Table 2.

The best-fit parameters for the DNA in construct for cyclization

DNA	Kink, °	Roll and tilt fluctuations, °	Twist fluctuations, °	Twist, °
B-DNA	−8.5 (±0.2)	4.56 (±0.03)	5.1 (±0.3)	34.13 (±0.09)
A-tracts	*	4.56 (±0.03)	5.1 (±0.3)	34.85

The fitting was performed by optimizing the magnitude and position of the kink for the unwanted curvature, twist of B DNA, and bending and twisting flexibilities, assuming a kink by roll and the same flexibilities for the A-tracts as those of B DNA. The bold A-tract twist is a fixed parameter for the optimization, shown here only for comparison. The base-pair fluctuations σ here are related to the persistence length P by P = 1/σ² with the helical rise l = 3.4 Å, or base pair as unit, and the torsional force constant C by C = lk_BT/σ², respectively (13). 

^*The parameters for the A-tract curvature are from ref. 29.