Nucleic Acid Double Helix - Base Pair Geometry

Base Pair Geometry

The geometry of a base, or base pair step can be characterized by 6 coordinates: Shift, slide, rise, tilt, roll, and twist. These values precisely define the location and orientation in space of every base or base pair in a nucleic acid molecule relative to its predecessor along the axis of the helix. Together, they characterize the helical structure of the molecule. In regions of DNA or RNA where the "normal" structure is disrupted, the change in these values can be used to describe such disruption.

For each base pair, considered relative to its predecessor, there are the following base pair geometries to consider:

• Shear
• Stretch
• Stagger
• Buckle
• Propeller twist: rotation of one base with respect to the other in the same base pair.
• Opening
• Shift: displacement along an axis in the base-pair plane perpendicular to the first, directed from the minor to the major groove.
• Slide: displacement along an axis in the plane of the base pair directed from one strand to the other.
• Rise: displacement along the helix axis.
• Tilt: rotation around this axis.
• vRoll: rotation around this axis.
• Twist: rotation around the helix axis.
• vx-displacement
• y-displacement
• inclination
• tip
• pitch: the number of base pairs per complete turn of the helix.

Rise and twist determine the handedness and pitch of the helix. The other coordinates, by contrast, can be zero. Slide and shift are typically small in B-DNA, but are substantial in A- and Z-DNA. Roll and tilt make successive base pairs less parallel, and are typically small. A diagram of these coordinates can be found in 3DNA website.

Note that "tilt" has often been used differently in the scientific literature, referring to the deviation of the first, inter-strand base-pair axis from perpendicularity to the helix axis. This corresponds to slide between a succession of base pairs, and in helix-based coordinates is properly termed "inclination".