The NMR Structure of a DNA Dodecamer in an Aqueous Dilute Liquid Crystalline Phase

Abstract

The solution structure of the DNA dodecamer d(CGCGAATTCGCG) 2 has been studied in an aqueous liquid crystalline medium containing 5% w/v bicelles. These phospholipid particles impose a small degree of orientation on the DNA duplex molecules with respect to the magnetic field and permit the measurement of dipolar interactions. Experiments were carried out on several samples with different isotopic labeling patterns, including two complementary samples, in which half of the nucleotides were uniformly enriched with 13 C and deuterated at the H2‘ ‘and H5‘ positions. From this, 198 13 C− 1 H and 10 15 N− 1 H one-bond dipolar coupling restraints were derived, in addition to 200 approximate 1 H− 1 H dipolar coupling and 162 structurally meaningful NOE restraints. Although loose empirical restraints for the phosphodiester backbone torsion angles were essential for obtaining structures that satisfy all experimental data, they do not contribute to the energetic penalty function of the final minimized structures. Except for additional regular Watson−Crick hydrogen bond restraints and standard van der Waals and electrostatic terms used in the molecular dynamics-based structure calculation, the structure is determined primarily by the dipolar couplings. The final structure is highly regular, without any significant bending or kinks, and with C2‘-endo/C1‘-exo sugar puckers corresponding to regular B-form DNA. Most local parameters, including sugar puckers, glycosyl torsion angles, and propeller twists, are also tightly determined by the NMR data. The precision of the determined structures is limited primarily by the uncertainty in the exact magnitude and rhombicity of the alignment tensor. This causes considerable spread in parameters such as the degree of base-pair opening and the width of the minor groove, which are relatively sensitive to the alignment tensor values used.