Interproton distance measurements in solution for a double-stranded DNA undecamer comprising a portion of the specific target site for the cycliC AMP receptor protein in the gal operon. A nuclear Overhauser enhancement study.

Using the proton-proton nuclear Overhauser effect, a large number (150) of interproton distances, both intra- and internucleotide, are determined in solution for a non-self-complementary DNA undecamer comprising a portion of the specific target site for the cAMP receptor protein in the gal operon. It is shown that these distances are very similar to those expected for classical B DNA (RMS difference of 0.5 A) but are significantly different from those expected for classical A DNA (RMS difference 1.1A). Glycosidic (chi) and C4'-C3' (delta) bond torsion angles are obtained by model building on the basis of the intranucleotide interproton distances. Whereas the sugar pucker exhibits little base-to-base variation with delta lying in the range 120 +/- 10 degrees, the glycosidic bond torsion angles of the pyrimidine and purine residues are significantly different, with chi pyr = -120 +/- 10 degrees and chi pur = -90 +/- 10 degrees.