Theoretical Calculation of the NMR Spectroscopy Parameters Allow Distinguish Between the Specific Direct and the Water-mediated Binding of Divalent Metal Cation to Guanine.

Vladimír Sychrovský1
, Jiří Šponer2,1 and Pavel Hobza1


1 Institute of Organic Chemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, 166 10, Prague 6, Czech Republic

2 Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic

The calculated intermolecular and intramolecular indirect NMR spin-spin coupling constants and NMR shifts were used for the discrimination between the inner-shell and the outer-shell binding motif of hydrated divalent cations Mg2+ or Zn2+ with guanine base. The intermolecular coupling constants 1J(X,O6) and 1J(X,N7) (X = Mg2+, Zn2+) can be unambiguously assigned to the specific inner-shell binding motif of the hydrated cation either with oxygen O6 or with nitrogen N7 of guanine. To obtain reliable shifts in NMR parameters hydrated guanine was utilized as the reference state. The calculated change of NMR spin-spin coupling constants due to the hydration and coordination of the cation with guanine is caused mainly by the variation of Fermi-contact coupling contribution while the variation of diamagnetic spin – orbit, paramagnetic spin – orbit and spin – dipolar coupling contributions is small. The change of s – character of guanine sigma bonding, sigma anti-bonding and lone pair orbitals upon the hydration and cation coordination (calculated using the Natural Bond Orbital analysis) correlates with the variation of Fermi – contact term. The calculated NMR shifts δ(N7) of -15.3 and -12.2 ppm upon the coordination of Mg2+ and Zn2+ ion, are similar to the NMR shift of 19.6 ppm toward the high - field measured by Tanaka for N7 of guanine upon the coordination of Cd2+ cation (Tanaka, Y.; Kojima, C.; Morita, E. H.; Kasai. Y.; Yamasaki, K.; Ono, A.; Kainosho, M.; Taira, K. J. Am. Chem. Soc. 2002, 124, 4595-4601). The present data indicate that measurements of NMR intermolecular coupling constants may be used to discriminate between the specific inner and outer-shell binding of divalent cations to nucleobases in DNA and RNA.


Vladimír Sychrovský, Jiří Šponer and Pavel Hobza, J. Am. Chem. Soc. 2004, in press.