1
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Dangerfield TL, Johnson KA. Design and interpretation of experiments to establish enzyme pathway and define the role of conformational changes in enzyme specificity. Methods Enzymol 2023; 685:461-492. [PMID: 37245912 DOI: 10.1016/bs.mie.2023.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We describe the experimental methods and analysis to define the role of enzyme conformational changes in specificity based on published studies using DNA polymerases as an ideal model system. Rather than give details of how to perform transient-state and single-turnover kinetic experiments, we focus on the rationale of the experimental design and interpretation. We show how initial experiments to measure kcat and kcat/Km can accurately quantify specificity but do not define its underlying mechanistic basis. We describe methods to fluorescently label enzymes to monitor conformational changes and to correlate fluorescence signals with rapid-chemical-quench flow assays to define the steps in the pathway. Measurements of the rate of product release and of the kinetics of the reverse reaction complete the kinetic and thermodynamic description of the full reaction pathway. This analysis showed that the substrate-induced change in enzyme structure from an open to a closed state was much faster than rate-limiting chemical bond formation. However, because the reverse of the conformational change was much slower than chemistry, specificity is governed solely by the product of the binding constant for the initial weak substrate binding and the rate constant for the conformational change (kcat/Km=K1k2) so that the specificity constant does not include kcat. The enzyme conformational change leads to a closed complex in which the substrate is bound tightly and is committed to the forward reaction. In contrast, an incorrect substrate is bound weakly, and the rate of chemistry is slow, so the mismatch is released from the enzyme rapidly. Thus, the substrate-induced-fit is the major determinant of specificity. The methods outlined here should be applicable to other enzyme systems.
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Affiliation(s)
- Tyler L Dangerfield
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States
| | - Kenneth A Johnson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States.
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2
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Dangerfield T, Johnson KA. Substrate Specificity and Kinetics of RNA Hydrolysis by SARS-CoV-2 NSP10/14 Exonuclease. ACS BIO & MED CHEM AU 2022; 2:600-606. [PMID: 36570070 PMCID: PMC9718090 DOI: 10.1021/acsbiomedchemau.2c00046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 11/18/2022]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the virus that causes COVID-19, continues to evolve resistance to vaccines and existing antiviral therapies at an alarming rate, increasing the need for new direct-acting antiviral drugs. Despite significant advances in our fundamental understanding of the kinetics and mechanism of viral RNA replication, there are still open questions regarding how the proofreading exonuclease (NSP10/NSP14 complex) contributes to replication fidelity and resistance to nucleoside analogs. Through single turnover kinetic analysis, we show that the preferred substrate for the exonuclease is double-stranded RNA without any mismatches. Double-stranded RNA containing a 3'-terminal remdesivir was hydrolyzed at a rate similar to a correctly base-paired cognate nucleotide. Surprisingly, single-stranded RNA or duplex RNA containing a 3'-terminal mismatch was hydrolyzed at rates 125- and 45-fold slower, respectively, compared to the correctly base-paired double-stranded RNA. These results define the substrate specificity and rate of removal of remdesivir for the exonuclease and outline rigorous kinetic assays that could help in finding next-generation exonuclease inhibitors or nucleoside analogs that are able to evade excision. These results also raise important questions about the role of the polymerase/exonuclease complex in proofreading during viral replication. Addressing these questions through rigorous kinetic analysis will facilitate the search for desperately needed antiviral drugs to combat COVID-19.
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3
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Dangerfield TL, Kirmizialtin S, Johnson KA. Conformational dynamics during misincorporation and mismatch extension defined using a DNA polymerase with a fluorescent artificial amino acid. J Biol Chem 2021; 298:101451. [PMID: 34838820 PMCID: PMC8715121 DOI: 10.1016/j.jbc.2021.101451] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/09/2021] [Accepted: 11/23/2021] [Indexed: 11/29/2022] Open
Abstract
High-fidelity DNA polymerases select the correct nucleotide over the structurally similar incorrect nucleotides with extremely high specificity while maintaining fast rates of incorporation. Previous analysis revealed the conformational dynamics and complete kinetic pathway governing correct nucleotide incorporation using a high-fidelity DNA polymerase variant containing a fluorescent unnatural amino acid. Here we extend this analysis to investigate the kinetics of nucleotide misincorporation and mismatch extension. We report the specificity constants for all possible misincorporations and characterize the conformational dynamics of the enzyme during misincorporation and mismatch extension. We present free energy profiles based on the kinetic measurements and discuss the effect of different steps on specificity. During mismatch incorporation and subsequent extension with the correct nucleotide, the rates of the conformational change and chemistry are both greatly reduced. The nucleotide dissociation rate, however, increases to exceed the rate of chemistry. To investigate the structural basis for discrimination against mismatched nucleotides, we performed all atom molecular dynamics simulations on complexes with either the correct or mismatched nucleotide bound at the polymerase active site. The simulations suggest that the closed form of the enzyme with a mismatch bound is greatly destabilized due to weaker interactions with active site residues, nonideal base pairing, and a large increase in the distance from the 3'-OH group of the primer strand to the α-phosphate of the incoming nucleotide, explaining the reduced rates of misincorporation. The observed kinetic and structural mechanisms governing nucleotide misincorporation reveal the general principles likely applicable to other high-fidelity DNA polymerases.
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Affiliation(s)
- Tyler L Dangerfield
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas, USA
| | - Serdal Kirmizialtin
- Chemistry Program, Division of Science, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kenneth A Johnson
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas, USA.
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4
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Giatti S, Di Domizio A, Diviccaro S, Falvo E, Caruso D, Contini A, Melcangi RC. Three-Dimensional Proteome-Wide Scale Screening for the 5-Alpha Reductase Inhibitor Finasteride: Identification of a Novel Off-Target. J Med Chem 2021; 64:4553-4566. [PMID: 33843213 PMCID: PMC8154553 DOI: 10.1021/acs.jmedchem.0c02039] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Finasteride, a 5-alpha
reductase (5α-R) inhibitor, is a widely
used drug for treating androgen-dependent conditions. However, its
use is associated with sexual, psychological, and physical complaints,
suggesting that other mechanisms, in addition to 5α-R inhibition,
may be involved. Here, a multidisciplinary approach has been used
to identify potential finasteride off-target proteins. SPILLO-PBSS
software suggests an additional inhibitory activity of finasteride
on phenylethanolamine N-methyltransferase (PNMT),
the limiting enzyme in formation of the stress hormone epinephrine.
The interaction of finasteride with PNMT was supported by docking
and molecular dynamics analysis and by in vitro assay,
confirming the inhibitory nature of the binding. Finally, this inhibition
was also confirmed in an in vivo rat model. Literature
data indicate that PNMT activity perturbation may be correlated with
sexual and psychological side effects. Therefore, results here obtained
suggest that the binding of finasteride to PNMT might have a role
in producing the side effects exerted by finasteride treatment.
