Similarities and differences in interaction of K+ and Na+ with condensed ordered DNA. A molecular dynamics computer simulation study

• Published in: Nucleic acids research 2006-01, Vol.34 (2), p.686-696
• Main Authors: Cheng, Yuhua, Korolev, Nikolay, Nordenskiöld, Lars
• Format: Article
• Language: English
• Subjects: Base Pairing; Cations - chemistry; Computer Simulation; Diffusion; DNA - chemistry; Models, Molecular; Nucleic Acid Conformation; Phosphates - chemistry; Potassium - chemistry; Sodium - chemistry; Water - chemistry
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkj434

Four 20 ns molecular dynamics simulations have been performed with two counterions, K+ or Na+, at two water contents, 15 or 20 H2O per nucleotide. A hexagonal simulation cell comprised of three identical DNA decamers [d(5′-ATGCAGTCAG) × d(5′-TGACTGCATC)] with periodic boundary condition along the DNA helix was used. The simulation setup mimics the DNA state in oriented DNA fibers or in crystals of DNA oligomers. Variation of counterion nature and water content do not alter averaged DNA structure. K+ and Na+ binding to DNA are different. K+ binds to the electronegative sites of DNA bases in the major and the minor grooves, while Na+ interacts preferentially with the phosphate groups. Increase of water causes a shift of both K+ and Na+ from the first hydration shell of O1P/O2P and of the DNA bases in the minor groove with lesser influence for the cation binding to the bases in the major groove. Mobility of both water and cations in the K–DNA systems is faster than in the Na–DNA systems: Na+ organizes and immobilizes water structure around itself and near DNA while for K+ water is less organized and more dynamic.