Abstract
Advanced Molecular Dynamics (MD) simulation protocols have been used to assess the ring puckering of cyclic D-ribose when the sugar is adsorbed on the most stable (0001) facet of calcium hydroxyapatite (HAp). In addition, sugar(...)mineral interactions, which are crucial for transfection processes and prebiotic chemistry, have been studied for systems in which the Ca2+ ions of the above mentioned ...
Abstract
Advanced Molecular Dynamics (MD) simulation protocols have been used to assess the ring puckering of cyclic D-ribose when the sugar is adsorbed on the most stable (0001) facet of calcium hydroxyapatite (HAp). In addition, sugar(...)mineral interactions, which are crucial for transfection processes and prebiotic chemistry, have been studied for systems in which the Ca2+ ions of the above mentioned HAp facet were totally or partially replaced by Mg2+. The latter replacement is spatially and quantitatively limited and has been found to cause important alterations in the conformational behavior of D-ribose that are similar to those suffered in hairpin RNA from A to B helical structures. Accordingly, replacement of Ca2+ by Mg2+ has a dramatic effect on the functionality of the nucleic acid. These changes have been related to both the substitution site on the surface and the amount of ions. Our results show that when replacement by Mg2+ occurs in OH--coordinated Ca2+ ions, Mg2+...D-ribose interactions are strong enough to prevent the interactions between the hydroxyl groups of the sugar and the remaining Ca2+ ions.
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