Papers
Topics
Authors
Recent
Gemini 2.5 Flash
Gemini 2.5 Flash
157 tokens/sec
GPT-4o
8 tokens/sec
Gemini 2.5 Pro Pro
46 tokens/sec
o3 Pro
4 tokens/sec
GPT-4.1 Pro
38 tokens/sec
DeepSeek R1 via Azure Pro
28 tokens/sec
2000 character limit reached

Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs. cgDNA+ (2401.05208v1)

Published 10 Jan 2024 in cond-mat.soft, cond-mat.stat-mech, and q-bio.BM

Abstract: Coarse-grained models have emerged as valuable tools to simulate long DNA molecules while maintaining computational efficiency. These models aim at preserving interactions among coarse-grained variables in a manner that mirrors the underlying atomistic description. We explore here a method for testing coarse-grained vs. all-atom models using stiffness matrices in Fourier space ($q$-stiffnesses), which are particularly suited to probe DNA elasticity at different length scales. We focus on a class of coarse-grained rigid base DNA models known as cgDNA and its most recent version cgDNA+. Our analysis shows that while cgDNA+ follows closely the $q$-stiffnesses of the all-atom model, the original cgDNA shows some deviations for twist and bending variables which are rather strong in the $q \to 0$ (long length scale) limit. The consequence is that while both cgDNA and cgDNA+ give a suitable description of local elastic behavior, the former misses some effects which manifest themselves at longer length scales. In particular, cgDNA performs poorly on the twist stiffness with a value much lower than expected for long DNA molecules. Conversely, the all-atom and cgDNA+ twist is strongly length scale dependent: DNA is torsionally soft at a few base pair distances, but becomes more rigid at distances of a few dozens base pairs. Our analysis shows that the bending persistence length in all-atom and cgDNA+ is somewhat overestimated.

