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• W2069664050 endingPage "4150" @default.
• W2069664050 startingPage "4143" @default.
• W2069664050 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." @default.
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• W2069664050 date "1999-11-01" @default.
• W2069664050 modified "2023-10-06" @default.
• W2069664050 title "NMR-derived solution structure of a 17mer hydroxymethyluracil-containing DNA" @default.
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• W2069664050 doi "https://doi.org/10.1093/nar/27.21.4143" @default.
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