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DNA Replication WATOC 2011

J
jordipoater

This study uses quantum chemical modeling to analyze the selectivity of DNA replication through hydrogen bonding, -stacking, and solvation effects. The researchers modeled the formation of Watson-Crick base pairs in the presence of another stacked pair, both in vacuum and in solution. They found that in vacuum, some mismatched pairs had higher affinity than correct pairs, but solvation corrected this by weakening incorrect interactions more. Hydrogen bonding patterns and solvent effects mainly drive selectivity, while stacking provides overall stability. A primer strand with a purine terminus also interacts more favorably with incoming nucleotides.

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Analysis of the Selectivity in the DNA Replication Mechanism through Solvation, -Stacking and Hydrogen Bonding Effects J. Poater, M. Swart, C. Fonseca Guerra, F. M. Bickelhaupt
DNA Replication ≒ DNA replication is at the core of life. ≒ Despite groundbreaking studies, this complex biochemical process is still incompletely understood. ≒ High fidelity with which DNA replication occurs. Specificity of the hydrogen-bonding interactions in the Watson-Crick AT and GC. Steric-shape complementarity of DNA bases and fit into active-site pocket of the DNA polymerase. Solvent effects and - stacking.
Objectives of this work ≒ We aim at uncovering and quantifying the effects on DNA replication of (de)solvation, - stacking and hydrogen bonding. Our model system: Thermochemistry analysis of the formation of a Watson-Crick base pair in the presence of another -stacked base pair in vacuo and in solution. And selectivity of the primer strand to form the W-C base pair instead of mismatched pair without enzyme. J. Poater, M. Swart, C. Fonseca-Guerra, F. M. Bickelhaupt, Chem. Commun.2011, 47, 7326-7328
Objectives of this work ≒ This is the first high-level quantum chemical study on DNA replication covering not only the formation of DNA base pairs but also - stacking interactions in a model system consisting of four DNA bases. ≒ Investigations on chemical primer extension, both computational (this work) and experimental, are relevant also for understanding the role of polymerase because they reveal how replication fidelity is affected in the absence of the enzyme. J. Poater, M. Swart, C. Fonseca-Guerra, F. M. Bickelhaupt, Chem. Commun.2011, 47, 7326-7328
Computational details ≒ ADF software package ≒ BP86-D/TZ2P level of theory ≒ Continuum solvation model: COSMO (takes effectively into account cavitation, internal energy and entropy effects of the solvent and yields an estimate of the Gibbs free energies )
Incoming nucleotide selectivity
H ≒ X + Y1/Z-Y2 X-Y1/Z-Y2 N with X = A, T, G, C and F; and Y1/Z-Y2 = A/T-A, T/A-T, G/C-G H N TW and C/G-C.
≒ In the gas phase, both G and C have a pronouncedly higher affinity for the correct Watson-Crick counterpart.
≒ Instead, both A and T have a higher affinity in the gas phase to form hydrogen-bonded mismatches with G. Although this is corrected in solvation.
≒ Solvation leads to a general reduction of all affinities. Note however that this weakening is more pronounced for the G-C than for the A-T pair.
≒ Stacking interactions appear to be important for the strength of the affinity of the template-primer complex but less so for the selectivity.
≒ Only after including solvent effects, all primer-template complexes have the highest affinity for forming WC pairs a not mismatches.
≒ Only in one case, there is a mismatch that is slightly more favorable than a Wa t s o n - C r i c k p a i r, n a m e l y, t h e formation of A-rA in A-rA/A-T instead of the correct A-T/A-T.
≒ "nearest neighbor" effect: the affinity of the primer-template complex for the correct incoming DNA base depends on which DNA base is situated at the terminal position of the primer strand.
≒ The twist slightly stabilizes most of the affinities but, more importantly, this twist is necessary for shifting the preference of Y1 = A in Y1/Z-Y2 from the incorrect G to the correct incoming base T.
≒ The apolar isoster of T that has been experimentally found by Kool et al. to correctly incorporate into template- primer complexes, forming A-F pairs, in the presence of DNA polymerase.
≒ COSMO simulations do not account for intrinsic thermal and entropy effects stemming from the model systems.
Conclusions ≒ The intrinsic affinity (i.e., in the absence of an enzyme) of the template-primer complex to select the correct natural DNA base derives from the cooperative action of hydrogen-bonding patterns and solvent effects. ≒ Stacking interactions play a less pronounced role for the selectivity but they are important for the overall stability. ≒ A primer strand with a purine terminus interacts more favorably with an incoming nucleotide than a primer strand with a pyrimidine base. ≒ The correct incorporation of nonpolar isosters, e.g., 1,3- difluorotoluene (F, an isoster of T), can not be explained without invoking an additional mechanism, such as, steric fit of the new base pair into the polymerase active-site pocket. J. Poater, M. Swart, C. Fonseca-Guerra, F. M. Bickelhaupt, Chem. Commun.2011, 47, 7326-7328
Acknowledgments M. Swart C. Fonseca-Guerra F.M. Bickelhaupt
http://iqc.udg.edu/xgironaseminar

