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Effect of magnesium ions on the structure of DNA thin films: an infrared spectroscopy study

Utilizing Fourier transform infrared spectroscopy we have investigated the vibrational spectrum of thin dsDNA films in order to track the structural changes upon addition of magnesium ions. In the range of low magnesium concentration ([magnesium]/[phosphate] = [Mg]/[P] < 0.5), both the red shift...

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Autores principales: Serec, Kristina, Babić, Sanja Dolanski, Podgornik, Rudolf, Tomić, Silvia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5041487/
https://www.ncbi.nlm.nih.gov/pubmed/27484473
http://dx.doi.org/10.1093/nar/gkw696
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author Serec, Kristina
Babić, Sanja Dolanski
Podgornik, Rudolf
Tomić, Silvia
author_facet Serec, Kristina
Babić, Sanja Dolanski
Podgornik, Rudolf
Tomić, Silvia
author_sort Serec, Kristina
collection PubMed
description Utilizing Fourier transform infrared spectroscopy we have investigated the vibrational spectrum of thin dsDNA films in order to track the structural changes upon addition of magnesium ions. In the range of low magnesium concentration ([magnesium]/[phosphate] = [Mg]/[P] < 0.5), both the red shift and the intensity of asymmetric PO(2) stretching band decrease, indicating an increase of magnesium-phosphate binding in the backbone region. Vibration characteristics of the A conformation of the dsDNA vanish, whereas those characterizing the B conformation become fully stabilized. In the crossover range with comparable Mg and intrinsic Na DNA ions ([Mg]/[P] ≈ 1) B conformation remains stable; vibrational spectra show moderate intensity changes and a prominent blue shift, indicating a reinforcement of the bonds and binding in both the phosphate and the base regions. The obtained results reflect the modified screening and local charge neutralization of the dsDNA backbone charge, thus consistently demonstrating that the added Mg ions interact with DNA via long-range electrostatic forces. At high Mg contents ([Mg]/[P] > 10), the vibrational spectra broaden and show a striking intensity rise, while the base stacking remains unaffected. We argue that at these extreme conditions, where a charge compensation by vicinal counterions reaches 92–94%, DNA may undergo a structural transition into a more compact form.
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spelling pubmed-50414872016-09-30 Effect of magnesium ions on the structure of DNA thin films: an infrared spectroscopy study Serec, Kristina Babić, Sanja Dolanski Podgornik, Rudolf Tomić, Silvia Nucleic Acids Res Structural Biology Utilizing Fourier transform infrared spectroscopy we have investigated the vibrational spectrum of thin dsDNA films in order to track the structural changes upon addition of magnesium ions. In the range of low magnesium concentration ([magnesium]/[phosphate] = [Mg]/[P] < 0.5), both the red shift and the intensity of asymmetric PO(2) stretching band decrease, indicating an increase of magnesium-phosphate binding in the backbone region. Vibration characteristics of the A conformation of the dsDNA vanish, whereas those characterizing the B conformation become fully stabilized. In the crossover range with comparable Mg and intrinsic Na DNA ions ([Mg]/[P] ≈ 1) B conformation remains stable; vibrational spectra show moderate intensity changes and a prominent blue shift, indicating a reinforcement of the bonds and binding in both the phosphate and the base regions. The obtained results reflect the modified screening and local charge neutralization of the dsDNA backbone charge, thus consistently demonstrating that the added Mg ions interact with DNA via long-range electrostatic forces. At high Mg contents ([Mg]/[P] > 10), the vibrational spectra broaden and show a striking intensity rise, while the base stacking remains unaffected. We argue that at these extreme conditions, where a charge compensation by vicinal counterions reaches 92–94%, DNA may undergo a structural transition into a more compact form. Oxford University Press 2016-09-30 2016-08-02 /pmc/articles/PMC5041487/ /pubmed/27484473 http://dx.doi.org/10.1093/nar/gkw696 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Structural Biology
Serec, Kristina
Babić, Sanja Dolanski
Podgornik, Rudolf
Tomić, Silvia
Effect of magnesium ions on the structure of DNA thin films: an infrared spectroscopy study
title Effect of magnesium ions on the structure of DNA thin films: an infrared spectroscopy study
title_full Effect of magnesium ions on the structure of DNA thin films: an infrared spectroscopy study
title_fullStr Effect of magnesium ions on the structure of DNA thin films: an infrared spectroscopy study
title_full_unstemmed Effect of magnesium ions on the structure of DNA thin films: an infrared spectroscopy study
title_short Effect of magnesium ions on the structure of DNA thin films: an infrared spectroscopy study
title_sort effect of magnesium ions on the structure of dna thin films: an infrared spectroscopy study
topic Structural Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5041487/
https://www.ncbi.nlm.nih.gov/pubmed/27484473
http://dx.doi.org/10.1093/nar/gkw696
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