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Thermodynamic Properties of Model DNA

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Coarse-Grained Modelling of DNA and DNA Self-Assembly

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Abstract

The attractive stacking interaction between adjacent bases causes single strands to form helical stacks at low temperature, with this order being disrupted as the temperature increases. The literature is divided on both the nature of the attraction and the thermodynamics of the transition. The relative contributions of van der Waals, induced dipole, hydrophobic and permanent polar/electrostatic interactions remain unclear.

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Notes

  1. 1.

    Bases were counted as stacked if their stacking interaction was less than \(-0.1\) reduced units, or approximately \(-0.60\)  kcal mol\(^{-1}\) (relative to a typical stacked interaction of \(-6\)  kcal mol\(^{-1}\)). Adjusting the cutoff to \(-1.2 \)  kcal mol\(^{-1}\) had a negligible effect.

  2. 2.

    Simulations are performed in the canonical ensemble, and hence should be described in terms of energy and entropy changes. I assume that, as dilute DNA strands contribute a very small partial pressure, discrepancies between constant volume and constant pressure results are small: we therefore use the term ‘enthalpy’ to describe what are in fact energies in the model, for consistency with experimental literature.

  3. 3.

    Averaging over the parameters of Ref. [20] gives an extremely convenient metric for comparison. An alternative approach (at least for the purposes of comparing \(T_m\)) would be to average over the \(T_m\) of all possible sequences. This second method gives results which are approximately 0.5 K lower for a 5 bp duplex and quickly converges on the first as duplex size increases.

  4. 4.

    Simulations of duplexes with more than 12 bp necessitated using a larger periodic cell, and hence a lower concentration. The fraction of bound duplexes was scaled to the higher concentration assuming the separate species are approximately ideal, as justified in Chap. 4. Extrapolation to a range of temperatures was performed using single histogram re-weighting: the accuracy of such a method was checked for 8 bp duplexes, and no significant systematic errors were found.

  5. 5.

    For example, if the melting transition of an 8-bp duplex was as wide as predicted by Ref. [20], one would expect the statistical weight of an 8-bp duplex in my model to be increased by around a factor of two at 341 K. This is the approximate melting temperature of a hairpin with an 8-bp stem and a 6-base loop: increasing the statistical weight of the hairpin by a factor of two would translate into an increase in \(T_m\) of around 2 K.

  6. 6.

    Note that the experiments were performed in a range of concentrations of denaturing urea, then extrapolated to zero urea concentration.

  7. 7.

    Hairpin stems contained 12 bp and loops consisted of six bases. For each system, four VMMC simulations were performed for \(4 \times 10^{10}\) steps, using umbrella sampling to improve equilibration.

References

  1. W. Saenger. Principles of Nucleic Acid Structure. Springer-Verlag, New York, 1984.

    Google Scholar 

  2. K. M. Guckan et al. Factors contributing to aromatic stacking in water: evaluation in the context of DNA. J. Am. Chem. Soc., 122(10):2213–2222, 2000.

    Google Scholar 

  3. G. Vesnaver and K. J. Breslauer. The contribution of DNA single-stranded order to the thermodynamics of duplex formation. Proc. Natl. Acad. Sci. U.S.A, 88:3569–3573, 1991.

    Google Scholar 

  4. M. Leng and G. Felsenfeld. A study of polyadenylic acid at neutral ph. J. Mol. Biol., 15(2):455–466, 1966.

    Google Scholar 

  5. R. M. Epand and H. A. Scheraga. Enthalpy of stacking in single-stranded polyriboadenylic acid. J. Am. Chem. Soc., 89(15):3888–3892, 1967.

    Google Scholar 

  6. D. Pörschke. The nature of stacking interactions in polynucleotides. molecular states in oligo- and polyribocytidylic acids by relaxation analysis. Biochemistry, 15(7):1495–1499, 1976.

    Google Scholar 

  7. S. M. Freier et al. Solvent effects on the kinetics and thermodynamics of stacking in poly(cyticylic acid). Biochemistry, 20:1419–1426, 1981.

    Google Scholar 

  8. C. S. M. Olsthoorn et al. Circular dichroism study of stacking properties of oligodeoxyadenylates and polydeoxyadenylate. Eur. J. Biochem., 115(2):309–321, 1981.

