Analysis of DNA bending by transient electric birefringence

Transient electric birefringence has been used to analyze DNA bending in six restriction fragments containing 171, 174, 207, 263, 289, and 471 bp in three different low ionic strength buffers. The target fragments contain sequences corresponding to the apparent bend centers in pUC19 and Litmus 28, previously identified by the circular permutation assay (Strutz, K.; Stellwagen, N. C. Electrophoresis 1996, 17, 989–995) . The target fragments migrate anomalously slowly in polyacrylamide gels and exhibit birefringence relaxation times that are shorter than those of restriction fragments of the same size, taken from nonbent regions of the same plasmids. Apparent bend angles ranging from 30° to 41° were calculated for the target fragments by τ‐ratio method. The bend angles of four of the target fragments were independent of temperature from 4°C to 20°C, but decreased when the temperature was increased to 37°C. The bend angles of the other two target fragments were independent of temperature over the entire range examined, 4°–37°C. Hence, the thermal stability of sequence‐dependent bends in random‐sequence DNA is variable. The bend angles of five of the six target fragments were independent of the presence or absence of Mg 2+ ions in the solution, indicating most of the target fragments were stably bent or curved, rather than anisometrically flexible. Restriction fragments containing 219 and 224 bp, with sequences somewhat offset from the sequence of the 207 bp fragment, were also studied. Comparison of the τ‐ratios of these overlapping fragments allowed both the bend angle and bend position to be independently determined. These methods should be useful for analyzing sequence‐dependent bending in other random‐sequence DNAs. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 270–288, 2003