search for possible solutions to the phase problem. By use of all the intensities and phase values from the dif-
fraction pattern, it is then possible to calculate the electron density within all points in the unit cell by Fourier
transformation. The quality and resolution of the electron density map depends on the number of reflections
that can be included in the Fourier transformation and on the accuracy of their intensities and phases.
Oligonucleotides in crystals usually form close contacts with neighbouring molecules and their interactions
can include base–base hydrogen bonding. Thus, the effect of crystal packing can be a more serious source of
structural distortion. A difficulty in the interpretation of oligonucleotide crystal structures is the unknown
extent to which crystallization conditions and crystal packing may have affected the structure. For example
crystallization of nucleic acids usually requires a precipitant solvent, which often decreases the effective
hydration of the molecule. For example dehydration of DNA can cause a structural change from a B-type to
an A-type structure (Section 2.2). Occasionally oligonucleotides are crystallized in two different crystal forms.
Provided the molecular structures are similar despite the different packing interactions, one may conclude
that packing can be neglected in such cases as an important factor in the control of conformation. Crystal
packing forces can sometimes be viewed as a blessing rather than a curse.^23 For example the GC/AT junction
seems to be a flexible hinge, and packing forces can stabilize either straight or bent conformations, thus pro-
viding a source of information about DNA deformability.
If two or more crystal forms are available and/or the crystallographic asymmetric unit of a specific form
contains several independent subunits, it may be possible to sample multiple conformations of the same
molecule. Thus, alternative packing forces may trap particular conformational states of a molecule to yield
dynamic information. Such an analysis has provided insights into the conformational basis for a bulge-
mediated RNA self-cleavage reaction.^24
11.4 Hydrodynamic and Separation Methods
11.4.1 Centrifugation
Analytical ultracentrifugation(AUC) is a powerful analytical tool that allows the hydrodynamic or thermo-
dynamic solution state behaviour of proteins and nucleic acids to be characterised.25,26The AUC technique
should not be confused with preparative procedures carried out by use of standard ultracentrifuges.
Physical and Structural Techniques Applied to Nucleic Acids 439
Figure 11.11 Steps in X-ray crystallographic structure solution. (a) A crystal. (b) An X-ray photograph. (c) Spot
intensity measurement. (d) An electron density map. (e) A structural model