Structure of a tethered cationic 3-aminopropyl chain incorporated into an oligodeoxynucleotide: evidence for 3'-orientation in the major groove accompanied by DNA bending.

Journal Article (Journal Article)

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 omega-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 (31)P NMR resonance in the 3'-direction at the phosphodiester linkage between nucleotides C(9) and G(10). Molecular dynamics calculations restrained by distances obtained from (1)H NOE data and torsion angles obtained from (1)H NMR (3)J coupling data, and in which the omega-amino group was constrained to be proximate to G(10)O(6), predicted from the (31)P 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 A, which indicated that in this dodecamer the Z3dU amino group did not participate in a salt bridge to its 5'-phosphate.

Full Text

Duke Authors

Cited Authors

  • Li, Z; Huang, L; Dande, P; Gold, B; Stone, MP

Published Date

  • July 24, 2002

Published In

Volume / Issue

  • 124 / 29

Start / End Page

  • 8553 - 8560

PubMed ID

  • 12121096

International Standard Serial Number (ISSN)

  • 0002-7863

Digital Object Identifier (DOI)

  • 10.1021/ja0201707


  • eng

Conference Location

  • United States