Structure and Dynamics of Nucleic Acids
Theoretical Study on the Factors Controlling the Stability of the Borate Complexes of Ribose, Arabinose, Lyxose, and Xylose
Published: CHEMISTRY-A EUROPEAN JOURNAL 14, 9990-9998 Authors: Sponer, JE., Sumpter, BG., Leszczynski, J., Sponer, J., Fuentes-Cabrera, M. Year: 2008
Recent experimental studies suggest that complexation with borate minerals stabilizes ribose, and that the borate complex of ribose is more stable than those of related aldopentoses, that is, arabinose, lyxose, and xylose. These findings have revived the debate on the plausibility of the RNA-world theory, because the), provide an explanation for the stabilization and selection of ribose in prebiotic conditions. In this paper we unravel the factors that make the ribose-borate complex the most stable one. For this purpose, we have investigated the structure and stability of the ribose-, arabinose-, lyxose-, and xylose-borate complexes using density functional theory and a continuum solvent approach. The computed results reveal that in the aldopentose-borate complexes, the electrostatic field of the borate is strong enough to change the orientation of the nearby hydroxyl groups compared to noncomplexed aldopentoses. In addition, we show that the distinct stability of the ribose-borate 2:1 complex can be attributed to 1) a strong hydrogen bond between the ribose 3-OH and one of the negatively charged borate oxygen atoms, and 2) a favorable contact between the aqueous medium and the 5-CH2OH group due to the space separation between the 5-CH2OH group and the borate anion.