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DNA Replication WATOC 2011

  • 1. Analysis of the Selectivity in the DNA Replication Mechanism through Solvation, -Stacking and Hydrogen Bonding Effects J. Poater, M. Swart, C. Fonseca Guerra, F. M. Bickelhaupt
  • 2. DNA Replication ≒ DNA replication is at the core of life. ≒ Despite groundbreaking studies, this complex biochemical process is still incompletely understood. ≒ High fidelity with which DNA replication occurs. Specificity of the hydrogen-bonding interactions in the Watson-Crick AT and GC. Steric-shape complementarity of DNA bases and fit into active-site pocket of the DNA polymerase. Solvent effects and - stacking.
  • 3. Objectives of this work ≒ We aim at uncovering and quantifying the effects on DNA replication of (de)solvation, - stacking and hydrogen bonding. Our model system: Thermochemistry analysis of the formation of a Watson-Crick base pair in the presence of another -stacked base pair in vacuo and in solution. And selectivity of the primer strand to form the W-C base pair instead of mismatched pair without enzyme. J. Poater, M. Swart, C. Fonseca-Guerra, F. M. Bickelhaupt, Chem. Commun.2011, 47, 7326-7328
  • 4. Objectives of this work ≒ This is the first high-level quantum chemical study on DNA replication covering not only the formation of DNA base pairs but also - stacking interactions in a model system consisting of four DNA bases. ≒ Investigations on chemical primer extension, both computational (this work) and experimental, are relevant also for understanding the role of polymerase because they reveal how replication fidelity is affected in the absence of the enzyme. J. Poater, M. Swart, C. Fonseca-Guerra, F. M. Bickelhaupt, Chem. Commun.2011, 47, 7326-7328
  • 5. Computational details ≒ ADF software package ≒ BP86-D/TZ2P level of theory ≒ Continuum solvation model: COSMO (takes effectively into account cavitation, internal energy and entropy effects of the solvent and yields an estimate of the Gibbs free energies )
  • 7. H ≒ X + Y1/Z-Y2 X-Y1/Z-Y2 N with X = A, T, G, C and F; and Y1/Z-Y2 = A/T-A, T/A-T, G/C-G H N TW and C/G-C.
  • 8. ≒ In the gas phase, both G and C have a pronouncedly higher affinity for the correct Watson-Crick counterpart.
  • 9. ≒ Instead, both A and T have a higher affinity in the gas phase to form hydrogen-bonded mismatches with G. Although this is corrected in solvation.
  • 10. ≒ Solvation leads to a general reduction of all affinities. Note however that this weakening is more pronounced for the G-C than for the A-T pair.
  • 11. ≒ Stacking interactions appear to be important for the strength of the affinity of the template-primer complex but less so for the selectivity.
  • 12. ≒ Only after including solvent effects, all primer-template complexes have the highest affinity for forming WC pairs a not mismatches.
  • 13. ≒ Only in one case, there is a mismatch that is slightly more favorable than a Wa t s o n - C r i c k p a i r, n a m e l y, t h e formation of A-rA in A-rA/A-T instead of the correct A-T/A-T.
  • 14. ≒ "nearest neighbor" effect: the affinity of the primer-template complex for the correct incoming DNA base depends on which DNA base is situated at the terminal position of the primer strand.
  • 15. ≒ The twist slightly stabilizes most of the affinities but, more importantly, this twist is necessary for shifting the preference of Y1 = A in Y1/Z-Y2 from the incorrect G to the correct incoming base T.
  • 16. ≒ The apolar isoster of T that has been experimentally found by Kool et al. to correctly incorporate into template- primer complexes, forming A-F pairs, in the presence of DNA polymerase.
  • 17. ≒ COSMO simulations do not account for intrinsic thermal and entropy effects stemming from the model systems.
  • 18. Conclusions ≒ The intrinsic affinity (i.e., in the absence of an enzyme) of the template-primer complex to select the correct natural DNA base derives from the cooperative action of hydrogen-bonding patterns and solvent effects. ≒ Stacking interactions play a less pronounced role for the selectivity but they are important for the overall stability. ≒ A primer strand with a purine terminus interacts more favorably with an incoming nucleotide than a primer strand with a pyrimidine base. ≒ The correct incorporation of nonpolar isosters, e.g., 1,3- difluorotoluene (F, an isoster of T), can not be explained without invoking an additional mechanism, such as, steric fit of the new base pair into the polymerase active-site pocket. J. Poater, M. Swart, C. Fonseca-Guerra, F. M. Bickelhaupt, Chem. Commun.2011, 47, 7326-7328
  • 19. Acknowledgments M. Swart C. Fonseca-Guerra F.M. Bickelhaupt