Dynamical Ordering of Metal Ions around DNA Double Helix

Scientific Report at NAS of Ukraine Presidium Meeting 2 October 2013

Authors

  • S.M. Perepelytsya Bogolyubov Institute for Theoretical Physics of the National Academy of Sciences of Ukraine, Kyiv

DOI:

https://doi.org/10.15407/visn2014.01.089

Keywords:

DNA, counterions, lattice, conformational vibrations, low-frequency spectra, texture

Abstract

DNA double helix with the ions of metals that neutralize the negatively charged phosphate groups of the macromolecule backbone has been studied. The results have been shown that metal ions may form a dynamical ordered structure along DNA, resembling to the lattice of ionic crystal (ion-phosphate lattice). The specific vibrational modes of DNA ionphosphate lattice have been found and their frequencies have been shown to be in the low-frequency spectra range (< 200 cm-1). The role of salts of alkali metal chlorides in the formation of fractal structures, observed on a surface after evaporation of aqueous solutions of DNA, has been explained within the framework of developed approach of dynamical ordering of ions around DNA.

References

Watson J.D., Crick F.H.C. A structure of deoxyribose nucleic acid. Nature. 1953. 171: 737–38. http://doi.org/10.1038/171737a0

Wilkins M.H.F., Stokes A.R., Wilson H.R. Molecular structure of deoxypentose nucleic acid. Nature. 1953. 171: 738–40. http://doi.org/10.1038/171738a0

Franklin R.E., Gosling R.G. Molecular configuration in sodium thymonucleate. Nature. 1953. 171: 740–41. http://doi.org/10.1038/171740a0

Perepelytsya S.M., Volkov S.N. Ion mode in the DNA low-frequency vibration spectra. Ukr. J. Phys. 2004. 49(11): 1072.

Perepelytsya S.M., Volkov S.N. Counterion vibrations in the DNA low-frequency spectra. Eur. Phys. J. E. 2007. 24: 261–69. http://doi.org/10.1140/epje/i2007-10236-x

Perepelytsya S.M., Volkov S.N. Conformational vibrations of DNA with counterions in cross-stranded position. Ukr. J. Phys. 2010. 55: 1182.

Perepelytsya S.M., Volkov S.N. Conformational vibrations of ionic lattice in DNA: Manifestation in the low-frequency Raman spectra. J. Mol. Liq. 2011. 164: 113–19. http://doi.org/10.1016/j.molliq.2011.04.015

Perepelytsya S.M., Volkov S.N. Vibrations of ordered counterions around left- and right-handed DNA double helix. J. Phys: Conf. Series. 2013. 438: 012013. http://doi.org/10.1088/1742-6596/438/1/012013

Perepelytsya S.M., Volkov S.N. Dynamics of ion-phosphate lattice of DNA in left-handed the double helix for. Ukr. J. Phys. 2013. 58: 554–61. http://doi.org/10.15407/ujpe58.06.0554

Kittel C. Introduction to Solid State Physics (Wiley, 1953).

Volkov S.N., Kosevich A.M. Molekulyarnaya biologiya (Molecular Biology). 1987. 21: 797–806.

Volkov S.N., Kosevich A.M. Theory of low-frequency vibrations in DNA macromolecules. J. Biomolec. Struct. Dyn. 1991. 8: 1069–83. http://doi.org/10.1080/07391102.1991.10507866

Volkov S.N. Biopolym. Cell. 1991; 7(1): 40-49.

Powell J.W., Edwards G.S., Genzel L., Kremer F., Wittlin A. Investigation of far-infrared vibrational modes in poly-nucleotides. Phys. Rev. A. – 1987. 35(9): 3929–39. http://doi.org/10.1103/PhysRevA.35.3929

Urabe H., Kato M., Tominaga Y., Kajiwara K. Counterion dependence of water of hydration in DNA gel. J. Chem. Phys. 1990. 92(1): 776–74. http://doi.org/10.1063/1.458430

Weidlich T., Lindsay S.M., Rui Q., Rupprecht A., Peticolas W.L., Thomas G.A. A Raman study of low frequency interhelical modes in A-, B-, and C- DNA. J. Biomolec. Struct. Dyn. 1990. 8(1):139–71. http://doi.org/10.1080/07391102.1990.10507795

Weidlich T., Powell J.W., Genzel L., Rupprecht A. Counerion effects on the Far-IR vibrational spectra of poly(rI)poly(rC). Biopolymers. 1990. 30: 477–80. http://doi.org/10.1002/bip.360300324

Bulavin L.A., Volkov S.N., Kutuvy S.Yu., Perepelytsya S.M. Observation of the DNA ion-phosphate vibrations. Dopovidi NANU. 2007. (10): 69–73. arXiv:0805.0696v1.

Bulavin L.A., Aktan A.Yu, Zabashta Yu.F. In: Medical Physics. Vol. 2. (Kuiv, 2011). [in Ukrainian].

Perepelytsya S.M., Volkov S.N. Biofizychnyy Visnyk (Biophysical Bulletin). 2009. 23(2): 5–19. [in Russian].

Perepelytsya S.M., Volkov S.N. Intensities of DNA ion-phosphate modes in low-frequency Raman spectra. Eur. Phys. J. E. 2010. 31: 201–06. http://doi.org/10.1140/epje/i2010-10566-6

Perepelytsya S.M., Glibitskiy G.M., Volkov S.N. Texture formation in DNA films with alkali metal chlorides. Biopolymers. 2013. 99(6): 508–16. http://doi.org/10.1002/bip.22209

Tarasevich Yu.Yu. Mechanisms and models of the dehydration self-organization in biological fluids. Physics-Uspekhi (Advances in Physical Sciences). 2004. 47(7): 717-28. http://doi.org/10.1070/PU2004v047n07ABEH001758

Glibitskiy G.M. Na-DNA films with ions of metals. Biofizychnyy Visnyk (Biophysical Bulletin). 2008. 21(2): 29–34.

Published

2014-01-23