FOOTNOTE

Deoxyribose sugar residues, both as individual molecules or joined within the polymer structure, can assume either C2' endo or C3' endo pucker conformations. Both conformations have similar energies. Through the use of the pseudorotational parameter (a mathematical parameter that defines the sugar conformation), one can explore the energies of the complete range of conformational states. These calculations show energy minima at C2' and C3' endo regions. These are connected by a minimal energy pathway having a barrier of about 1.5 kcal/mole.

In B-DNA, sugar residues are in the C2' endo family of structures, whereas, in A-DNA, they are in the C3' endo family. The transition region separating these two sugar pucker conformations is, therefore, a key source of nonlinearity that separates the A- and B- conformational states.

Beta-DNA utilizes a similar source of nonlinearity (i.e., the beta-structural element contains both C3' endo and C2' endo sugar puckers) to distinguish it from the A- and B- forms. Its metastability reflects the presence of additional energies in its structure that necessitate the partial unstacking of alternate base pairs (within beta-structural elements) in its lowest energy form.

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