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Exploring the Counterion Atmosphere around DNA: What Can Be Learned from Molecular Dynamics Simulations?

Manuel Rueda ^*, Elena Cubero ^* , Charles A. Laughton  and Modesto Orozco ^* 

^* Molecular Modelling and Bioinformatics Unit, Institut de Recerca Biomèdica, Parc Científic de Barcelona, Barcelona 08028, Spain; Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Barcelona 08028, Spain; and School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, United Kingdom

Correspondence: Address reprint requests to Modesto Orozco, E-mail: modesto{at}mmb.pcb.ub.es.

The counterion distribution around a DNA dodecamer (5'-CGCGAATTCGCG-3') is analyzed using both standard and novel techniques based on state of the art molecular dynamics simulations. Specifically, we have explored the population of Na⁺ in the minor groove of DNA duplex, and whether or not a string of Na⁺ can replace the spine of hydration in the narrow AATT minor groove. The results suggest that the insertion of Na⁺ in the minor groove is a very rare event, but that when once the ion finds specific sites deep inside the groove it can reside there for very long periods of time. According to our simulation the presence of Na⁺ inside the groove does not have a dramatic influence in the structure or dynamics of the duplex DNA. The ability of current MD simulations to obtain equilibrated pictures of the counterion atmosphere around DNA is critically discussed.

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