DNA structure from A to B.

P . Shing Ho and his colleagues at Oregon State and Berkeley publish in this issue of PNAS an interesting study (1) of helical structure in the DNA hexamer GGCGCC, finding that various states that appear to be logical intermediates between A-DNA and B-DNA can be induced by methylation or bromination of cytosine or by crystal packing. Their results bear on three issues that have been argued over in the past: (i) the differences between A-DNA and BDNA and transitions between them, (ii) the intrinsic sequence-dependent malleability of a DNA duplex, and (iii) the effects of local helix packing on DNA fine-structure. The six x-ray crystal structure analyses that provided the proposed intermediates in this and an earlier study (2) are listed in Table 1. The first three are straightforward, with one DNA helix per asymmetric unit or eight helices per tetragonal unit cell. The next three, however, are unusual. These crystals have three or four distinct hexamer helices per asymmetric unit, identical in sequence and crystallizing conditions, but differing in their local environment within the resulting crystals. Vargason et al. (1, 2) interpret these helical structures as intermediates between true A and B structures, characterizing them as composite (helices e and f), extended (helices g and h), or AyB intermediates (helices i, j, and k). Helices a–d are the B form, and helices l and m are the A form. Together these are stated to form a series of 13 hexamers (see their figure 2 in ref. 1) that bridges the entire range from B-DNA to A-DNA. (The reuse of label i in their table 2 in ref. 1 would appear to be a nomenclature error; if so, their structural progression then has 14 members rather than 13.) All three unique helices in the tetragonal crystals of GGCGGG 1 spermine adopt the B form. But the four independent molecules in each of the trigonal crystal forms having methylated or brominated C-3 exhibit at least three different helical types, which leaves the reader puzzled and wishing to know more. Three of the four helices in one crystal are said to form ‘‘a planar canopy in the a-b plane,’’ whereas the fourth helix rises perpendicular to this canopy along the c axis. Of the three helices in the canopy, one is A-DNA whereas the other two are AyB intermediates similar to that reported earlier for CATGGGCCCATG (3) and proposed for CCCCGGGG and GGGGCCCC in solution (4, 5). This perturbation of DNA helix structure by crystal environment cries out for careful analysis. The resulting 13 (or 14) helical structures can be grouped into a series extending from B-DNA to A-DNA, which is attempted in figures 2 and 3 of Vargason et al. (1). The most compelling parameter for their sequential arrangement is x-displacement or the displacement of a base pair away from the helix axis in the direction of the base pair short axis. This feature makes B-DNA (with near-zero x-displacement) a stack of base pairs along the helix axis and gives A-DNA (with large negative x-displacement) its central hole (6, 7). If a single parameter must be chosen with which to follow the B-to-A helix transition, then x-displacement obviously is the parameter of choice. The inclination of a base pair away from perpendicularity to the helix axis, measured along its long axis (see definitions and diagrams in refs. 8–11), is less helpful than one would expect. It has been common or received knowledge from fiber diffraction that base pairs in B-DNA were perpendicular to the helix axis, whereas those in A-DNA were inclined by 15° to 20°. Yet single crystal structure analyses have failed to bear that out; observed inclinations of base pairs in A-DNA crystals are much less, generally in the range of 5° to 12°. The present study of Vargason et al. (1) shows little or no correlation between helix type and base pair inclination angle, unless the composite and extended helices e–h are arbitrarily deleted from the analysis. Part of the problem with inclination as a parameter is that, in short helical segments such as these hexamers, inclination can be confused with local helix bending. The change in base pair orientation from one end of helix d to the other is easy to see in their figure 2 (1), for example. It can be ascribed to inclination, but much the same appearance would result if the helix segment were simply bent at its center in a direction that compresses the major groove at the right. Indeed, if the hexamer helix were bent at its center, then the inclination relative to an overall unbent axis would have one sense at the beginning of the helix, the opposite sense one-half turn of helix later, and the original sense again after a full turn. Careful examination of their figure 3 shows that this reversal of inclination is exactly what is observed in helix d and to a lesser extent in helices c, e, g, and h. Hence there is no compelling evidence for changes in inclination along the B-to-A series, but only for local helix bending, the latter probably induced by crystal packing. This inclination vs. bending issue illustrates how longer runs of helix than a half-turn hexamer become critical. The parameter slide or relative motion of two stacked base pairs along their long axes (see refs. 8–11) does appear to map the transition between B and A well. This