Studies on the hydrodynamic properties of DNA show that general-sequence DNA migrates through
gels more slowly than expected which is because the DNA helix occupies a cylindrical volume that has a
larger diameter than that of a simple B-helix (Section 11.4.3). This phenomenon is a result of DNA writhing,
which involves a continuously curved distortion of the helix axis to generate a spiral form and is nicely illus-
trated by the extension of a coiled telephone wire (Figure 2.24b). It follows that the repeated alternation of
straight A-tracts with short sections of general sequence, each having half of a writhing turn, will generate
curved DNA (Figure 2.24c). A detailed structural analysis of this explanation says that curvature of B-DNA
involves rolling of base pairs, compresses the major groove (which corresponds to positive roll), has a
sequence-determined continuum in the bending behaviour, and shows anisotropy of flexible bending.
2.3.3.2 DNA Bending. Such intrinsic, sequence-dependent curvature must be distinguished from the
bending of DNA, which results from the application of an external force. Dickerson has also examined the
bending of the DNA helix that occurs in many crystal structures of the B-form. It is associated with
the step from a GC to an AT base pair and results from rolling one base pair over the next along their
long axes in a direction that compresses the major groove (Figure 2.19c). He suggests that this junction is
a flexible hinge that is capable of bending or not bending. Such ‘facultative bending’responds to the influ-
ence of local forces, typically interactions with other macromolecules, for example control proteins or a
nucleosome core. By contrast, poly(dA) tracts are known to resist bending in nucleosome reconstitution
experiments. It can thus be seen that sequence-dependent variation in DNA bendabilityis an important fac-
tor in DNA recognition by proteins.
One important conclusion emerges: DNA has evolved conformationally to interact with other macro-
molecules. A free, linear DNA helix in solution may, in fact, be the least biologically relevant state of all.^24
Slipped structureshave been postulated to occur at direct repeat sequences, and they have been found
up-stream of important regulatory sites. The structures described (Figure 2.24a) are consistent with the
pattern of cleavage by single-strand nucleases but otherwise are not well characterised.
Purine–pyrimidine tractsmanifest an unusual structure at low temperature with a long-range, sequence-
dependent single base shift in base-pairing in the major groove. For the dodecamer d(ACCGGCGCCACA)
d(TGTGGCGCCGGT), the bases in the d(CA)ntract have high propeller twist (–32°) and are so strongly
tilted in the 3-direction that there is disruption of Watson–Crick pairing in the major groove and forma-
tion of interactions with the 5-neighbour of the complementary base. This alteration propagates along the
B-form helix for at least half a turn with a domino-like motion. As a result, the DNA structure is normal
when viewed from the minor groove and mismatched when seen from the major groove. Since (CA)ntracts
are involved both in recombination and in transcription, this new recognition pattern has to be considered
in the analysis of the various processes involved with reading of genetic information.
Anisomorphic DNAis the description given to DNA conformations associated with direct repair, DR2,
sequences at ‘joint regions’ in viral DNA, which are known to have unusual chemical and physical properties.
The two complementary strands have different structures and this leads to structural aberrations at the centre
of the tandem sequences that can be seen under conditions of torsional stress induced by negative supercoiling.
Hairpin loopsare formed by oligonucleotide single strands which have a segment of inverted comple-
mentary sequence. For example, the 16-mer d(CGCGCGTTTTCGCGCG) has a hexamer repeat and its
crystal structure shows a hairpin with a loop of four Ts and a Z-DNA hexamer stem (Figure 2.25a). When
such inverted sequences are located in a DNA duplex, the conditions exist for formation of a cruciform.
Cruciformsinvolve intra-strand base-pairing and generate two stems and two hairpin loops from a sin-
gle unwound duplex region.^26 The inverted sequence repeats are known as palindromes, which have a
given DNA duplex sequence followed after a short break by the same duplex sequence in the opposite
direction. This is illustrated for a segment of the bacterial plasmid pBR322 (Figure 2.25b), where a palin-
drome of two undecamer sequences exists.
X-ray, NMR and sedimentation studies of such stem–loop structures show that the four arms are aligned
in pairs to give an oblique X structure with continuity of base-stacking and helical axes across the junc-
tions (Section 6.8.1). Also, the loops have an optimum size of from four to six bases. Residues in the loops
40 Chapter 2