.A. Biochemistry. 1996; 35: 12762-12777Crossref PubMed Scopus (176) Google Scholar). Recently, crystallographic structures of rat and human pol β have been determined at 3.6- and 2.3-Å resolutions (15Pelletier H. Sawaya M.R. Kumar A. Wilson S.H. Kraut J.A. Science. 1994; 264: 1891-1903Crossref PubMed Scopus (756) Google Scholar, 16Pelletier H. Sawaya M.R. Wolfle W. Wilson S.H. Kraut J.A. Biochemistry. 1996; 35: 12762-12777Crossref PubMed Scopus (176) Google Scholar). A characteristic feature of the pol β structure is the presence of a small 8-kDa domain, which is connected with the tip of the fingers through a tether of 14 amino acids (15Pelletier H. Sawaya M.R. Kumar A. Wilson S.H. Kraut J.A. Science. 1994; 264: 1891-1903Crossref PubMed Scopus (756) Google Scholar, 16Pelletier H. Sawaya M.R. Wolfle W. Wilson S.H. Kraut J.A. Biochemistry. 1996; 35: 12762-12777Crossref PubMed Scopus (176) Google Scholar). Solution studies showed that the 8-kDa domain has a high affinity for a ss nucleic acid, thus providing evidence that it is the template-binding domain, while the catalytic activity and dsDNA affinity reside in the large 31-kDa domain (17Kumar A. Abbotts J. Karawya E.M. Wilson S.H. Biochemistry. 1990; 29: 7156-7159Crossref PubMed Scopus (89) Google Scholar, 18Casas-Finet J.R. Kumar A. Morris G. Wilson S.H. Karpel R.L. J. Biol. Chem. 1991; 266: 19618-19625Abstract Full Text PDF PubMed Google Scholar). The quantitative analysis of the interactions of human pol β with a ssDNA has not been directly addressed before. The only information about the interactions of the enzyme with a ss nucleic acid comes from studies of the interactions of an analogous rat enzyme with the fluorescent polyribonucleotide, poly(rεA) (17Kumar A. Abbotts J. Karawya E.M. Wilson S.H. Biochemistry. 1990; 29: 7156-7159Crossref PubMed Scopus (89) Google Scholar, 18Casas-Finet J.R. Kumar A. Morris G. Wilson S.H. Karpel R.L. J. Biol. Chem. 1991; 266: 19618-19625Abstract Full Text PDF PubMed Google Scholar). These studies indicated that the enzyme forms a single type of complex with ∼11 nucleotide residues occluded by the protein (18Casas-Finet J.R. Kumar A. Morris G. Wilson S.H. Karpel R.L. J. Biol. Chem. 1991; 266: 19618-19625Abstract Full Text PDF PubMed Google Scholar). The in vivo role of pol β is related to its ability to fill short ssDNA gaps, <6 nucleotides, during nucleotide excision repair (2Friedberg E.C. Walker G.C. Siede W. DNA Repair and Mutagenesis. ASM Press, Washington, DC1995Google Scholar, 3Budd M.E. Campbell J.L. Mutat. Res. 1997; 384: 157-167Crossref PubMed Scopus (53) Google Scholar, 5Sobol R.W. Horton J.K. Kühn R. Hua G. Singhal R.K. Prasad R. Rajewsky K. Wilson S.H. Nature. 1996; 379: 183-186Crossref PubMed Scopus (783) Google Scholar, 19Prasad R. Beard W.A. Wilson S.H. J. Biol. Chem. 1994; 269: 18096-18101Abstract Full Text PDF PubMed Google Scholar,20Singhal R.K. Wilson S.H. J. Biol. Chem. 1993; 268: 15906-15911Abstract Full Text PDF PubMed Google Scholar). Fundamental questions of the pol β mechanism relate to the problem of how the enzyme, which is proposed to form a single type of complex with a ssDNA (18Casas-Finet J.R. Kumar A. Morris G. Wilson S.H. Karpel R.L. J. Biol. Chem. 1991; 266: 19618-19625Abstract Full Text PDF PubMed Google Scholar), efficiently recognizes small ssDNA gaps, much smaller than the indicated site size of the complex. Another important question is: does the enzyme have the ability to adjust to the decreasing accessibility of the ssDNA in the vanishing gap during DNA synthesis? Elucidation of the pol β-ssDNA recognition processes constitutes a first step toward understanding the molecular mechanism of the enzyme. In this article, we report the quantitative analysis of human pol β interactions with the ssDNA using the thermodynamically rigorous fluorescence titration technique (21Bujalowski W. Jezewska M.J. Biochemistry. 1995; 34: 8513-8519Crossref PubMed Scopus (121) Google Scholar, 22Jezewska M.J. Kim U.-S. Bujalowski W. Biochemistry. 1996; 36: 2129-2145Crossref Scopus (83) Google Scholar, 23Jezewska M.J. Bujalowski W. Biochemistry. 1996; 35: 2117-2128Crossref PubMed Scopus (84) Google Scholar, 24Jezewska M.J. Bujalowski W. Biophys. Chem. 1997; 64: 253-269Crossref PubMed Scopus (37) Google Scholar). We provide direct evidence that human pol β binds the ssDNA in two binding modes, (pol β)16 and (pol β)5, which differ in the number of occluded nucleotide residues in the complex. Thus, the enzyme can switch between high and low site size binding modes. This ability may be crucial for efficient recognition of the small ssDNA gaps on damaged DNA and for a processive DNA synthesis. Both binding modes differ in affinities and abilities to induce conformational changes in the ssDNA. These differences strongly suggest that, in the (pol β)16 mode, the 31-kDa catalytic domain of the enzyme is involved in interactions with the ssDNA. We thank Gloria Drennan Davis for help in preparing the manuscript." @default.
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W2040444329 title "Human DNA Polymerase β Recognizes Single-stranded DNA Using Two Different Binding Modes" @default.
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