Definition Search Book Streamline Icon: https://streamlinehq.com
References (42)
  1. M. Pasi et al., “μ𝜇\muitalic_μABC: A systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA,” Nucl. Acids Res. 42, 12272–12283 (2014).
  2. J. Curuksu, M. Zacharias, R. Lavery, and K. Zakrzewska, “Local and global effects of strong DNA bending induced during molecular dynamics simulations,” Nucl. Acids Res. 37, 3766–3773 (2009).
  3. J. Spiriti, H. Kamberaj, A. M. De Graff, M. Thorpe, and A. Van Der Vaart, “DNA bending through large angles is aided by ionic screening,” J. Chem. Theor. Comput. 8, 2145–2156 (2012).
  4. A. Karolak and A. van der Vaart, “Enhanced sampling simulations of DNA step parameters,” J. Comput. Chem. 35, 2297–2304 (2014).
  5. A. Peguero-Tejada and A. van der Vaart, “Biasing simulations of DNA base pair parameters with application to propellor twisting in AT/AT, AA/TT, and AC/GT steps and their uracil analogs,” J. Chem. Inf. Model. 57, 85–92 (2017).
  6. A. Voorspoels, J. Vreede, and E. Carlon, “Rigid base biasing in molecular dynamics enables enhanced sampling of DNA conformations,” J. Chem. Theor. Comput. 19, 902–909 (2023).
  7. T. E. Ouldridge, A. A. Louis, and J. P. Doye, “DNA nanotweezers studied with a coarse-grained model of DNA,” Phys. Rev. Lett. 104, 178101 (2010).
  8. O. Henrich, Y. A. G. Fosado, T. Curk, and T. E. Ouldridge, “Coarse-grained simulation of DNA using LAMMPS,” Eur. Phys. J. E 41, 57 (2018).
  9. P. D. Dans, A. Zeida, M. R. Machado, and S. Pantano, “A coarse grained model for atomic-detailed DNA simulations with explicit electrostatics,” J. Chem. Theor. Comput. 6, 1711–1725 (2010).
  10. Y. A. G. Fosado, D. Michieletto, J. Allan, C. Brackley, O. Henrich, and D. Marenduzzo, “A single nucleotide resolution model for large-scale simulations of double stranded DNA,” Soft Matter 12, 9458–9470 (2016).
  11. D. Chakraborty, N. Hori, and D. Thirumalai, “Sequence-dependent three interaction site model for single-and double-stranded DNA,” J. Chem. Theory Comput. 14, 3763–3779 (2018).
  12. S. Assenza and R. Pérez, ‘‘Accurate sequence-dependent coarse-grained model for conformational and elastic properties of double-stranded DNA,” J. Chem. Theor. Comput. 18, 3239–3256 (2022).
  13. R. Frederickx, T. In’t Veld, and E. Carlon, “Anomalous dynamics of DNA hairpin folding,” Phys. Rev. Lett. 112, 198102 (2014).
  14. C. Matek, T. E. Ouldridge, J. P. K. Doye, and A. A. Louis, “Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA,” Scientific Reports 5, 7655 (2015).
  15. A. Córdoba, D. M. Hinckley, J. Lequieu, and J. J. de Pablo, “A molecular view of the dynamics of dsDNA packing inside viral capsids in the presence of ions,” Biophys. J. 112, 1302–1315 (2017).
  16. L. Coronel, A. Suma, and C. Micheletti, “Dynamics of supercoiled DNA with complex knots: large-scale rearrangements and persistent multi-strand interlocking,” Nucl. Acids Res. 46, 7533 (2018).
  17. M. Caraglio, E. Skoruppa, and E. Carlon, “Overtwisting induces polygonal shapes in bent DNA,” J. Chem. Phys 150, 135101 (2019).
  18. D. Petkevičiūtė, M. Pasi, O. Gonzalez, and J. Maddocks, “cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA,” Nucl. Acids Res. 42, e153–e153 (2014).
  19. R. Sharma, A. S. Patelli, L. De Bruin, and J. H. Maddocks, “cgNA+ web: A visual interface to the cgNA+ sequence-dependent statistical mechanics model of double-stranded nucleic acids,” J. Mol. Biol. , 167978 (2023).
  20. W. K. Olson et al., “A standard reference frame for the description of nucleic acid base-pair geometry,” J. Mol. Biol. 313, 229–237 (2001).
  21. A. S. Patelli, A sequence-dependent coarse-grain model of B-DNA with explicit description of bases and phosphate groups parametrised from large scale Molecular Dynamics simulations, Ph.D. thesis, EPFL, Lausanne (2019).
  22. O. Gonzalez, D. Petkeviciute, and J. H. Maddocks, “A sequence-dependent rigid-base model of DNA,” J. Chem. Phys. 138 (2013).
  23. E. Skoruppa, A. Voorspoels, J. Vreede, and E. Carlon, “Length-scale-dependent elasticity in DNA from coarse-grained and all-atom models,” Phys. Rev. E 103, 042408 (2021).
  24. M. Segers, A. Voorspoels, T. Sakaue, and E. Carlon, “Mechanical properties of nucleic acids and the non-local twistable wormlike chain model,” J. Chem. Phys. 156, 234105 (2022).
  25. H. Dohnalová and F. Lankaš, “Deciphering the mechanical properties of B-DNA duplex,” WIREs Comput Mol Sci. , e1575 (2021).
  26. B. Eslami-Mossallam, H. Schiessel, and J. van Noort, “Nucleosome dynamics: Sequence matters,” Adv. Colloid Interface Sci. 232, 101–113 (2016).
  27. Y. A. Gutiérrez Fosado, F. Landuzzi, and T. Sakaue, “Coarse graining DNA: Symmetry, nonlocal elasticity, and persistence length,” Phys. Rev. Lett. 130, 058402 (2023).
  28. M. Segers, E. Skoruppa, J. A. Stevens, M. Vangilbergen, A. Voorspoels, and E. Carlon, “Comment on "Flexibility of short DNA helices with finite-length effect: From base pairs to tens of base pairs",” J. Chem. Phys. 155, 027101 (2021).
  29. Z. Bryant, M. D. Stone, J. Gore, S. B. Smith, N. R. Cozzarelli, and C. Bustamante, “Structural transitions and elasticity from torque measurements on DNA,” Nature 424, 338–341 (2003).
  30. J. Lipfert, J. W. Kerssemakers, T. Jager, and N. H. Dekker, “Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments,” Nat. Methods 7, 977–980 (2010).
  31. X. Gao, Y. Hong, F. Ye, J. T. Inman, and M. D. Wang, “Torsional Stiffness of Extended and Plectonemic DNA,” Phys. Rev. Lett. 127, 028101 (2021).
  32. J. S. Mitchell, J. Glowacki, A. E. Grandchamp, R. S. Manning, and J. H. Maddocks, “Sequence-dependent persistence lengths of DNA,” J. Chem. Theory Comput. 13, 1539–1555 (2017).
  33. S. Kim, E. Broströmer, D. Xing, J. Jin, S. Chong, H. Ge, S. Wang, C. Gu, L. Yang, Y. Q. Gao, et al., “Probing allostery through DNA,” Science 339, 816–819 (2013).
  34. G. Rosenblum, N. Elad, H. Rozenberg, F. Wiggers, and H. Hofmann, “Allostery through DNA drives phenotype switching,” Nature Comm. 12, 1–12 (2021).
  35. J. Lipfert, G. M. Skinner, J. M. Keegstra, T. Hensgens, T. Jager, D. Dulin, M. Köber, Z. Yu, S. P. Donkers, F.-C. Chou, R. Das, and N. H. Dekker, “Double-stranded RNA under force and torque: Similarities to and striking differences from double-stranded DNA,” Proc. Natl. Acad. Sci. USA 111, 15408–15413 (2014).
  36. K. Liebl and M. Zacharias, “The development of nucleic acids force fields: From an unchallenged past to a competitive future,” Biophys. J. 122, 2841 (2023).
  37. M. Abrahams, T. Murtola, R. Schulz, S. Páll, J. Smith, B. Hess, and E. Lindahl, “GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers,” SoftwareX 1-2, 19–25 (2015).
  38. I. Ivani et al., “Parmbsc1: a refined force field for DNA simulations,” Nat. Methods 13, 55–58 (2016).
  39. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, “Comparison of simple potential functions for simulating liquid water,” J. Chem. Phys. 79, 926–935 (1983).
  40. G. Bussi, D. Donadio, and M. Parrinello, “Canonical sampling through velocity rescaling,” J. Chem. Phys. 126, 014101 (2007).
  41. M. Parrinello and A. Rahman, “Polymorphic transitions in single crystals: A new molecular dynamics method,” J. Appl. Phys. 52, 7182–7190 (1981).
  42. R. Lavery, M. Moakher, J. Maddocks, D. Petkeviciute, and D. Zakrzewska, “Conformational analysis of nucleic acids revisited: Curves+,” Nucl. Acids Res. 37, 5917–5929 (2009).

Summary

We haven't generated a summary for this paper yet.

Ai Sparkles Streamline Icon: https://streamlinehq.com Summarize Now
X Twitter Logo Streamline Icon: https://streamlinehq.com

Tweets