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Affiliation(s)
- Silvia Giatti
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, via Balzaretti 9, 20133 Milano, Italy
| | - Alessandro Di Domizio
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, via Balzaretti 9, 20133 Milano, Italy.,SPILLOproject, via Stradivari 17, Paderno Dugnano, 20037 Milano, Italy
| | - Silvia Diviccaro
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, via Balzaretti 9, 20133 Milano, Italy
| | - Eva Falvo
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, via Balzaretti 9, 20133 Milano, Italy
| | - Donatella Caruso
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, via Balzaretti 9, 20133 Milano, Italy
| | - Alessandro Contini
- Dipartimento Di Scienze Farmaceutiche, Università degli Studi di Milano, 20133 Milano, Italy
| | - Roberto Cosimo Melcangi
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, via Balzaretti 9, 20133 Milano, Italy
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5
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Dangerfield TL, Johnson KA. Conformational dynamics during high-fidelity DNA replication and translocation defined using a DNA polymerase with a fluorescent artificial amino acid. J Biol Chem 2020; 296:100143. [PMID: 33273013 PMCID: PMC7857513 DOI: 10.1074/jbc.ra120.016617] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 12/21/2022] Open
Abstract
We address the role of enzyme conformational dynamics in specificity for a high-fidelity DNA polymerase responsible for genome replication. We present the complete characterization of the conformational dynamics during the correct nucleotide incorporation forward and reverse reactions using stopped-flow and rapid-quench methods with a T7 DNA polymerase variant containing a fluorescent unnatural amino acid, (7-hydroxy-4-coumarin-yl) ethylglycine, which provides a signal for enzyme conformational changes. We show that the forward conformational change (>6000 s−1) is much faster than chemistry (300 s−1) while the enzyme opening to allow release of bound nucleotide (1.7 s−1) is much slower than chemistry. These parameters show that the conformational change selects a correct nucleotide for incorporation through an induced-fit mechanism. We also measured conformational changes occurring after chemistry and during pyrophosphorolysis, providing new insights into processive polymerization. Pyrophosphorolysis occurs via a conformational selection mechanism as the pyrophosphate binds to a rare pretranslocation state of the enzyme–DNA complex. Global data fitting was achieved by including experiments in the forward and reverse directions to correlate conformational changes with chemical reaction steps. This analysis provided well-constrained values for nine rate constants to establish a complete free-energy profile including the rates of DNA translocation during processive synthesis. Translocation does not follow Brownian ratchet or power stroke models invoking nucleotide binding as the driving force. Rather, translocation is rapid and thermodynamically favorable after enzyme opening and pyrophosphate release, and it appears to limit the rate of processive synthesis at 4 °C.
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Affiliation(s)
- Tyler L Dangerfield
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas, Austin, Texas, USA
| | - Kenneth A Johnson
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas, Austin, Texas, USA.
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6
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Haratipour P, Minard C, Nakhjiri M, Negahbani A, Chamberlain BT, Osuna J, Upton TG, Zhao M, Kashemirov BA, McKenna CE. Completing the β,γ-CXY-dNTP Stereochemical Probe Toolkit: Synthetic Access to the dCTP Diastereomers and 31P and 19F NMR Correlations with Absolute Configurations. J Org Chem 2020; 85:14592-14609. [PMID: 33125847 DOI: 10.1021/acs.joc.0c01204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleoside 5'-triphosphate (dNTP) analogues in which the β,γ-oxygen is mimicked by a CXY group (β,γ-CXY-dNTPs) have provided information about DNA polymerase catalysis and fidelity. Definition of CXY stereochemistry is important to elucidate precise binding modes. We previously reported the (R)- and (S)-β,γ-CHX-dGTP diastereomers (X = F, Cl), prepared via P,C-dimorpholinamide CHCl (6a, 6b) and CHF (7a, 7b) bisphosphonates (BPs) equipped with an (R)-mandelic acid as a chiral auxiliary, with final deprotection using H2/Pd. This method also affords the β,γ-CHCl-dTTP (11a, 11b), β,γ-CHF (12a, 12b), and β,γ-CHCl (13a, 13b) dATP diastereomers as documented here, but the reductive deprotection step is not compatible with dCTP or the bromo substituent in β,γ-CHBr-dNTP analogues. To complete assembly of the toolkit, we describe an alternative synthetic strategy featuring ethylbenzylamine or phenylglycine-derived chiral BP synthons incorporating a photolabile protecting group. After acid-catalyzed removal of the (R)-(+)-α-ethylbenzylamine auxiliary, coupling with activated dCMP and photochemical deprotection, the individual diastereomers of β,γ-CHBr- (33a, 33b), β,γ-CHCl- (34a, 34b), β,γ-CHF-dCTP (35a, 35b) were obtained. The β,γ-CH(CH3)-dATPs (44a, 44b) were obtained using a methyl (R)-(-)-phenylglycinate auxiliary. 31P and 19F NMR Δδ values are correlated with CXY stereochemistry and pKa2-4 values for 13 CXY-bisphosphonic acids and imidodiphosphonic acid are tabulated.
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Affiliation(s)
- Pouya Haratipour
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Corinne Minard
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Maryam Nakhjiri
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Amirsoheil Negahbani
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Brian T Chamberlain
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Jorge Osuna
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Thomas G Upton
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Michelle Zhao
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Boris A Kashemirov
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Charles E McKenna
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
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7
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Räz MH, Sandell ES, Patil KM, Gillingham DG, Sturla SJ. High Sensitivity of Human Translesion DNA Synthesis Polymerase κ to Variation in O 6-Carboxymethylguanine Structures. ACS Chem Biol 2019; 14:214-222. [PMID: 30645109 DOI: 10.1021/acschembio.8b00802] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Carboxymethylation of DNA, including the formation of the DNA adduct O6-carboxymethylguanine ( O6-CMG), is associated with lifestyle factors, such as diet. It can impede replicative polymerases (Pols) and lead to replication fork stalling, or an alternative means for replication to proceed by translesion DNA synthesis (TLS). TLS requires specialized DNA Pols characterized by open and preformed active sites capable of preferential bypass of alkylated DNA adducts but that have high error rates, leading to mutations. Human TLS Pols can bypass O6-CMG with varying degrees of accuracy, but it is not known how the chemical structure of the O6-CMG adduct influences polymerase proficiency or fidelity. To better understand how adduct structure determines dNTP selection at lesion sites, we prepared DNA templates with a series of O6-CMG structural analogs and compared the primer extension patterns of Y- and X-family Pols in response to these modifications. The results indicate that the structure of the DNA adduct had a striking effect on dNTP selection by Pol κ and that an increased steric size influences the fidelity of Pol η, whereas Pol ι and β function were only marginally affected. To test the hypothesis that specific hydrogen bonding interactions between the templating base and the incoming dNTP are a basis of this selection, we modeled the structural analogs with incoming dNTP in the Pol κ active site. These data indicate that the base pairing geometry and stabilization by a dense hydrogen bonding network are important molecular features for dNTP incorporation, providing a basis for understanding error-free bypass of O6-CMG by Pol κ.
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Affiliation(s)
- Michael H. Räz
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092, Zürich, Switzerland
| | - Emma S. Sandell
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092, Zürich, Switzerland
| | - Kiran M. Patil
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Dennis G. Gillingham
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Shana J. Sturla
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092, Zürich, Switzerland
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8
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Bull CL, Funnell NP, Ridley CJ, Pulham CR, Coster PL, Tellam JP, Marshall WG. Pressure-induced isosymmetric phase transition in biurea. CrystEngComm 2019. [DOI: 10.1039/c9ce01028a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An isosymmetric phase transition of biurea has been found in which the molecules appear to “snap” from one conformer to another upon compression.
