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. Author manuscript; available in PMC: 2011 Mar 28.
Published in final edited form as: Nat Protoc. 2008;3(7):1213–1227. doi: 10.1038/nprot.2008.104

Figure 1.

Figure 1

Pictorial definitions of rigid-body parameters used to describe the geometry of complementary (or non-complementary) base pairs and sequential base pair steps. The base pair reference frame (lower left) is constructed such that the x-axis points away from the (shaded) minor groove edge of a base or base pair and the y-axis points toward the sequence strand (I). The relative position and orientation of successive base pair planes are described with respect to both a dimer reference frame (upper right) and a local helical frame (lower right). Images illustrate positive values of the designated parameters. Reproduced with permission from Nucleic Acids Research.