Bent DNA – Bending Index

This method predicts the bending of free DNA. If short stretches of a particular bent sequence repeat with a period close to the 10.5-bp pitch of the B-DNA double helix, it follows that local bending of a helix will sum to produce a persistent curvature of the whole sequence. According to Trifonov and Sussman (1980), certain dinucleotides, such as AA, when repeated with a period close to 10.5 bp, form a curvature in DNA as a result of a “wedge” angle inherent in AA dinucleotides.

Bent DNA – Bending Index computes the helical trajectory over the arc length. At the same time, the angle formed by two vectors parallel to the helical midpoint at the ends of the arc is measured. Using an arc length that exceeds the helical periodicity eliminates this periodicity bias for longer DNA segments. The method makes no attempt to predict the super coil structure of DNA. Nor does it take into account involvement of DNA-binding proteins on chromatin structure. Bent DNA – Bending Index should be used with the assumption that the DNA is free of proteins.

To change method parameters:

1. Double click on the method name in the Method Curtain or select the method display and then Analysis > Method Parameters.

2. Specify Arc Length, the window size used for each trajectory point determination.

3. Specify Threshold, the minimum value for calling a region “bent,” using values ranging from 0 to 180.