mechanism of action is unknown. However, it is likely that polyamines play an analogous role to histones
in that they may neutralise some of the negative charges on the DNA backbone and hence promote DNA
packaging. Direct binding of polyamines to DNA and the resulting modulation of protein–DNA inter-
actions appears to play an important role in cell proliferation.^9
9.5 Hydration Effects and Water–DNA Interactions
Hydration of DNAis essential for it to maintain its folded conformation.^9 Indeed the hydration state and
interactions with ions can exert large effects on nucleic acid conformation and hence influence the nature
of interactions with other ligands such as proteins (Section 10.4.2). Early fibre diffraction studies (Section 1.4)
showed that relative humidity has an effect on DNA conformation, such that B-type DNA is found at high
humidity values (above 85%) whereas A-form DNA occurs with lower humidity (between 75–80%) and
DNA becomes disordered if the relative humidity is lowered to between 55 and 75%. In addition, base-
composition and salt concentration affect the values of relative humidity under which one or other con-
formation is favoured.
In practice, it is very challenging to study water–DNA interactionsexperimentally. Useful data have
been obtained from gravimetric studies and infrared (IR) spectra of DNA films as a function of relative
humidity. Visualization of specific water molecules from X-ray diffraction analysis of single DNA crys-
tals has also proved difficult in the past. This is because a crystal is derived typically from aqueous solu-
tion that also contains cations such as Mg^2 or spermine, and alcohols such as 2-methyl-2,4-pentanediol
(MPD7). Thus at resolutions of 2 Å or above, it is difficult to distinguish whether a particular electron den-
sity corresponds to water, a cation, or a spermine molecule.
Much of our present understanding of DNA hydration (as well as other biophysical characteristics of DNA)
has come from studies of the Dickerson–Drew dodecamer(Section 2.2.4, Figure 2.17). This oligonucleotide
duplex, with the sequence d(CGCGAATTCGCG) 2 , provided the first published B-DNA X-ray crystal struc-
ture. It is the best studied DNA sequence with over 68 isomorphous members of the d(CGCXAATTYGCG) 2
(XG or A; YC or T) dodecamer family, and numerous biophysical and binding studies have been
carried out with it in solution. In the early 1980s, Dickerson and co-workers obtained several structures of
this sequence, for example, at room temperature, at 16 K or at 7°C for the 9-bromo derivative in MPD7.^10
Hydration was not readily visible in the room temperature structure due to high Bvalues. However the
16 K and MPD7 structures were extensively hydrated with 65 solvent peaks and an average of three waters
per phosphate. In the major groove, 19 solvent molecules formed a first hydration layer around nitrogen
and oxygen atoms of the bases in that groove. A second hydration layer contained a further 36 solvent mol-
ecules that formed clusters spanning the major groove. In the minor groove, a zigzag pattern of water mol-
ecules formed a “spine of hydration” in all the structures (Section 2.2.4, Figure 2.18). This concept of a spine
of hydration has become pervasive in DNA chemistry and is often invoked to explain a multitude of effects
related to DNA stability and ligand binding.
346 Chapter 9
Figure 9.2 Structures of two outside-edge electrostatic DNA binding ligands, spermine and spermidine