    Google Scholar 

  9. J. Zhou et al. Conformational changes in single-strand DNA as a function of temperature by SANS. Biophys. J., 90(2):544–551, 2006.

    Google Scholar 

  10. P. J. Mikulecky and A. L. Feig. Heat capacity changes associated with nucleic acid folding. Biopolymers, 82(1):38–58, 2006.

    Google Scholar 

  11. J. Applequist and V. Damle. Thermodynamics of the one-stranded helix-coil equilibrium in polyadenylic acid. J. Am. Chem. Soc., 88(17):3895–3900, 1966.

    Google Scholar 

  12. J. A. Holbrook et al. Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: Interpretation in terms of coupled processes of formation and association of single-stranded helices. Biochemistry, 38(26):8409–8422, 1999.

    Google Scholar 

  13. I. Jelesarov et al. The energetics of HMG box interactions with DNA: thermodynamic description of the target dna duplexes. J. Mol. Biol., 294(4):981–995, 1999.

    Google Scholar 

  14. J. Norberg and L. Nilsson. Potential of mean force calculations of the stacking-unstacking process in single-stranded deoxyribodinucleoside monophosphates. Biophys. J., 69(6):2277–2285, 1995.

    Google Scholar 

  15. S. Sen and L. Nilsson. MD simulations of homomorphous PNA, DNA, and RNA single strands: characterization and comparison of conformations and dynamics. J. Am. Chem. Soc., 123(30):7414–7422, 2001.

    Google Scholar 

  16. J. M. Martínez, S. K. C. Elmroth, and L. Kloo. Influence of sodium ions on the dynamics and structure of single-stranded DNA oligomers: A molecular dynamics study. J. Am. Chem. Soc., 123(49):12279–12289, 2001.

    Google Scholar 

  17. S. Tonzani and G. C. Schatz. Electronic excitations and spectra in single-stranded DNA. Journal of the American Chemical Society, 130(24):7607–7612, 2008.

    Google Scholar 

  18. O.-S. Lee and G. C. Schatz. Interaction between DNAs on a gold surface. The Journal of Physical Chemistry C, 113(36):15941–15947, 2009.

    Google Scholar 

  19. D. Poland and H. A. Scheraga. Theory of Helix-Coil Transitions in Biopolymers: Statistical Mechanical Theory of Order-disorder Transitions in Biological Macromolecules. Academic Press, New York, 1970.

    Google Scholar 

  20. J. SantaLucia, Jr. and D. Hicks. The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct., 33:415–40, 2004.

    Google Scholar 

  21. R. D. Blake and S. G. Delcourt. Thermal stability of DNA. Nucl. Acids Res., 26(14):3323–3332, 1998.

    Google Scholar 

  22. M. D. Frank-Kamenetskii. Simplification of the empirical relationship between melting temperature of DNA, its GC content and concentration of sodium ions in solution. Biopolymers, 10:2623–2624, 1971.

    Google Scholar 

  23. E. J. Sambriski, D. C. Schwartz, and J. J. de Pablo. A mesoscal model of DNA and its renaturation. Biophys. J., 96:1675–1690, 2009.

    Google Scholar 

  24. D. Andreatta et al. Ultrafast dynamics in DNA: Fraying at the end of the helix. J. Am. Chem. Soc., 128(21):6885–6892, 2006.

    Google Scholar 

  25. S. Nonin, J.-L. Leroy, and M. Gueron. Terminal base pairs of oligodeoxynucleotides: Imino proton exchange and fraying. Biochemistry, 34(33):10652–10659, 1995.

    Google Scholar 

  26. D. J. Patel and C. W. Hilbers. Proton nuclear magnetic resonance investigations of fraying in double-stranded d-ApTpGpCpApT in aqueous solution. Biochemistry, 14(12):2651–2656, 1975.

    Google Scholar 

  27. A. Tikhomirova, N. Taulier, and T. V. Chalikian. Energetics of nucleic acid stability: The effect of \(\Delta {\rm C}_P\). J. Am. Chem. Soc., 126(50):16387–16394, 2004.

    Google Scholar 

  28. R. R. Sinden. DNA structure and function. Academic Press Inc., London, 1994.

    Google Scholar 

  29. T. E. Ouldridge, A. A. Louis, and J. P. K. Doye. DNA nanotweezers studied with a coarse-grained model of DNA. Phys. Rev. Lett., 104:178101, 2010.

