"...the tyranny of the lattice...".

Abstract

A systematic comparison of crystal structures of nine different B-DNA dodecamers, in three different space groups, with and without A-tracts, shows that crystal packing or lattice forces are of secondary importance for helix axis bending, minor-groove width, and propeller twist. While other local helix parameters may be influenced or even established by crystal packing, the properties just enumerated are determined primarily by base sequence. One and the same crystal packing scheme can accommodate a bend in one of two different directions, or no bend at all. A-tract regions of B-DNA are inherently straight and unbent, with base-pair inclination no different from that of general-sequence B-DNA. Where bends are observed at junctions between G.C and A.T regions, they always involve a roll about base-pair long axes in a direction that compresses the wide major groove and, hence, are 90 degrees away from that necessary for the correctness of the junction model of A-tract bending. The G.C/A.T junction appears to be a flexible hinge, capable of adopting either a straight or a bent conformation under the local influence of weak crystal packing forces. Such forces therefore are a source of information about DNA deformability and not a curse to be deplored. But as an indication of the weakness of crystal packing forces, introduction of a single bromine atom in the major groove is sufficient to eliminate a bend, although brominated and unbrominated crystals are isomorphous.

Distribution of bending propensity in DNA sequences

“…Also, protein-induced bending at TATA sequences seems to be especially pronounced [13][14][15][16][17]. The lowest bendability value, on the other hand, is associated with poly(dA) motifs, which is also in agreement with experimental data, obtained by nucleosome studies [9,17] and X-ray crystallography [20,21]. It is interesting to note that the motifs of highest helical asymmetry index are in fact the properly positioned combinations of these two type of segments (i.e.…”

How sequence defines structure: A crystallographic map of DNA structure and conformation

“…Thus, the crystal lattice serves less as a tyrant (15,16) here than as an experimental facilitator that leaves no doubt concerning the structure(s) of each sequence.…”

“…The potential problems, however, are those purported to be inherent in DNA crystallography, including the potential that lattice interactions greatly influence or actually induce the conformation observed in the crystal (15)(16)(17). The results demonstrate that the sequence motif designed for this study is highly crystallizable and samples DNA structures and conformational variations within these structural classes broadly, apparently independent of such overt crystal lattice effects.…”

The structure of a stable intermediate in the A ↔ B DNA helix transition

“…It is pointless to contend whether crystal or solution studies identify the ''true'' structural features of a given DNA sequence; these studies provide different snapshots of the range of conformations adaptable by a selectively flexible molecule. Indeed, the vaunted ''tyranny of the lattice'' should be appreciated as a source of information about molecular deformability (24).…”