A Palladium-mediated DNA Base Pair of a β-C-Nucleoside Possessing a 2-Aminophenol as the Nucleobase

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Abstract
An approach we have used in this study for the incorporation of metal ions into DNA, is the direct modification of a DNA base itself, turning it into a metal-chelating nucleobase wherein two nucleobases are paired through metal coordination. Herein we report the X-ray crystal structure of a synthetic intermediate 6 for the aminophenol bearing nucleoside 3 and its metal coordination properties with Pd2+. The anomeric configuration of the nucleoside was unequivocally determined to be β-form by the X-ray analysis of 6; the structure has been resolved by direct methods (S1R97) and expanded using Fourier techniques (DIRDIF94) using 2628 independent reflections with I>2.00 [sgrave](I) and 425 parameters. Final R (Rw) was 0.037 (0.043): orthorhombic, space group P212121 (#19) with a=16.562(1) Å, b=16.933(1) Å, c=11.205(1) Å, and V=3142.2(4) Å3; Dc =1.369g/cm3 for Z=4, and molecular weight 647.65. This result is consistent with the tentative assignment by our previous 1H NOE differentiation experiments. Detailed 1H NMR studies showed that the nucleoside forms a stable 2:1 complex with Pd2+ with concomitant deprotonation of its phenolic proton. Although there are two possible structures (cis or trans) for the square-planar Pd2+ complex, the ratio of cis to trans was approximately 1:1. The electrospray ionization time-of-flight mass spectrum of the complex also provided clear evidence for the 2:1 complexation.