Dynamics of Ion-Phosphate Lattice of DNA in Left-Handed Double Helix Form
DOI:
https://doi.org/10.15407/ujpe58.06.0554Keywords:
left-handed double helix, ion-phosphate lattice, DNAAbstract
The conformational vibrations of Z-DNA with counterions are studied in the framework of a phenomenological model developed. The structure of a left-handed double helix with counterions neutralizing the negatively charged phosphate groups of DNA is considered as an ion-phosphate lattice. The frequencies and the Raman intensities for the modes of Z-DNA with Na+ and Mg2+ ions are calculated, and the low-frequency Raman spectra are built. At the spectral interval about the frequency 150 cm^-1; a new mode of ion-phosphate vibrations, which characterizes the vibrations of Mg2+ counterions, is found. The results of our calculations show that the intensities of Z-DNA modes are sensitive to the concentration of magnesium counterions. The obtained results describe well the experimental Raman spectra of Z-DNA.
References
<li> W. Saenger, Principles of Nucleic Acid Structure (Springer, New York, 1984). <a href="https://doi.org/10.1007/978-1-4612-5190-3">https://doi.org/10.1007/978-1-4612-5190-3</a></li>
<li> Yu.P. Blagoi, V.L. Galkin, G.O. Gladchenko et al., The Complexes of Nucleic Acids and Metals in Solutions (Naukova Dumka, Kiev, 1991) (in Russian).</li>
<li> V.I. Ivanov, L.E. Minchenkova, A.K. Schyolkina, and A.I. Poletayev, Biopolymers 12, 89 (1973). <a href="https://doi.org/10.1002/bip.1973.360120109">https://doi.org/10.1002/bip.1973.360120109</a></li>
<li> V.Ya. Maleev, M.A. Semenov, A.I. Gasan, and V.A. Kashpur, Biofizika 38, 768 (1993).</li>
<li> L.D. Williams and L.J. Maher, Annu. Rev. Biophys. Biomol. Struct. 29, 497 (2000). <a href="https://doi.org/10.1146/annurev.biophys.29.1.497">https://doi.org/10.1146/annurev.biophys.29.1.497</a></li>
<li> A. Rich and S. Zhang, Nature Reviews 4, 566 (2003). <a href="https://doi.org/10.1038/nrg1115">https://doi.org/10.1038/nrg1115</a></li>
<li> V. Tereshko et al., Nucleic Acids Res. 29, 1208 (2001). <a href="https://doi.org/10.1093/nar/29.5.1208">https://doi.org/10.1093/nar/29.5.1208</a></li>
<li> V. Tereshko, G. Minasov, and M. Egli, J. Am. Chem. Soc. 121, 470 (1999). <a href="https://doi.org/10.1021/ja9832919">https://doi.org/10.1021/ja9832919</a></li>
<li> N.V. Hud and M. Polak, Current Opinion Struct. Biol. 11, 293 (2001). <a href="https://doi.org/10.1016/S0959-440X(00)00205-0">https://doi.org/10.1016/S0959-440X(00)00205-0</a></li>
<li> G.S. Manning, Q. Rev. Biophys. 11, 179 (1978). <a href="https://doi.org/10.1017/S0033583500002031">https://doi.org/10.1017/S0033583500002031</a></li>
<li> M.D. Frank-Kamenetskii, V.V. Anshelevich, and A.V. Lukashin, Sov. Phys. Usp. 151, 595 (1987). <a href="https://doi.org/10.3367/UFNr.0151.198704b.0595">https://doi.org/10.3367/UFNr.0151.198704b.0595</a></li>
<li> Y. Levin, Rep. Prog. Phys. 65, 1577 (2002). <a href="https://doi.org/10.1088/0034-4885/65/11/201">https://doi.org/10.1088/0034-4885/65/11/201</a></li>
<li> <li> A.A. Kornyshev et al., Rev. Mod. Phys. 79, 943 (2007). <a href="https://doi.org/10.1103/RevModPhys.79.943">https://doi.org/10.1103/RevModPhys.79.943</a></li>
<li> R. Das, T.T. Mills, L.W. Kwok et al., Phys. Rev. Lett. 90, 188103 (2003). <a href="https://doi.org/10.1103/PhysRevLett.90.188103">https://doi.org/10.1103/PhysRevLett.90.188103</a></li>
<li> K. Andersen, R. Das, H.Y. Park et al., Phys. Rev. Lett. 93, 248103 (2004). <a href="https://doi.org/10.1103/PhysRevLett.93.248103">https://doi.org/10.1103/PhysRevLett.93.248103</a></li>
