A palladium-mediated DNA base pair of a beta-C-nucleoside possessing a 2-aminophenol as the nucleobase

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 met al coordination. Herein we report the X-ray crystal structure of a syntheti c intermediate 6 for the aminophenol-bearing nucleoside 3 and its metal coo rdination properties with Pd2+. The anomeric configuration of the nucleosid e was unequivocally determined to be beta -form by the X-ray analysis of 6; the structure has been resolved by direct methods (S1R97) and expanded usi ng Fourier techniques (DIRDIF94) using 2628 independent reflections with I >2.00 sigma (I) and 425 parameters. Final R (R-w) was 0.037 (0.043): orthor hombic space group P2(1)2(1)2(1) (#19) with a=16.562(1) Angstrom, b=16.933( 1) Angstrom, c=11.205(1) Angstrom, and V=3142.2(4) Angstrom (3); D-c=1.369g /cm(3) for Z=4, and molecular weight 647.65. This result is consistent with the tentative assignment by our previous H-1 NOE differentiation experimen ts. Detailed H-1 NMR studies showed that the nucleoside forms a stable 2:1 complex with Pd2+ with concomitant deprotonation of its phenolic proton. Al though there are two possible structures (cis or trans) for the square-plan ar Pd2+ complex, the ratio of cis to trans was approximately 1:1. The elect rospray ionization time-of-flight mass spectrum of the complex also provide d clear evidence for the 2:1 complexation.