A two-dimensional NMR study of the solution structure of a DNA dodecamer comprising the concensus sequence for the specific DNA-binding sites of the glucocorticoid receptor protein

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Abstract
A two‐dimensional 500‐MHz 1H‐NMR study on the non‐self‐complementary double‐stranded DNA dodecamer 5′d(C‐C‐A‐G‐A‐A‐C‐A‐G‐T‐G‐G)5′d(C‐C‐A‐C‐T‐G‐T‐T‐C‐T‐G‐G), is presented. This oligonucleo‐tide contains the consensus octanucleotide sequence 5′d(A‐G‐A‐A‐C‐A‐G‐T) for the specific DNA‐binding sites of the glucocorticoid receptor protein [Payvar, F. et al. (1984) Cell 35, 381–392]. Using a combination of two‐dimensional pure phase absorption nuclear Overhauser enhancement (NOESY) and homonuclear J‐correlated (COSY) spectroscopy all non‐exchangeable base (with the exception of the adenine H2 protons), methyl and deoxyribose H1′, H2′, H2″, H3′ and H4′ resonances are assigned unambiguously using a sequential resonance assignment strategy. From the relative intensities of the cross peaks in the pure phase absorption NOESY spectra at two mixing times it is shown that the dodecamer adopts a B‐type conformation in solution.