HENRY M. SOBELL

BETA-DNA, A KEY STRUCTURAL INTERMEDIATE IN DNA MELTING

Beta-DNA is a distinctly different structural form from either B- or A- DNA. Evidence for its existence comes from studies of intercalation by drugs and dyes and the binding of certain proteins to DNA.

Although double-stranded, beta-DNA is unique in being both hyperflexible and metastable. Its hyperflexibility suggests a resemblance to a liquid-like phase, a phase in-between the more rigid B- and A- forms (i.e., both solid-like phases) and the melted single-stranded form (i.e., a gas-like phase). Both properties necessitate beta-DNA to be "pinned" by an intercalator or held by a protein in order to be studied in detail.

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-puckering 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 forms contain base pairs partially unstacked, while higher energy forms contain base pairs completely unstacked.

Why is beta-DNA an obligatory intermediate in DNA melting?

This is because beta-DNA lies on the minimal energy pathway connecting B-DNA with single-stranded melted DNA. Three distinctly different sources of nonlinearity appear as DNA chains unwind, and these determine the sequence of conformational changes that occur along this pathway.

The first two sources of nonlinearity stem from changes in the sugar-pucker conformations and base-pair stacking. These changes require small energies (i.e., kT), and appear as part of the initial structural distortions accompanying DNA unwinding. Starting with B-DNA, the effect of unwinding DNA is to counter-balance this with an equal but opposite right-handed superhelical writhing to keep the linking invariant. This is achieved through a modulated beta-alternation in sugar puckering along the chains, accompanied by the gradual partial unstacking of alternate base pairs.

The lowest energy beta-DNA structure emerges as an end result. Its metastability reflects the presence of additional energies in its structure that necessitate the partial unstacking of alternate base pairs.

The third source of nonlinearity arises from the stretching and the ultimate rupture of hydrogen bonds connecting base pairs.

At first, beta-DNA accommodates further unwinding through the gradual loss of superhelical writhing. This reflects the appearance of beta-structural elements having increasingly higher energy -- these have base pairs further unstacked and unwound. Eventually, however, a limit is reached and further unwinding begins to stretch hydrogen-bonds that connect base-pairs. Continued unwinding results in the disruption of these hydrogen-bonds, and the appearance of single-stranded DNA. This final sequence of conformational changes defines the boundary that connects beta-DNA to single-stranded melted DNA.

The highest energy beta-DNA form corresponds to a transition state intermediate in DNA melting (see APPENDIX A), while the lowest energy beta-DNA form is an obligatory structural intermediate in the B- to A- transition (see next section).