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Affiliation(s)
- Craig L. Bull
- ISIS Neutron and Muon Facility
- Rutherford Appleton Laboratory
- Chilton
- U. K
| | | | | | - Colin R. Pulham
- EastCHEM School of Chemistry
- Joseph Black Building
- Edinburgh
- UK
| | - Paul L. Coster
- EastCHEM School of Chemistry
- Joseph Black Building
- Edinburgh
- UK
| | - James P. Tellam
- ISIS Neutron and Muon Facility
- Rutherford Appleton Laboratory
- Chilton
- U. K
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9
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Raper AT, Reed AJ, Suo Z. Kinetic Mechanism of DNA Polymerases: Contributions of Conformational Dynamics and a Third Divalent Metal Ion. Chem Rev 2018; 118:6000-6025. [DOI: 10.1021/acs.chemrev.7b00685] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Austin T. Raper
- Department of Chemistry and Biochemistry, Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Andrew J. Reed
- Department of Chemistry and Biochemistry, Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Zucai Suo
- Department of Chemistry and Biochemistry, Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
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10
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Wu WJ, Yang W, Tsai MD. How DNA polymerases catalyse replication and repair with contrasting fidelity. Nat Rev Chem 2017. [DOI: 10.1038/s41570-017-0068] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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11
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Qian Y, Johnson KA. The human mitochondrial single-stranded DNA-binding protein displays distinct kinetics and thermodynamics of DNA binding and exchange. J Biol Chem 2017; 292:13068-13084. [PMID: 28615444 DOI: 10.1074/jbc.m117.791392] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 06/08/2017] [Indexed: 11/06/2022] Open
Abstract
The human mitochondrial ssDNA-binding protein (mtSSB) is a homotetrameric protein, involved in mtDNA replication and maintenance. Although mtSSB is structurally similar to SSB from Escherichia coli (EcoSSB), it lacks the C-terminal disordered domain, and little is known about the biophysics of mtSSB-ssDNA interactions. Here, we characterized the kinetics and thermodynamics of mtSSB binding to ssDNA by equilibrium titrations and stopped-flow kinetic measurements. We show that the mtSSB tetramer can bind to ssDNA in two distinct binding modes: (SSB)30 and (SSB)60, defined by DNA binding site sizes of 30 and 60 nucleotides, respectively. We found that the binding mode is modulated by magnesium ion and NaCl concentration, but unlike EcoSSB, the mtSSB does not show negative intersubunit cooperativity. Global fitting of both the equilibrium and kinetic data afforded estimates for the rate and equilibrium constants governing the formation of (SSB)60 and (SSB)30 complexes and for the transitions between the two binding modes. We found that the mtSSB tetramer binds to ssDNA with a rate constant near the diffusion limit (2 × 109 m-1 s-1) and that longer DNA (≥60 nucleotides) rapidly wraps around all four monomers, as revealed by FRET assays. We also show that the mtSSB tetramer can directly transfer from one ssDNA molecule to another via an intermediate with two DNA molecules bound to the mtSSB. In conclusion, our results indicate that human mtSSB shares many physicochemical properties with EcoSSB and that the differences may be explained by the lack of an acidic, disordered C-terminal tail in human mtSSB protein.
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Affiliation(s)
- Yufeng Qian
- Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas, Austin, Texas 78712
| | - Kenneth A Johnson
- Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas, Austin, Texas 78712.
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12
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Shawon J, Khan AM, Rahman A, Hoque MM, Khan MAK, Sarwar MG, Halim MA. Molecular Recognition of Azelaic Acid and Related Molecules with DNA Polymerase I Investigated by Molecular Modeling Calculations. Interdiscip Sci 2016; 10:525-537. [PMID: 27696206 DOI: 10.1007/s12539-016-0186-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/20/2016] [Accepted: 09/12/2016] [Indexed: 12/18/2022]
Abstract
Molecular recognition has central role on the development of rational drug design. Binding affinity and interactions are two key components which aid to understand the molecular recognition in drug-receptor complex and crucial for structure-based drug design in medicinal chemistry. Herein, we report the binding affinity and the nonbonding interactions of azelaic acid and related compounds with the receptor DNA polymerase I (2KFN). Quantum mechanical calculation was employed to optimize the modified drugs using B3LYP/6-31G(d,p) level of theory. Charge distribution, dipole moment and thermodynamic properties such as electronic energy, enthalpy and free energy of these optimized drugs are also explored to evaluate how modifications impact the drug properties. Molecular docking calculation was performed to evaluate the binding affinity and nonbonding interactions between designed molecules and the receptor protein. We notice that all modified drugs are thermodynamically more stable and some of them are more chemically reactive than the unmodified drug. Promise in enhancing hydrogen bonds is found in case of fluorine-directed modifications as well as in the addition of trifluoroacetyl group. Fluorine participates in forming fluorine bonds and also stimulates alkyl, pi-alkyl interactions in some drugs. Designed drugs revealed increased binding affinity toward 2KFN. A1, A2 and A3 showed binding affinities of -8.7, -8.6 and -7.9 kcal/mol, respectively against 2KFN compared to the binding affinity -6.7 kcal/mol of the parent drug. Significant interactions observed between the drugs and Thr358 and Asp355 residues of 2KFN. Moreover, designed drugs demonstrated improved pharmacokinetic properties. This study disclosed that 9-octadecenoic acid and drugs containing trifluoroacetyl and trifluoromethyl groups are the best 2KFN inhibitors. Overall, these results can be useful for the design of new potential candidates against DNA polymerase I.
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Affiliation(s)
- Jakaria Shawon
- Division of Computer-Aided Drug Design, BICCB, Green Research Centre, 38 Green Road West, Dhaka, 1205, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Akib Mahmud Khan
- Division of Computer-Aided Drug Design, BICCB, Green Research Centre, 38 Green Road West, Dhaka, 1205, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Adhip Rahman
- Division of Computer-Aided Drug Design, BICCB, Green Research Centre, 38 Green Road West, Dhaka, 1205, Bangladesh
| | - Mohammad Mazharol Hoque
- Division of Computer-Aided Drug Design, BICCB, Green Research Centre, 38 Green Road West, Dhaka, 1205, Bangladesh
| | - Mohammad Abdul Kader Khan
- Department of General Studies, Jubail University College, Jubail Industrial City, 31961, Saudi Arabia
| | - Mohammed G Sarwar
- Fakultät für Chemie und Biochemie, Organische Chemie I, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Mohammad A Halim
- Division of Computer-Aided Drug Design, BICCB, Green Research Centre, 38 Green Road West, Dhaka, 1205, Bangladesh.
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France.
