| Abstract
| - The solution structure of the DNA dodecamer d(CGCGAATTCGCG)2 has been studied in an aqueousliquid crystalline medium containing 5% w/v bicelles. These phospholipid particles impose a small degree oforientation on the DNA duplex molecules with respect to the magnetic field and permit the measurement ofdipolar 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 13C anddeuterated at the H2‘ ‘and H5‘ positions. From this, 198 13C−1H and 10 15N−1H one-bond dipolar couplingrestraints were derived, in addition to 200 approximate 1H−1H dipolar coupling and 162 structurally meaningfulNOE restraints. Although loose empirical restraints for the phosphodiester backbone torsion angles were essentialfor obtaining structures that satisfy all experimental data, they do not contribute to the energetic penalty functionof the final minimized structures. Except for additional regular Watson−Crick hydrogen bond restraints andstandard 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, withoutany significant bending or kinks, and with C2‘-endo/C1‘-exo sugar puckers corresponding to regular B-formDNA. Most local parameters, including sugar puckers, glycosyl torsion angles, and propeller twists, are alsotightly determined by the NMR data. The precision of the determined structures is limited primarily by theuncertainty in the exact magnitude and rhombicity of the alignment tensor. This causes considerable spread inparameters such as the degree of base-pair opening and the width of the minor groove, which are relativelysensitive to the alignment tensor values used.
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