Abstract
In this study, we performed a simulation of stretching dynamics in double-stranded DNA fragments in a high-gradient liquid flow in the neighborhood of collapsing cavitation bubbles. We used calculated profiles of elastic tension along the polymer fragment model to determine the rates of mechanochemical cleavage at different positions in DNA restriction fragments. The obtained cleavage rate curves are qualitatively consistent with experimentally observed profiles of ultrasonic cleavage rates of DNA restriction fragments, which we showed earlier to be position-dependent. Based on the sum of our data, we propose a model that links the sequence specificity of ultrasonic DNA cleavage that has been proven experimentally to the sequence-specific conformational dynamics of β-D-deoxyribose in a B-form of the double helix. Furthermore, quantitative assessments of ultrasonic DNA cleavage rates for different conformational states of β-D-deoxyribose calculated based on the proposed model qualitatively agree with the experimental data.
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References
S. L. Grokhovsky, Mol. Biol. (Moscow) 40(2), 276 (2006).
S. L. Grokhovsky, I. A. Il’icheva, D. Yu. Nechipurenko, L. A. Panchenko, R. V. Polozov, and Yu. D. Nechi- purenko, Biophysics (Moscow) 53(3), 250 (2008).
S. L. Grokhovsky, I. A. Il’icheva, D. Yu. Nechipurenko, et al., Biophys. J. 100(1), 117 (2011).
J. R. Thomas, J. Phys. Chem. 63(10), 1725 (1959).
S. L. Grokhovsky, I. A. Il’icheva, D. Yu. Nechipurenko, et al., in Gel Electrophoresis: Principles and Basics, Ed. by S. Magdeldin (InTech, Croatia, 2012 pp. 217–238.
S. L. Grokhovsky, I. A. Il’icheva, D. Yu. Nechipurenko, et al., in Ultrasonics: Theory, Techniques, and Practical Applications, Ed. by Hanako Ayabito and Mitsuko Katsukawa (Nova Science, New York, 2013), p. 24.
H. G. Flynn, in Physical Acoustics, Ed. by W.P. Masson, (Academic Press, New York, 1964), Vol. 1, part B, pp. 57–172.
C. E. Brennen, Cavitation and Bubble Dynamics (Oxford Univ. Press, Oxford, 1995).
M. Doi and S. F. Edwards, The Theory of Polymer Dynamics (Clarendon Press, Oxford, 1986).
M. X. Fernandes, A. Ortega, M. C. López Martinez, and J. Garcia de la Torre, Nucleic Acids Res. 30(8), 1782 (2002).
C. Bustamante, J. F. Marko, E. D. Siggia, and S. Smith, Science 265, 1599 (1994).
H. B. Hakim, S. M. Lindsay, and J. Powell, Bipolymers 23, 1185 (1984).
S. B. Smith, Y. Cui, and C. Bustamante, Science 271, 795 (1996).
S. W. Schmidt, M. K. Beyer, and H. Clausen-Schaumann, J. Am. Chem. Soc. 130, 3664 (2008).
A. M. Basedow and E. B. Ebert, in Advances in Polymers Science, Vol. 22, Edited by A. Abe, A.-C. Albertsson, and J. Genzer (Springer, Berlin, 1977), pp. 83–148.
I. A. Il’icheva, D. Yu. Nechipurenko, and S. L. Grokhovsky. J. Biomol. Struct. Dyn. 27, 391 (2009).
O. C. Richards and P. D. Boyer, J. Mol. Biol. 11, 327 (1965).
C. Richardson, J. Mol. Biol. 15, 49 (1966).
Z. Wu, F. Delaglio, N. Tjandra, et al., J. Biomol. NMR 26(4), 297 (2003).
M. S. Poptsova, I. A. Il’icheva, D. Yu. Nechipurenko, et al., Sci. Reports 4, 4532 (2014).
A. M. Basedow and E. B. Ebert, in Advances in Polymers Science, Vol. 22, Ed. by A. Abe, A.-C., Albertsson, and J. Genzer (Springer, Berlin, 1977), pp. 83–148.
Y. K. Lentza, L. R. Wordenb, T. J. Anchordoquya, and C. S. Lengsfeld, J. Aerosol Sci. 36, 973 (2005).
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Original Russian Text © D.Yu. Nechipurenko, I.A. Il’icheva, M.V. Khodikov, M.S. Poptsova, Yu.D. Nechipurenko, S.L. Grokhovsky, 2014, published in Biofizika, 2014, Vol. 59, No. 6, pp. 1061–1070.
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Nechipurenko, D.Y., Il’icheva, I.A., Khodikov, M.V. et al. Modeling of mechanochemical DNA cleavage by the action of ultrasound. BIOPHYSICS 59, 861–868 (2014). https://doi.org/10.1134/S000635091406013X
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DOI: https://doi.org/10.1134/S000635091406013X