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13
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Huang J, Yennie CJ, Delaney S. Klenow Fragment Discriminates against the Incorporation of the Hyperoxidized dGTP Lesion Spiroiminodihydantoin into DNA. Chem Res Toxicol 2015; 28:2325-33. [PMID: 26572218 DOI: 10.1021/acs.chemrestox.5b00330] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Defining the biological consequences of oxidative DNA damage remains an important and ongoing area of investigation. At the foundation of understanding the repercussions of such damage is a molecular-level description of the action of DNA-processing enzymes, such as polymerases. In this work, we focus on a secondary, or hyperoxidized, oxidative lesion of dG that is formed by oxidation of the primary oxidative lesion, 2'-deoxy-8-oxo-7,8-dihydroguanosine (8-oxodG). In particular, we examine incorporation into DNA of the diastereomers of the hyperoxidized guanosine triphosphate lesion spiroiminodihydantoin-2'-deoxynucleoside-5'-triphosphate (dSpTP). Using kinetic parameters, we describe the ability of the Klenow fragment of Escherichia coli DNA polymerase I lacking 3' → 5' exonuclease activity (KF(-)) to utilize (S)-dSpTP and (R)-dSpTP as building blocks during replication. We find that both diastereomers act as covert lesions, similar to a Trojan horse: KF(-) incorporates the lesion dNTP opposite dC, which is a nonmutagenic event; however, during the subsequent replication, it is known that dSp is nearly 100% mutagenic. Nevertheless, using kpol/Kd to define the nucleotide incorporation specificity, we find that the extent of oxidation of the dGTP-derived lesion correlates with its ability to be incorporated into DNA. KF(-) has the highest specificity for incorporation of dGTP opposite dC. The selection factors for incorporating 8-oxodGTP, (S)-dSpTP, and (R)-dSpTP are 1700-, 64000-, and 850000-fold lower, respectively. Thus, KF(-) is rigorous in its discrimination against incorporation of the hyperoxidized lesion, and these results suggest that the specificity of cellular polymerases provides an effective mechanism to avoid incorporating dSpTP lesions into DNA from the nucleotide pool.
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Affiliation(s)
- Ji Huang
- Department of Chemistry, Brown University , Providence, Rhode Island 02912, United States
| | - Craig J Yennie
- Department of Chemistry, Brown University , Providence, Rhode Island 02912, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University , Providence, Rhode Island 02912, United States
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14
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Tsai MD. How DNA polymerases catalyze DNA replication, repair, and mutation. Biochemistry 2014; 53:2749-51. [PMID: 24716436 DOI: 10.1021/bi500417m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica , Nankang, Taipei 115, Taiwan , and Institute of Biochemical Sciences, National Taiwan University , Taipei 106, Taiwan
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15
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Abstract
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This review will summarize our structural
and kinetic studies of
RB69 DNA polymerase (RB69pol) as well as selected variants of the
wild-type enzyme that were undertaken to obtain a deeper understanding
of the exquisitely high fidelity of B family replicative DNA polymerases.
We discuss how the structures of the various RB69pol ternary complexes
can be used to rationalize the results obtained from pre-steady-state
kinetic assays. Our main findings can be summarized as follows. (i)
Interbase hydrogen bond interactions can increase catalytic efficiency
by 5000-fold; meanwhile, base selectivity is not solely determined
by the number of hydrogen bonds between the incoming dNTP and the
templating base. (ii) Minor-groove hydrogen bond interactions at positions n – 1 and n – 2 of the primer
strand and position n – 1 of the template
strand in RB69pol ternary complexes are essential for efficient primer
extension and base selectivity. (iii) Partial charge interactions
among the incoming dNTP, the penultimate base pair, and the hydration
shell surrounding the incoming dNTP modulate nucleotide insertion
efficiency and base selectivity. (iv) Steric clashes between mismatched
incoming dNTPs and templating bases with amino acid side chains in
the nascent base pair binding pocket (NBP) as well as weak interactions
and large gaps between the incoming dNTPs and the templating base
are some of the reasons that incorrect dNTPs are incorporated so inefficiently
by wild-type RB69pol. In addition, we developed a tC°–tCnitro Förster resonance energy transfer assay to monitor
partitioning of the primer terminus between the polymerase and exonuclease
subdomains.
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Affiliation(s)
- Shuangluo Xia
- Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06520-8024, United States
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16
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Egli M. The steric hypothesis for DNA replication and fluorine hydrogen bonding revisited in light of structural data. Acc Chem Res 2012; 45:1237-46. [PMID: 22524491 DOI: 10.1021/ar200303k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In DNA, bases pair in a molecular interaction that is both highly predictable and exquisitely specific. Therefore researchers have generally believed that the insertion of the matching nucleotide opposite a template base by DNA polymerases (pols) required Watson-Crick (W-C) hydrogen bond formation. However pioneering work by Kool and co-workers using hydrophobic base analogs such as the thymine (T) isostere 2,4-difluorotoluene (F) showed that shape rather than H-bonding served as the primary source of specificity in DNA replication by certain pols. This steric hypothesis for DNA replication has gained popularity, perhaps discouraging further experimental studies to address potential limitations of this new idea. The idea that shape trumps H-bonding in terms of pol selectivity largely hinges on the belief that fluorine is a poor H-bond acceptor. However, the shape complementarity model was embraced in the absence of any detailed structural data for match (F:A) and mismatch pairs (F:G, F:C, F:T) in DNA duplexes or at active sites of pols. Although the F and T nucleosides are roughly isosteric, it is unclear whether F:A and T:A pairs exhibit similar geometries. If the F:A pair is devoid of H-bonding, it will be notably wider than a T:A pair. Because shape and size and H-bonding are intimately related, it may not be possible to separate these two properties. Thus the geometries of an isolated F:A pair in water may differ considerably from an F:A pair embedded in a stretch of duplex DNA, at the tight active site of an A-family replicative pol, or within the spacious active site of a Y-family translesion pol. The shape complementarity model may have more significance for pol accuracy than efficiency: this model appears to be most relevant for replicative pols that use specific residues to probe the identity of the nascent base pair from the minor groove side. However, researchers have not fully considered the importance of such interactions that include H-bonds compared with W-C H-bonds in terms of pol fidelity and the shape complementarity model. This Account revisits the steric hypothesis for DNA replication in light of recent structural data and discusses the role of fluorine as an H-bond acceptor. Over the last 5 years, crystal structures have emerged for nucleic acid duplexes with F paired opposite to natural bases or located at the active sites of DNA pols. These data permit a more nuanced understanding of the role of shape in DNA replication and the capacity of fluorine to form H-bonds. These studies and additional research involving RNA or other fluorine-containing nucleoside analogs within duplexes indicate that fluorine engages in H-bonding in many cases. Although T and F are isosteric at the nucleoside level, replacement of a natural base by F in pairs often changes their shapes and sizes, and dF in DNA behaves differently from rF in RNA. Similarly, the pairing geometries observed for F and T opposite dATP, dGTP, dTTP, or dCTP and their H-bonding patterns at the active site of a replicative pol differ considerably.
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
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17
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Kirmizialtin S, Nguyen V, Johnson KA, Elber R. How conformational dynamics of DNA polymerase select correct substrates: experiments and simulations. Structure 2012; 20:618-27. [PMID: 22483109 PMCID: PMC3322391 DOI: 10.1016/j.str.2012.02.018] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 02/21/2012] [Accepted: 02/23/2012] [Indexed: 11/26/2022]
Abstract
Nearly every enzyme undergoes a significant change in structure after binding it's substrate. Experimental and theoretical analyses of the role of changes in HIV reverse transcriptase structure in selecting a correct substrate are presented. Atomically detailed simulations using the Milestoning method predict a rate and free energy profile of the conformational change commensurate with experimental data. A large conformational change occurring on a millisecond timescale locks the correct nucleotide at the active site but promotes release of a mismatched nucleotide. The positions along the reaction coordinate that decide the yield of the reaction are not determined by the chemical step. Rather, the initial steps of weak substrate binding and protein conformational transition significantly enrich the yield of a reaction with a correct substrate, whereas the same steps diminish the reaction probability of an incorrect substrate.