    Google Scholar 

  30. S. J. Green, J. Bath, and A. J. Turberfield. Coordinated chemoechanical cycles: a mechanism for autonomous molecular motion. Phys. Rev. Lett., 101(23):238101, 2008.

    Google Scholar 

  31. J. Bois et al. Topological constraints in nucleic acid hybridization kinetics. Nucl. Acids Res., 33(13):4090–4095, 2005.

    Google Scholar 

  32. D. K. Hendrix, S. E. Brenner, and S. R. Holbrook. RNA structural motifs: building blocks of a modular biomolecule. Q. Rev. Biophys., 38(03):221–243, 2005.

    Google Scholar 

  33. S. Kuznetsov et al. A semiflexible polymer model applied to loop formation in DNA hairpins. Biophys. J., 81:2864–2875, 2001.

    Google Scholar 

  34. Y. You et al. Design of LNA probes that improve mismatch discrimination. Nucl. Acids Res., 34(8):e60, 2006.

    Google Scholar 

  35. T. Naiser et al. Position dependent mismatch discrimination on DNA microarrays - experiments and model. BMC Bioinformatics, 9(1):509, 2008.

    Google Scholar 

  36. R. A. Dimitrov and M. Zuker. Predictio of hybridization and melting for double-stranded nucleic acids. Biophys. J., 87:215–226, 2004.

    Google Scholar 

  37. N. R. Markham and M. Zuker. DINAMelt web server for nucleic acid meting prediction. Nucl. Acids Res., 33:W577–W581, 2005.

    Google Scholar 

  38. N. Peyret. Prediction of nucleic acid hybridization: parameters and algorithms. PhD thesis, Wayne State University, 2000.

    Google Scholar 

  39. D. V. Pyshnyi and E. M. Ivanova. Thermodynamic parameters of coaxial stacking on stacking hybridization of oligodeoxyribonucleotides. Russ. Chem. B+, 51:1145–1155, 2002.

    Google Scholar 

  40. D. V. Pyshnyi and E. M. Ivanova. The influence of nearest neighbors on the efficiency of coaxial stacking at contiguous stacking hybridization of oligodeoxyribonucleotides. Nucleos. Nucleot. Nucl., 23(6–7):1057–1064, 2004.

    Google Scholar 

  41. M. J. Lane et al. The thermodynamic advantage of DNA oligonucleotide ‘stacking hybridization’ reactions: Energetics of a DNA nick. Nucl. Acids Res., 25(3):611–616, 1997.

    Google Scholar 

  42. V. A. Vasiliskov, D. V. Prokopenko, and A. D. Mirzabekov. Parallel multiplex thermodynamic analysis of coaxial base stacking in DNA duplexes by oligodeoxyribonucleotide microchips. Nucl. Acids Res., 29(11):2303–2313, 2001.

    Google Scholar 

  43. S. Woo and P. W. K. Rothemund. Programmable molecular recognition based on the geometry of DNA nanostructures. Nature Chem., 3:620–627, 2011.

    Google Scholar 

  44. E. Protozanova, P. Yakovchuk, and M. D. Frank-Kamenetskii. Stacked-unstacked equilibrium at the nick site of DNA. J. Mol. Biol., 342(3):775–785, 2004.

    Google Scholar 

  45. P. Yakovchuk, E. Protozanova, and M. D. Frank-Kamenetskii. Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucl. Acids Res., 34(2):564–574, 2006.

    Google Scholar 

  46. T. E. Ouldridge, A. A. Louis, and J. P. K. Doye. Structural, mechanical and thermodynamic properties of a coarse-grained model of DNA. J. Chem. Phys., 134:085101, 2011.

    Google Scholar 

  47. N. Peyret et al. Nearest-neighbour thermodynamics and NMR of DNA sequences with internal AA, CC, GG and TT mismatches. Biochemistry, 38:3468–3477, 1999.

    Google Scholar 

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  1. University of Oxford, Oxford, UK

    Dr. Thomas E. Ouldridge

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Ouldridge, T.E. (2012). Thermodynamic Properties of Model DNA. In: Coarse-Grained Modelling of DNA and DNA Self-Assembly. Springer Theses. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30517-7_6

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  • DOI: https://doi.org/10.1007/978-3-642-30517-7_6

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