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Base sequence specificity of counterion binding to DNA: what can MD simulations tell us?
Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Stockholms universitet, Science for Life Laboratory (SciLifeLab). University of Cagliari, Italy.
Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Università di Cagliari, Italy.
Vise andre og tillknytning
Rekke forfattare: 7
2016 (engelsk)Inngår i: Canadian journal of chemistry (Print), ISSN 0008-4042, E-ISSN 1480-3291, Vol. 94, nr 12, 1181-1188 s.Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

Nucleic acids are highly charged biopolymers whose secondary structure is strongly dependent on electrostatic interactions. Solvent molecules and ions are also believed to play an important role in mediating and directing both sequence recognition and interactions with other molecules, such as proteins and a variety of ligands. Therefore, to fully understand the biological functions of DNA, it is necessary to understand the interactions with the surrounding counterions. It is well known that monovalent counterions can bind to the minor groove of DNA with consecutive sequences of four, or more, adenine and thymine (A-tracts) with relatively long residence times. However, much less is known about their binding to the backbone and to the major groove. In this work, we used molecular dynamics simulations to both investigate the interactions between the backbone and major groove of DNA and one of its physiological counterions (Na+) and evaluate the relationship between these interactions and the nucleotide sequence. Three dodecamers, namely CGAAAATTTTCG, CGCTCTAGAGCG, and CGCGAATTCGCG, were simulated using the Toukan-Rahman flexible SPC water model and Smith and Dang parameters for Na+, revealing a significant sequence dependence on the ion binding to both backbone and major groove. In the absence of experimental data on the atomistic details of the studied interactions, the reliability of the results was evaluated performing the simulations with additional sets of potential parameters for ions and solvent, namely the A. qvist or the Joung and Cheatham ion parameters and the TIP3P water model. This allowed us to evaluate the results by verifying which features are preserved independently from the parameters adopted.

sted, utgiver, år, opplag, sider
2016. Vol. 94, nr 12, 1181-1188 s.
Emneord [en]
DNA-counterion interactions, DNA sequence specificity, ion parameters, molecular dynamics
HSV kategori
Identifikatorer
URN: urn:nbn:se:su:diva-139302DOI: 10.1139/cjc-2016-0296ISI: 000390320300026OAI: oai:DiVA.org:su-139302DiVA: diva2:1074273
Tilgjengelig fra: 2017-02-15 Laget: 2017-02-15 Sist oppdatert: 2017-02-15bibliografisk kontrollert

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Laaksonen, AattoPorcu, MassimilianoLyubartsev, Alexander P.
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