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Another useful tool for studying DNA is CD (Circular dichroism). This type of spectroscopy measures how a molecule selectively absorbs left- or righthanded circularly polarised light. It is sensitive to molecular chirality and, in the case of DNA, was notably used to predict that the Z form was a left-handed double helix. It can provide data on the orientation of the base pairs with respect to the helical axis, but quantitative interpretation of the data is not easy since it DNA structure, dynamics and recognition 19 Table 3 Energetics of DNA Stabilising factors: Base pairing (electrostatics/LJ) Base stacking (hydrophobic) Ion binding (electrostatics) Solvation entropy Destabilising factors: Phosphate repulsion (electrostatics) Solvation enthalpy (electrostatics/LJ) DNA strand entropy is still difficult to calculate the theoretical CD spectra corresponding to a given molecular conformation.
As an example, a 15 base pair DNA double helix (containing roughly 1000 atoms) requires a solvent shell of roughly 5000 water molecules. The simulated system is contained within a box, which is typically a rectangular prism or a truncated octahedron. Artefacts linked to edge-effects are avoided by symmetrically reproducing the box in all directions. These so-called “periodic boundary conditions” mean that a solvent molecule or ion leaving the simulation box on one side will simultaneously re-enter the box on the opposite side.
If you are interested in this area, look up the work of Peter Nielsen on PNA (peptide nucleic acid) where the sugar-phosphate backbone has been replaced with modified peptide linkages, without damaging the possibility of base pairing with conventional polynucleotides. A final structure which should be mentioned is the so-called Holliday junction (figure 6) which can be formed as a response to negative superhelical stress at inverted sequence repeats. Stress leads to local unpairing and the extrusion of two single strands which can then reform base pairs leading to a four helix junction.