HENRY M. SOBELL
THE STRUCTURE AND PROPERTIES OF BETA-DNA
Beta-DNA is a distinctly different structural phase from either A- or B- DNA. It is both metastable and hyperflexible and, for this reason, must be held ("pinned") by a suitable intercalator or DNA binding protein to be studied in detail. The underlying source of nonlinearity that separates beta-DNA from either A- or B-DNA is the presence of both C2' endo and C3' endo sugar pucker conformations.
The structure is composed of repeating units called beta-structural elements. These are a family of base-paired dinucleotide structures, each possessing the same mixed sugar-pucker pattern (i.e., C3' endo (3'-5') C2' endo) and having similar backbone conformational angles, but varying in the degree of base unstacking. Lower energy beta-structural elements contain base pairs partially unstacked, while higher energy beta-structural elements contain base pairs completely unstacked.
Why is beta-DNA a metastable structural phase?
This reflects the presence of additional energies in its lowest energy structure that necessitate base pairs within beta-structural elements to remain partially unstacked. For example, partial base pair unstacking may be required to relieve strain energy in the sugar-phosphate backbone (and/or elsewhere in the structure) as the lowest energy beta-DNA structure emerges from A- or B-DNA.
Why is beta-DNA a hyperflexible structural phase?
The presence of partial base pair unstacking acts to weaken van der Waals forces stabilizing stacking interactions between base pairs. In addition, the altered sugar-phosphate backbone stereochemistry present within each beta-structural element allows DNA to stretch and to unwind due to the presence of unhindered rotation around glycosidic bonds and other sugar-phosphate linkages. These combined effects give the beta-structural element hinge-like properties, and explain why beta-DNA is a hyperflexible structural phase.