Figure 2

Deviations of DNA structure from the average B-form DNA that play a role modeling three-dimensional structures of specific DNA sequences. The figure illustrates physical parameters of B-form DNA structure that are altered in preferred sites for integration of insertional vectors. (a) B-form DNA. (b) A-DNA. Interactions between neighboring nucleotides govern the variable energy needed to convert from B-DNA to A-DNA. The propensity of a sequence of B-form DNA to adopt the A-form is referred to as A-philicity [134]. (c) Parameters of base pair orientation affected by protein-DNA binding. 'Twist' (horizontal looping arrow) refers to the rotation of base pairs around a central axis (heavy vertical black line); the average rotation between two base pairs is 36°. 'Tilt' (dotted lines) refers to the inclination of the base pairs with respect to the central axis; the average tilt is 0° between base pairs, which are normally parallel in B-form DNA. 'Rise' (vertical double arrowhead) is the distance between adjacent base pairs; the normal spacing is slightly more than 3.3 Å, but it can be more than 3.4 Å at preferred target sites. 'Slide' (horizontal double arrowhead) refers to the shifting of the axis of a base pair out of alignment with the central axis. 'Roll' (vertical looping arrow) refers to rotation of the nucleotide plane around a horizontal axis. A given base pair may be distorted in more than one of these parameters. V _step analysis is a method of examining these, and other physical parameters such as 'shift', in terms of a single number that derives from the transition from one base pair to another [131,137]. (d) DNA bendability