Incorporation of 5-(hydroxymethyl)-2′-deoxyuridine into DNA in place of thymine by SPO1, a Bacillus subtilis bacteriophage, allows the viral DNA to bind selectively to transcription factor 1. We have synthesized a TF1-binding site: d(5′-ACCHACHCHHHGHAGGT-3′)-d(5′-ACCHACAAAGAGHAGGT-3′) and studied this molecule using NMR spectroscopy. The chemical shifts of exchangeable and non-exchangeable protons were sequentially assigned. Absence of corresponding NOEs in the imino-imino region suggested that the end base pairs did not form Watson-Crick hydrogen bond. Restrained molecular dynamics calculation yielded a family of B-DNA structures whose r.m.s.d. was 0.66 Å (all atoms) for the internal 15 bp. The helical twist was 38.5° per step. The base pairs were situated directly on the helix axis (X-displacement × -0.2 Å). All sugars exhibited C2′-endo puckering with P = 167.3° and vmax × 38.2°. The OH groups of all hmU bases resided on the 3′ side of the base plane and may affect the base orientation relative to the sugar plane as the average x value for all hmU was 4° more positive than that of other nucleosides (258° versus 254°). Positive roll angles (p) and small flanking twists (ω) at hmU suggested that the two hmU-A base pair steps open toward the minor grooves.
NMR-derived solution structure of a 17mer Hydroxymethyluracil-containing DNA
PEPE, Antonietta;
1999-01-01
Abstract
Incorporation of 5-(hydroxymethyl)-2′-deoxyuridine into DNA in place of thymine by SPO1, a Bacillus subtilis bacteriophage, allows the viral DNA to bind selectively to transcription factor 1. We have synthesized a TF1-binding site: d(5′-ACCHACHCHHHGHAGGT-3′)-d(5′-ACCHACAAAGAGHAGGT-3′) and studied this molecule using NMR spectroscopy. The chemical shifts of exchangeable and non-exchangeable protons were sequentially assigned. Absence of corresponding NOEs in the imino-imino region suggested that the end base pairs did not form Watson-Crick hydrogen bond. Restrained molecular dynamics calculation yielded a family of B-DNA structures whose r.m.s.d. was 0.66 Å (all atoms) for the internal 15 bp. The helical twist was 38.5° per step. The base pairs were situated directly on the helix axis (X-displacement × -0.2 Å). All sugars exhibited C2′-endo puckering with P = 167.3° and vmax × 38.2°. The OH groups of all hmU bases resided on the 3′ side of the base plane and may affect the base orientation relative to the sugar plane as the average x value for all hmU was 4° more positive than that of other nucleosides (258° versus 254°). Positive roll angles (p) and small flanking twists (ω) at hmU suggested that the two hmU-A base pair steps open toward the minor grooves.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