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Affiliation(s)
- Serdal Kirmizialtin
- Department of Chemistry and Biochemistry and Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, 1 University Station, Austin, Texas 78712
| | - Virginia Nguyen
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway, MBB 3.122, Austin, Texas 78712, USA
| | - Kenneth A. Johnson
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway, MBB 3.122, Austin, Texas 78712, USA
| | - Ron Elber
- Department of Chemistry and Biochemistry and Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, 1 University Station, Austin, Texas 78712
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18
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Xia S, Eom SH, Konigsberg WH, Wang J. Structural basis for differential insertion kinetics of dNMPs opposite a difluorotoluene nucleotide residue. Biochemistry 2012; 51:1476-85. [PMID: 22304682 DOI: 10.1021/bi2016487] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We have recently challenged the widely held view that 2,4-difluorotoluene (dF) is a nonpolar isosteric analogue of the nucleotide dT, incapable of forming hydrogen bonds (HBs). To gain a further understanding for the kinetic preference that favors dAMP insertion opposite a templating dF, a result that mirrors the base selectivity that favors dAMP insertion opposite dT by RB69 DNA polymerase (RB69pol), we determined presteady-state kinetic parameters for incorporation of four dNMPs opposite dF by RB69pol and solved the structures of corresponding ternary complexes. We observed that both the F2 and F4 substituent of dF in these structures serve as HB acceptors forming HBs either directly with dTTP and dGTP or indirectly with dATP and dCTP via ordered water molecules. We have defined the shape and chemical features of each dF/dNTP pair in the RB69pol active site without the corresponding phosphodiester-linkage constraints of dF/dNs when they are embedded in isolated DNA duplexes. These features can explain the kinetic preferences exhibited by the templating dF when the nucleotide incorporation is catalyzed by wild type RB69pol or its mutants. We further show that the shapes of the dNTP/dF nascent base pair differ markedly from the corresponding dNTP/dT in the pol active site and that these differences have a profound effect on their incorporation efficiencies.
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Affiliation(s)
- Shuangluo Xia
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, United States
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19
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Abstract
Evolution balances DNA replication speed and accuracy to optimize replicative fitness and genetic stability. There is no selective pressure to improve DNA replication fidelity beyond the background mutation rate from other sources, such as DNA damage. However, DNA polymerases remain amenable to amino acid substitutions that lower intrinsic error rates. Here, we review these 'antimutagenic' changes in DNA polymerases and discuss what they reveal about mechanisms of replication fidelity. Pioneering studies with bacteriophage T4 DNA polymerase (T4 Pol) established the paradigm that antimutator amino acid substitutions reduce replication errors by increasing proofreading efficiency at the expense of polymerase processivity. The discoveries of antimutator substitutions in proofreading-deficient 'mutator' derivatives of bacterial Pols I and III and yeast Pol δ suggest there must be additional antimutagenic mechanisms. Remarkably, many of the affected amino acid positions from Pol I, Pol III, and Pol δ are similar to the original T4 Pol substitutions. The locations of antimutator substitutions within DNA polymerase structures suggest that they may increase nucleotide selectivity and/or promote dissociation of primer termini from polymerases poised for misincorporation, leading to expulsion of incorrect nucleotides. If misincorporation occurs, enhanced primer dissociation from polymerase domains may improve proofreading in cis by an intrinsic exonuclease or in trans by alternate cellular proofreading activities. Together, these studies reveal that natural selection can readily restore replication error rates to sustainable levels following an adaptive mutator phenotype.
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Affiliation(s)
- Alan J Herr
- Department of Pathology, University of Washington, Seattle, USA
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20
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Euro L, Farnum GA, Palin E, Suomalainen A, Kaguni LS. Clustering of Alpers disease mutations and catalytic defects in biochemical variants reveal new features of molecular mechanism of the human mitochondrial replicase, Pol γ. Nucleic Acids Res 2011; 39:9072-84. [PMID: 21824913 PMCID: PMC3241644 DOI: 10.1093/nar/gkr618] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mutations in Pol γ represent a major cause of human mitochondrial diseases, especially those affecting the nervous system in adults and in children. Recessive mutations in Pol γ represent nearly half of those reported to date, and they are nearly uniformly distributed along the length of the POLG1 gene (Human DNA Polymerase gamma Mutation Database); the majority of them are linked to the most severe form of POLG syndrome, Alpers–Huttenlocher syndrome. In this report, we assess the structure–function relationships for recessive disease mutations by reviewing existing biochemical data on site-directed mutagenesis of the human, Drosophila and yeast Pol γs, and their homologs from the family A DNA polymerase group. We do so in the context of a molecular model of Pol γ in complex with primer–template DNA, which we have developed based upon the recently solved crystal structure of the apoenzyme form. We present evidence that recessive mutations cluster within five distinct functional modules in the catalytic core of Pol γ. Our results suggest that cluster prediction can be used as a diagnosis-supporting tool to evaluate the pathogenic role of new Pol γ variants.
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Affiliation(s)
- Liliya Euro
- Research Programs Unit, Molecular Neurology, Biomedicum-Helsinki, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
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21
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Lund TJ, Cavanaugh NA, Joubert N, Urban M, Patro JN, Hocek M, Kuchta RD. B family DNA polymerases asymmetrically recognize pyrimidines and purines. Biochemistry 2011; 50:7243-50. [PMID: 21761848 DOI: 10.1021/bi2006916] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We utilized a series of pyrimidine analogues modified at O(2), N-3, and N(4)/O(4) to determine if two B family DNA polymerases, human DNA polymerase α and herpes simplex virus I DNA polymerase, choose whether to polymerize pyrimidine dNTPs using the same mechanisms they use for purine dNTPs. Removing O(2) of a pyrimidine dNTP vastly decreased the level of incorporation by these enzymes and also compromised fidelity in the case of C analogues, while removing O(2) from the templating base had more modest effects. Removing the Watson-Crick hydrogen bonding groups of N-3 and N(4)/O(4) greatly impaired polymerization, both of the resulting dNTP analogues and of natural dNTPs opposite these pyrimidine analogues when present in the template strand. Thus, the Watson-Crick hydrogen bonding groups of a pyrimidine clearly play an important role in enhancing correct dNTP polymerization but are not essential for preventing misincorporation. These studies also indicate that DNA polymerases recognize bases extremely asymmetrically, both in terms of whether they are a purine or pyrimidine and whether they are in the template or are the incoming dNTP. The mechanistic implications of these results with regard to how polymerases discriminate between right and wrong dNTPs are discussed.
