Abstract
A novel deoxynucleoside, 2‘-deoxy-7-(hydroxymethyl)-7-deazaadenosine, was synthesized with the intent of using the analogue to mimic the role of “structural” waters in the major groove of DNA. The target compound was synthesized in four steps starting from 2-((ethoxymethylene)amino)-5-bromo-1-(2‘-deoxy-3‘,5‘-di-O-p-toluoyl-β-d-erythro-pentofuranosyl)pyrrole-3,4-dicarbonitrile. The structure was characterized by X-ray diffraction and proton NMR spectroscopic analyses. The crystal structure shows an intramolecular hydrogen bond between an amino proton on N6 and the oxygen of the hydroxymethyl group. When superimposed onto particular adenines in the structure of the tryptophan (trp) repressor/operator complex, the analogue places the oxygen of the hydroxymethyl group very near the oxygen contributed by the water in the protein/DNA complex. This analogue may be useful for probing the role of structural waters in other specific protein/DNA complexes and in DNA bending.
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