Figure 2From: DNA secondary structure is influenced by genetic variation and alters susceptibility to de novo translocation In vitro assay for secondary structure formation induced by negative supercoiling. (A) The palindromic region can form cruciform structures in the presence of negative torsion of the double-stranded DNA, which is relieved upon cruciform extrusion. (B) EMSA for plasmids during agarose gel electrophoresis. The arrow indicates the position for plasmids with a negative supercoil, while the bracket indicates that for a relaxed plasmid that corresponds to the fraction with cruciform extrusion. In general, relaxed plasmids show up as a ladder consisting of various topoisomers with different linking numbers, which appears as a smear due to the low resolution of gel electrophoresis. (C) Correlation between translocation frequency and secondary structure-forming propensity of the PATRR estimated by EMSA. The horizontal axis indicates the percentage of plasmid extruding a cruciform, while the vertical axis indicates the de novo translocation frequency in sperm. A linear correlation was observed and was statistically significant (r = 0.71, P = 0.03).Back to article page