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Affiliation(s)
- Travis J Lund
- Department of Chemistry and Biochemistry, University of Colorado, UCB 215, Boulder, Colorado 80309, USA
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22
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Xia S, Konigsberg WH, Wang J. Hydrogen-bonding capability of a templating difluorotoluene nucleotide residue in an RB69 DNA polymerase ternary complex. J Am Chem Soc 2011; 133:10003-5. [PMID: 21667997 DOI: 10.1021/ja2021735] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Results obtained using 2,4-difluorotoluene nucleobase (dF) as a nonpolar thymine isostere by Kool and colleagues challenged the Watson-Crick dogma that hydrogen bonds between complementary bases are an absolute requirement for accurate DNA replication. Here, we report crystal structure of an RB69 DNA polymerase L561A/S565G/Y567A triple mutant ternary complex with a templating dF opposite dTTP at 1.8 Å-resolution. In this structure, direct hydrogen bonds were observed between: (i) dF and the incoming dTTP, (ii) dF and residue G568 of the polymerase, and (iii) dF and ordered water molecules surrounding the nascent base pair. Therefore, this structure provides evidence that a templating dF can form novel hydrogen bonds with the incoming dTTP and with the enzyme that differ from those formed with a templating dT.
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Affiliation(s)
- Shuangluo Xia
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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23
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Pre-steady-state kinetic analysis of the incorporation of anti-HIV nucleotide analogs catalyzed by human X- and Y-family DNA polymerases. Antimicrob Agents Chemother 2010; 55:276-83. [PMID: 21078938 DOI: 10.1128/aac.01229-10] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nucleoside reverse transcriptase inhibitors (NRTIs) are an important class of antiviral drugs used to manage infections by human immunodeficiency virus, which causes AIDS. Unfortunately, these drugs cause unwanted side effects, and the molecular basis of NRTI toxicity is not fully understood. Putative routes of NRTI toxicity include the inhibition of human nuclear and mitochondrial DNA polymerases. A strong correlation between mitochondrial toxicity and NRTI incorporation catalyzed by human mitochondrial DNA polymerase has been established both in vitro and in vivo. However, it remains to be determined whether NRTIs are substrates for the recently discovered human X- and Y-family DNA polymerases, which participate in DNA repair and DNA lesion bypass in vivo. Using pre-steady-state kinetic techniques, we measured the substrate specificity constants for human DNA polymerases β, λ, η, ι, κ, and Rev1 incorporating the active, 5'-phosphorylated forms of tenofovir, lamivudine, emtricitabine, and zidovudine. For the six enzymes, all of the drug analogs were incorporated less efficiently (40- to >110,000-fold) than the corresponding natural nucleotides, usually due to a weaker binding affinity and a slower rate of incorporation for the incoming nucleotide analog. In general, the 5'-triphosphate forms of lamivudine and zidovudine were better substrates than emtricitabine and tenofovir for the six human enzymes, although the substrate specificity profile depended on the DNA polymerase. Our kinetic results suggest NRTI insertion catalyzed by human X- and Y-family DNA polymerases is a potential mechanism of NRTI drug toxicity, and we have established a structure-function relationship for designing improved NRTIs.
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24
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Brown JA, Pack LR, Sherrer SM, Kshetry AK, Newmister SA, Fowler JD, Taylor JS, Suo Z. Identification of critical residues for the tight binding of both correct and incorrect nucleotides to human DNA polymerase λ. J Mol Biol 2010; 403:505-15. [PMID: 20851705 DOI: 10.1016/j.jmb.2010.09.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 08/31/2010] [Accepted: 09/08/2010] [Indexed: 10/19/2022]
Abstract
DNA polymerase λ (Pol λ) is a novel X-family DNA polymerase that shares 34% sequence identity with DNA polymerase β. Pre-steady-state kinetic studies have shown that the Pol λ-DNA complex binds both correct and incorrect nucleotides 130-fold tighter, on average, than the DNA polymerase β-DNA complex, although the base substitution fidelity of both polymerases is 10(-)(4) to 10(-5). To better understand Pol λ's tight nucleotide binding affinity, we created single-substitution and double-substitution mutants of Pol λ to disrupt the interactions between active-site residues and an incoming nucleotide or a template base. Single-turnover kinetic assays showed that Pol λ binds to an incoming nucleotide via cooperative interactions with active-site residues (R386, R420, K422, Y505, F506, A510, and R514). Disrupting protein interactions with an incoming correct or incorrect nucleotide impacted binding to each of the common structural moieties in the following order: triphosphate≫base>ribose. In addition, the loss of Watson-Crick hydrogen bonding between the nucleotide and the template base led to a moderate increase in K(d). The fidelity of Pol λ was maintained predominantly by a single residue, R517, which has minor groove interactions with the DNA template.
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Affiliation(s)
- Jessica A Brown
- Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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25
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Ding H, Greenberg MM. DNA damage and interstrand cross-link formation upon irradiation of aryl iodide C-nucleotide analogues. J Org Chem 2010; 75:535-44. [PMID: 20067226 PMCID: PMC2813935 DOI: 10.1021/jo902071y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The 5-halopyrimidine nucleotides damage DNA upon UV-irradiation or exposure to gamma-radiolysis via the formation of the 2'-deoxyuridin-5-yl sigma-radical. The bromo and iodo derivatives of these molecules are useful tools for probing DNA structure and as therapeutically useful radiosensitizing agents. A series of aryl iodide C-nucleotides were incorporated into synthetic oligonucleotides and exposed to UV-irradiation and gamma-radiolysis. The strand damage produced upon irradiation of DNA containing these molecules is consistent with the generation of highly reactive sigma-radicals. Direct stand breaks and alkali-labile lesions are formed at the nucleotide analogue and flanking nucleotides. The distribution of lesion type and location varies depending upon the position of the aryl ring that is iodinated. Unlike 5-halopyrimidine nucleotides, the aryl iodides produce interstrand cross-links in duplex regions of DNA when exposed to gamma-radiolysis or UV-irradiation. Quenching studies suggest that cross-links are produced by gamma-radiolysis via capture of a solvated electron, and subsequent fragmentation to the sigma-radical. These observations suggest that aryl iodide C-nucleotide analogues may be useful as probes for excess electron transfer and radiosensitizing agents.
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Affiliation(s)
- Hui Ding
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA
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26
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Johnson KA. The kinetic and chemical mechanism of high-fidelity DNA polymerases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1041-8. [PMID: 20079883 DOI: 10.1016/j.bbapap.2010.01.006] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2009] [Revised: 12/15/2009] [Accepted: 01/04/2010] [Indexed: 10/19/2022]
Abstract
This review summarizes our current understanding of the structural, kinetic and thermodynamic basis for the extraordinary accuracy of high-fidelity DNA polymerases. High-fidelity DNA polymerases, such as the enzyme responsible for the replication of bacteriophage T7 DNA, discriminate against similar substrates with an accuracy that approaches one error in a million base pairs while copying DNA at a rate of approximately 300 base pairs per second. When the polymerase does make an error, it stalls, giving time for the slower proofreading exonuclease to remove the mismatch so that the overall error frequency approaches one in a billion. Structural analysis reveals a large change in conformation after nucleotide binding from an open to a closed state. Kinetic analysis has shown that the substrate-induced structural change plays a key role in the discrimination between correct and incorrect base pairs by governing whether a nucleotide will be retained and incorporated or rapidly released.
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Affiliation(s)
- Kenneth A Johnson
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas, 2500 Speedway, Austin, TX 78712, USA.
