Structural origins of adenine-tract bending

Abstract

DNA sequences containing short adenine tracts are intrinsically curved and play a role in transcriptional regulation. Despite many high-resolution NMR and x-ray studies, the origins of curvature remain disputed. Long-range restraints provided by 85 residual dipolar couplings were measured for a DNA decamer containing an adenine (A)(4)-tract and used to refine the structure. The overall bend in the molecule is a result of in-phase negative roll in the A-tract and positive roll at its 5' junction, as well as positive and negative tilt inside the A-tract and near its junctions. The bend magnitude and direction obtained from NMR structures is 9.0 degrees into the minor groove in a coordinate frame located at the third AT base pair. We evaluated long-range and wedge models for DNA curvature and concluded that our data for A-tract curvature are best explained by a "delocalized bend" model. The global bend magnitude and direction of the NMR structure are in excellent agreement with the junction model parameters used to rationalize gel electrophoretic data and with preliminary results of a cyclization kinetics assay from our laboratory.

Figure 1

Stereo view of the 10 lowest-energy A4 decamer structures calculated with dipolar couplings superimposed on inner 8 bp. The A-tract strand is facing toward the reader.

Figure 2

Structural parameters of 10 best A4 structures calculated with (black circles) and without (red squares) dipolar couplings. (A) local helical parameters. (B) Propeller twist and buckle. (C) Minor groove width (P–P distances). All parameters were calculated with 3DNA (28). Error bars represent three standard deviations of the mean.

Figure 3

Comparisons of experimental results with predictions of various models (for identical inner 8 bp of the A4 sequence). (A) Local helical parameters. (B) Global bend magnitudes and directions. Axes point in the direction of major groove at each base pair. Circles represent bends of 5, 10, and 15°. Global bends were modeled with madbend (36).

Figure 4

Comparisons of local base pair parameters of A4 (black circles) and A6 (red squares) (42) structures. Values of the A4 decamer have been translated onto the A6 dodecamer. All parameters were calculated with 3DNA (28).