NMR-derived solution structure of a 17mer hydroxymethyluracil-containing DNA

Incorporation of 5-(hydroxymethyl)-2'-deoxyuridine into DNA in place of thy mine by SPO1, a Bacillus subtilis bacteriophage, allows the viral DNA to bi nd selectively to transcription factor 1, We have synthesized a TF1-binding site: d(5'-ACCHACHCHHHGHAGGT-3')-d(5'-ACCHACAAAGAGHAGGT-3') and studied th is molecule using NMR spectroscopy. The chemical shifts of exchangeable and non-exchangeable protons were sequentially assigned. Absence of correspond ing NOEs in the imino-imino region suggested that the end base pairs did no t form Watson-Crick hydrogen bond. Restrained molecular dynamics calculatio n yielded a family of B-DNA structures whose r.m.s.d. was 0.66 Angstrom (al l atoms) for the internal 15 bp, The helical twist was 38.5 degrees per ste p. The base pairs were situated directly on the helix axis (X-displacement = -0.2 Angstrom), Ail sugars exhibited C2'-endo puckering with P = 167.3 de grees and upsilon(max) = 38.2 degrees, The OH groups of all hmU bases resid ed on the 3' side of the base plane and may affect the base orientation rel ative to the sugar plane as the average chi value for all hmU was 4 degrees more positive than that of other nucleosides (258 degrees versus 254 degre es). Positive roll angles (rho) and small flanking twists (omega) at hmU su ggested that the two hmU-A base pair steps open toward the minor grooves.