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27
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Kuchta RD. Nucleotide Analogues as Probes for DNA and RNA Polymerases. CURRENT PROTOCOLS IN CHEMICAL BIOLOGY 2010; 2:111-124. [PMID: 21822500 PMCID: PMC3149870 DOI: 10.1002/9780470559277.ch090203] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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 straight-forward, a key issue is to appropriately design the studies to answer the mechanistic question of interest. This article addresses the major issues involved in designing these studies, and some of the potential difficulties that arise in interpreting the data. Examples are given both of the type of analogues typically used, the experimental approaches with different polymerases, and issues with data interpretation.
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Affiliation(s)
- Robert D Kuchta
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309
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28
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Urban M, Joubert N, Hocek M, Alexander RE, Kuchta RD. Herpes simplex virus-1 DNA primase: a remarkably inaccurate yet selective polymerase. Biochemistry 2009; 48:10866-81. [PMID: 19835416 DOI: 10.1021/bi901476k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Herpes simplex virus-1 primase misincorporates the natural NTPs at frequencies of around one error per 30 NTPs polymerized, making it one of the least accurate polymerases known. We used a series of nucleotide analogues to further test the hypothesis that primase requires Watson-Crick hydrogen bond formation to efficiently polymerize a NTP. Primase could not generate base pairs containing a complete set of hydrogen bonds in an altered arrangement (isoguanine.isocytosine) and did not efficiently polymerize dNTPs completely incapable of forming Watson-Crick hydrogen bonds opposite templating bases incapable of forming Watson-Crick hydrogen bonds. Similarly, primase did not incorporate most NTPs containing hydrophobic bases incapable of Watson-Crick hydrogen bonding opposite natural template bases. However, 2-pyridone NTP and 4-methyl-2-pyridone NTP provided striking exceptions to this rule. The effects of removing single Watson-Crick hydrogen bonding groups from either the NTP or templating bases varied from almost no effect to completely blocking polymerization depending both on the parental base pair (G.C vs A.T/U) and which base pair of the growing primer (second, third, or fourth) was examined. Thus, primase does not absolutely need to form Watson-Crick hydrogen bonds to efficiently polymerize a NTP. Additionally, we found that herpes primase can misincorporate nucleotides both by misreading the template and by a primer-template slippage mechanism. The mechanistic and biological implications of these results are discussed.
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Affiliation(s)
- Milan Urban
- Department of Chemistry and Biochemistry, University of Colorado, UCB 215, Boulder, Colorado 80309, USA
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29
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Affiliation(s)
- Michal Hocek
- Department of Chemistry, WestChem, University of Glasgow, Glasgow G12 8QQ, United Kingdom, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, CZ-16610 Prague 6, Czech Republic
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30
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Heshmati E, Abdolmaleki P, Mozdarani H, Sarvestani AS. Effects of halogen substitution on Watson–Crick base pairing: A possible mechanism for radiosensitivity. Bioorg Med Chem Lett 2009; 19:5256-60. [DOI: 10.1016/j.bmcl.2009.06.105] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Revised: 05/21/2009] [Accepted: 06/18/2009] [Indexed: 11/15/2022]
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31
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Trostler M, Delier A, Beckman J, Urban M, Patro JN, Spratt TE, Beese LS, Kuchta RD. Discrimination between right and wrong purine dNTPs by DNA polymerase I from Bacillus stearothermophilus. Biochemistry 2009; 48:4633-41. [PMID: 19348507 DOI: 10.1021/bi900104n] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We used a series of dATP and dGTP analogues to determine how DNA polymerase I from Bacillus stearothermophilus (BF), a prototypical A family polymerase, uses N-1, N(2), N-3, and N(6) of purine dNTPs to differentiate between right and wrong nucleotide incorporation. Altering any of these nitrogens had two effects. First, it decreased the efficiency of correct incorporation of the resulting dNTP analogue, with the loss of N-1 and N-3 having the most severe effects. Second, it dramatically increased the rate of misincorporation of the resulting dNTP analogues, with alterations in either N-1 or N(6) having the most severe impacts. Adding N(2) to dNTPs containing the bases adenine and purine increased the degree of polymerization opposite T but also tremendously increased the degree of misincorporation opposite A, C, and G. Thus, BF uses N-1, N(2), N-3, and N(6) of purine dNTPs both as negative selectors to prevent misincorporation and as positive selectors to enhance correct incorporation. Comparing how BF discriminates between right and wrong dNTPs with both B family polymerases and low-fidelity polymerases indicates that BF has chosen a unique solution vis-a-vis these other enzymes and, therefore, that nature has evolved at least three mechanistically distinct solutions.
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Affiliation(s)
- Michael Trostler
- Department of Chemistry and Biochemistry, University of Colorado, UCB 215, Boulder, Colorado 80309, USA
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32
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Zhang H, Eoff RL, Kozekov ID, Rizzo CJ, Egli M, Guengerich FP. Structure-function relationships in miscoding by Sulfolobus solfataricus DNA polymerase Dpo4: guanine N2,N2-dimethyl substitution produces inactive and miscoding polymerase complexes. J Biol Chem 2009; 284:17687-99. [PMID: 19542237 DOI: 10.1074/jbc.m109014274] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Previous work has shown that Y-family DNA polymerases tolerate large DNA adducts, but a substantial decrease in catalytic efficiency and fidelity occurs during bypass of N2,N2-dimethyl (Me2)-substituted guanine (N2,N2-Me2G), in contrast to a single methyl substitution. Therefore, it is unclear why the addition of two methyl groups is so disruptive. The presence of N2,N2-Me2G lowered the catalytic efficiency of the model enzyme Sulfolobus solfataricus Dpo4 16,000-fold. Dpo4 inserted dNTPs almost at random during bypass of N2,N2-Me2G, and much of the enzyme was kinetically trapped by an inactive ternary complex when N2,N2-Me2G was present, as judged by a reduced burst amplitude (5% of total enzyme) and kinetic modeling. One crystal structure of Dpo4 with a primer having a 3'-terminal dideoxycytosine (Cdd) opposite template N2,N2-Me2G in a post-insertion position showed Cdd folded back into the minor groove, as a catalytically incompetent complex. A second crystal had two unique orientations for the primer terminal Cdd as follows: (i) flipped into the minor groove and (ii) a long pairing with N2,N2-Me2G in which one hydrogen bond exists between the O-2 atom of Cdd and the N-1 atom of N2,N2-Me2G, with a second water-mediated hydrogen bond between the N-3 atom of Cdd and the O-6 atom of N2,N2-Me2G. A crystal structure of Dpo4 with dTTP opposite template N2,N2-Me2G revealed a wobble orientation. Collectively, these results explain, in a detailed manner, the basis for the reduced efficiency and fidelity of Dpo4-catalyzed bypass of N2,N2-Me2G compared with mono-substituted N2-alkyl G adducts.
