On the competition between water, sodium ions, and spermine in binding to DNA: a molecular dynamics computer simulation study.
The interaction of DNA with the polyamine spermine(4+) (Spm(4+)), sodium ions, and water molecules has been studied using molecular dynamics computer simulations in a system modeling a DNA crystal. The simulation model consisted of three B-DNA decamers in a periodic hexagonal cell, containing 1200 water molecules, 8 Spm(4+), 32 Na(+), and 4 Cl(-) ions. The present paper gives a more detailed account of a recently published report of this system and compares results on this mixed Spm(4+)/Na(+)-cation system with an molecular dynamics simulation carried out for the same DNA decamer under similar conditions with only sodium counterions (Korolev et al., J. Mol. Biol. 308:907). The presence of Spm(4+) makes significant influence on the DNA hydration and on the interaction of the sodium ions with DNA. Spermine pushes water molecules out of the minor groove, whereas Na(+) attracts and organizes water around DNA. The major binding site of the Spm(4+) amino groups and the Na(+) ions is the phosphate group of DNA. The flexible polyamine spermine displays a high presence in the minor groove but does not form long-lived and structurally defined complexes. Sodium ions compete with Spm(4+) for binding to the DNA bases in the minor groove. Sodium ions also have several strong binding sites in the major groove. The ability of water molecules, Spm(4+), and Na(+) to modulate the local structure of the DNA double helix is discussed.
Korolev
Nikolay
N
Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S 106 91 Stockholm, Sweden.
Lyubartsev
Alexander P
AP
Laaksonen
Aatto
A
Nordenskiöld
Lars
L
D001483:Base Sequence; D001667:Binding, Competitive; D055592:Biophysical Phenomena; D001703:Biophysics; D002412:Cations / Q000378:metabolism; D003198:Computer Simulation; D003460:Crystallization; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D066298:In Vitro Techniques; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012964:Sodium / Q000378:metabolism*; D013096:Spermine / Q000378:metabolism*; D013816:Thermodynamics; D014867:Water / Q000378:metabolism
D002412:Cations; D014867:Water; D013096:Spermine; D004247:DNA; D012964:Sodium