Structure of a Tethered Cationic 3-Aminopropyl Chain Incorporated into an Oligodeoxynucleotide:  Evidence for 3‘-Orientation in the Major Groove Accompanied by DNA Bending

The structure of the dodecamer d(CGCGAATXCGCG)2, in which X = Z3dU, 5-(3-aminopropyl)-2‘-deoxyuridine, was determined. At neutral pH, Z3dU introduced a positive charge into the major groove. NMR spectroscopy revealed that the Z3dU ω-aminopropyl moiety oriented in the 3‘-direction from the site of modification. Watson−Crick base pairing remained intact throughout the dodecamer. The presence of the charged amino group in the major groove resulted in a 0.24 ppm upfield shift of one 31P NMR resonance in the 3‘-direction at the phosphodiester linkage between nucleotides C9 and G10. Molecular dynamics calculations restrained by distances obtained from 1H NOE data and torsion angles obtained from 1H NMR 3J coupling data, and in which the ω-amino group was constrained to be proximate to G10O6, predicted from the 31P NMR data and molecular modeling (Dande, P.; Liang, G.; Chen, F.-X.; Roberts, C.; Nelson, M. G.; Hashimoto, H.; Switzer, C.; Gold, B. Biochemistry 1997, 36, 6024−6032), were consistent with experimental NOEs. These refined structures exhibited bending. The distance from the amino group to the 5‘-phosphate oxygen of Z3dU was >5 Å, which indicated that in this dodecamer the Z3dU amino group did not participate in a salt bridge to its 5‘-phosphate.