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Affiliation(s)
- Huidong Zhang
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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Zhang H, Beckman J, Wang J, Konigsberg W. RB69 DNA polymerase mutants with expanded nascent base-pair-binding pockets are highly efficient but have reduced base selectivity. Biochemistry 2009; 48:6940-50. [PMID: 19522539 DOI: 10.1021/bi900422b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have investigated the effect of systematically enlarging the nascent base-pair-binding pocket (NBP) of a replicative DNA polymerase from bacteriophage RB69 (RB69 pol) on the incorporation efficiency (k(pol)/K(d,app)) for both correct and incorrect dNMPs. Accordingly, we replaced residues L561, Y567, and S565 in the NBP with Ala, Ala, and Gly, respectively. We combined L561A and Y567A to give a double mutant and then introduced the S565G mutation to give a triple mutant. The efficiency of incorrect dNMP insertion increased markedly relative to the wild type with the single mutants and increased further as the number of substitutions in the NBP increased. The difference in incorporation efficiency for mispairs between the mutants and the wild-type RB69 pol was due mainly to k(pol). Unexpectedly, enlarging the NBP had a minimal effect on the incorporation efficiency of correct dNMPs. Our kinetic data suggest that replicative DNA pols exert base discrimination via "negative selection" against mispairs by using residues in the NBP, particularly the three residues analyzed in this study, to allow rapid incorporation of only correct base pairs. This proposal differs from how geometry and "tightness of fit" of the NBP is often invoked to account for rapid incorporation of correct base pairs, namely, that a tighter fit within the NBP leads to an increase in insertion rates [Kool, E. T. (2002) Annu. Rev. Biochem. 71, 191-219]. We related our findings to that of a model translesion DNA pol, Sulfolobus solfataricus Dpo4. We concur with the main conclusion of a previous study [Mizukami, S., et al. (2006) Biochemistry 45, 2772-2778], namely, that lesion bypass pols exhibit low incorporation efficiencies for correct dNMPs (leading to relative promiscuity) not because of a more open NBP but because of a loose fit of substrates bound in the catalytic centers. This is a property not shared by RB69 pol and its mutants.
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Affiliation(s)
- Hong Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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Choi JY, Lim S, Eoff RL, Guengerich FP. Kinetic analysis of base-pairing preference for nucleotide incorporation opposite template pyrimidines by human DNA polymerase iota. J Mol Biol 2009; 389:264-74. [PMID: 19376129 PMCID: PMC4010588 DOI: 10.1016/j.jmb.2009.04.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2009] [Revised: 03/31/2009] [Accepted: 04/09/2009] [Indexed: 10/20/2022]
Abstract
DNA polymerase (pol) iota, a member of the mammalian Y-family of DNA polymerases involved in translesion DNA synthesis, has been previously suggested to peculiarly utilize Hoogsteen base pairing for DNA synthesis opposite template purines, unlike pols eta and kappa, which utilize Watson-Crick (W-C) base pairing. To investigate the possible roles of Hoogsteen, W-C, and wobble base-pairing modes in the selection of nucleotides opposite template pyrimidines by human pol iota, we carried out kinetic analyses of incorporation of modified purine nucleoside triphosphates including 7-deazapurines, inosine, 2-aminopurine, 2,6-diaminopurine, and 6-chloropurine, which affect H-bonding in base-pair formation opposite template pyrimidines. Carbon substitution at the N7 atom of purine nucleoside triphosphates, which disrupts Hoogsteen base pairing, only slightly inhibited DNA synthesis opposite template pyrimidines by pol iota, which was not substantially different from human pols eta and kappa. Opposite template T, only the relative wobble stabilities (inferred from the potential numbers of H-bonding, steric, and electrostatic interactions but not measured) of base pairs were positively correlated to the relative efficiencies of nucleotide incorporation by pol iota but not the relative W-C or Hoogsteen stabilities, unlike pols eta and kappa. In contrast, opposite C, only the relative W-C stabilities of base pairs were positively correlated to the relative efficiencies of nucleotide incorporation by pol iota, as with pols eta and kappa. These results suggest that pol iota might not indispensably require Hoogsteen base pairing for DNA synthesis opposite pyrimidines but rather might prefer wobble base pairing in the selection of nucleotides opposite T and W-C base pairing opposite C.
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Affiliation(s)
- Jeong-Yun Choi
- Department of Pharmacology, School of Medicine, Ewha Womans University, 911-1, Mok-6-dong, Yangcheon-gu, Seoul 158-710, Republic of Korea.
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Zhang H, Eoff RL, Kozekov ID, Rizzo CJ, Egli M, Guengerich FP. Structure-Function Relationships in Miscoding by Sulfolobus solfataricus DNA Polymerase Dpo4. J Biol Chem 2009. [DOI: 10.1074/jbc.m109.014274] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Krueger AT, Kool ET. Redesigning the architecture of the base pair: toward biochemical and biological function of new genetic sets. ACTA ACUST UNITED AC 2009; 16:242-8. [PMID: 19318205 DOI: 10.1016/j.chembiol.2008.12.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Revised: 12/04/2008] [Accepted: 12/04/2008] [Indexed: 11/16/2022]
Abstract
Recognition of the nucleic acid bases within the DNA scaffold comprises the basis for transmission of genetic information, dictating protein and cell assembly, organismal development, and evolution. Driven in part by the need to test our current understanding of this information transfer, chemists have begun to design and synthesize nonnatural bases and base pair structures to mimic the function of DNA without relying on Nature's purine-pyrimidine base pair scaffold. Multiple examples have been recently described that self-assemble stably and sequence specifically in vitro, and some isolated unnatural base pairs can be replicated in vitro as well. Moreover, recent experiments with unnatural bases in bacterial cells have demonstrated surprisingly efficient reading of the chemical information. This suggests the future possibility of redesigning and replacing the chemical information of an evolving cell while retaining biological function.
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Affiliation(s)
- Andrew T Krueger
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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Lee HR, Helquist SA, Kool ET, Johnson KA. Base pair hydrogen bonds are essential for proofreading selectivity by the human mitochondrial DNA polymerase. J Biol Chem 2007; 283:14411-6. [PMID: 17650503 PMCID: PMC2386942 DOI: 10.1074/jbc.m705006200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have characterized the role of Watson-Crick hydrogen bonding in the 3'-terminal base pair on the 3'-5' exonuclease activity of the human mitochondrial DNA polymerase. Nonpolar nucleoside analogs of thymidine (dF) and deoxyadenosine (dQ) were used to eliminate hydrogen bonds while maintaining base pair size and shape. Exonuclease reactions were examined using pre-steady state kinetic methods. The time dependence of removal of natural nucleotides from the primer terminus paired opposite the nonpolar analogs dF and dQ were best fit to a double exponential function. The double exponential kinetics as well as the rates of excision (3-6 s(-1) fast phase, 0.16-0.3 s(-1) slow phase) are comparable with those observed during mismatch removal of natural nucleotides even when the analog was involved in a sterically correct base pair. Additionally, incorporation of the next correct base beyond a nonpolar analog was slow (0.04-0.22 s(-1)), so that more than 95% of terminal base pairs were removed rather than extended. The polymerase responds to all 3'-terminal base pairs containing a nonpolar analog as if it were a mismatch regardless of the identity of the paired base, and kinetic partitioning between polymerase and exonuclease sites failed to discriminate between correct and incorrect base pairs. Thus, sterics alone are insufficient, whereas hydrogen bond formation is essential for proper proofreading selectivity by the mitochondrial polymerase. The enzyme may use the alignment and prevention of fraying provided by proper hydrogen bonding and minor groove hydrogen bonding interactions as critical criteria for correct base pair recognition.
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Affiliation(s)
- Harold R Lee
- Department of Chemistry and Biochemistry, Institute of Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
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