<li> K. Andresen, X. Qui, S.A. Pabit et al., Biophys. J. 95, 287 (2008). <a href="https://doi.org/10.1529/biophysj.107.123174">https://doi.org/10.1529/biophysj.107.123174</a></li>
<li> X. Qiu, L.W. Kwok, H.Y. Park et al., Phys. Rev. Lett. 101, 228101 (2008). <a href="https://doi.org/10.1103/PhysRevLett.101.228101">https://doi.org/10.1103/PhysRevLett.101.228101</a></li>
<li> P. Varnai and K. Zakrzewska, Nucleic Acids Res. 32, 4269 (2004). <a href="https://doi.org/10.1093/nar/gkh765">https://doi.org/10.1093/nar/gkh765</a></li>
<li> S.Y. Ponomarev, K.M. Thayer, and D.L. Beveridge, Proc. Natl. Acad. Sci. USA 101, 14771 (2004). <a href="https://doi.org/10.1073/pnas.0406435101">https://doi.org/10.1073/pnas.0406435101</a></li>
<li> C. Kittel, Introduction to Solid State Physics (Wiley, New York, 1954).</li>
<li> I.A. Heisler, K. Mazur, and S.R. Meech, J. Phys. Chem. 115, 2563 (2011). <a href="https://doi.org/10.1021/jp111239v">https://doi.org/10.1021/jp111239v</a></li>
<li> J.W. Powell, G.S. Edwards, L. Genzel et al., Phys. Rev. A 35, 3929 (1987). <a href="https://doi.org/10.1103/PhysRevA.35.3929">https://doi.org/10.1103/PhysRevA.35.3929</a></li>
<li> O.P. Lamba, A.H.-J. Wang, and G.J. Thomas, jr., Biopolymers 28, 667 (1989). <a href="https://doi.org/10.1002/bip.360280210">https://doi.org/10.1002/bip.360280210</a></li>
<li> T. Weidlich, S.M. Lindsay, Qi Rui et al., J. Biomol. Struct. Dyn. 8, 139 (1990). <a href="https://doi.org/10.1080/07391102.1990.10507795">https://doi.org/10.1080/07391102.1990.10507795</a></li>
<li> T. Weidlich, J.W. Powell, L. Genzel, and A. Rupprecht, Biopolymers 30, 477 (1990). <a href="https://doi.org/10.1002/bip.360300324">https://doi.org/10.1002/bip.360300324</a></li>
<li> S.N. Volkov and A.M. Kosevich, Molek. Biol. 21, 797 (1987).</li>
<li> S.N. Volkov and A.M. Kosevich, J. Biomol. Struct. Dyn. 8, 1069 (1991). <a href="https://doi.org/10.1080/07391102.1991.10507866">https://doi.org/10.1080/07391102.1991.10507866</a></li>
<li> S.N. Volkov, Biopolymers and Cell 7, 40 (1991). <a href="https://doi.org/10.7124/bc.0002B0">https://doi.org/10.7124/bc.0002B0</a></li>
<li> A.M. Kosevich and S.N. Volkov, Nonlinear Excitations in Biomolecules, edited by M. Peyrard (Springer, New York, 1995), Chapter 9.</li>
<li> S.M. Perepelytsya and S.N. Volkov, Ukr. J. Phys. 49, 1072 (2004); arXiv: q-bio.BM/0412022.</li>
<li> S.M. Perepelytsya and S.N. Volkov, Eur. Phys. J. E 24, 261 (2007). <a href="https://doi.org/10.1140/epje/i2007-10236-x">https://doi.org/10.1140/epje/i2007-10236-x</a></li>
<li> S.M. Perepelytsya and S.N. Volkov, Biofiz. Bull. 23(2), 5 (2009); arXiv: q-bio.BM/0805.0696v1.</li>
<li> S.M. Perepelytsya and S.N. Volkov, Eur. Phys. J. E 31, 201 (2010). <a href="https://doi.org/10.1140/epje/i2010-10566-6">CrossRef</a></li>
<li> S.M. Perepelytsya and S.N. Volkov, Ukr. J. Phys. 55, 1182 (2010).</li>
<li> S.M. Perepelytsya and S.N. Volkov, J. Molec. Liq. 5, 1182 (2011).</li>
<li> T. Weidlich, S.M. Lindsay, W.L. Peticolas, and G.A. Thomas, J. Biomolec. Struct. Dyn. 7, 849 (1990). <a href="https://doi.org/10.1002/3527603085">https://doi.org/10.1002/3527603085</a></li>
<li> A.M. Kosevich,Theory of Crystal Lattice (Wiley-VCH, Berlin, 1999). <a href="https://doi.org/10.1080/07391102.1990.10508528">https://doi.org/10.1080/07391102.1990.10508528</a></li>
<li> R.V. Gessner, C.A. Frederick, G.J. Quigley et al., J. Biol. Chem. 264, 7921 (1989).</li>
<li> N.A. Izmailov, Electrochemistry of Solutions (Khimiya, Moscow, 1976) (in Russian).</li>
</ol>
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