title: Interaction of cyclic cytosine-, guanine-, thymine-, uracil- and mixed guanine-cytosine base tetrads with K+, Na+ and Li+ ions -- a density functional study.
abstract: We have carried out B3LYP hybrid density functional studies of complexes formed by cyclic cytosine-, guanine-, thymine-, uracil- and mixed guanine cytosine-tetrads with Li+, Na+ and K+ ions to determine their structures and interaction energies. The conformations studied have been restricted to a hydrogen bond pattern closely related to the tetrads observed in experimental nucleic acid structures. A comparison of the alkali metal ion/tetrad complexes with the tetrads without cations indicates that alkali metal ions modulate the tetrad structures significantly and that even the hydrogen bond pattern may change. Guanine-tetrad cation complexes show the strongest interaction energy compared to other tetrads that occur less frequently in experimental structures. The most stable G-tetrad/metal ion structure adopts a nearly planar geometry that is especially suitable for tetraplex formation, which requires approximately parallel tetrad planes. In the cytosine-tetrad there is a very large central cavity suitable for cation recognition, but the complexes adopt a non-planar structure unsuitable for stacking, except possibly for ions with very large radii. Uracil and thymine tetrads show a significant different characteristics which may contribute to the differences between DNA and RNA
authors.affiliation: Revotar Biopharmaceuticals AG, Neuendorfstrasse 24a, D-16761, Hennigsdorf, Germany. m.meyer@revotar-ag.de
authors.forename: Michael
authors.initials: M
authors.lastname: Meyer
authors.forename: Jürgen
authors.initials: J
authors.lastname: Sühnel
mesh_terms: D000465:Algorithms; D020029:Base Pairing; D002414:Cations, Monovalent / Q000737:chemistry; D003596:Cytosine / Q000737:chemistry*; D006147:Guanine / Q000737:chemistry*; D006860:Hydrogen Bonding; D008094:Lithium / Q000737:chemistry; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D011188:Potassium / Q000737:chemistry; D012964:Sodium / Q000737:chemistry; D055672:Static Electricity; D013816:Thermodynamics; D013941:Thymine / Q000737:chemistry*; D014498:Uracil / Q000737:chemistry*
chemical_list: D002414:Cations, Monovalent; D014498:Uracil; D006147:Guanine; D003596:Cytosine; D008094:Lithium; D012964:Sodium; D013941:Thymine; D011188:Potassium