Physical and Structural Techniques Applied to Nucleic Acids 451
Figure 11.17 Matrix-assisted laser desorption/ionization time-of-flightmass spectrum of the crude products of a
chemical synthesis of 19-mer oligodeoxynucleotide d(GGATTACAGGTATGAGCCA) showing a major
component at 5879.8 (calculated 5876.8). This routine spectrum was obtained on an Applied
Biosystems Voyager DE workstation (linear, negative ion mode) with a standard 3-hydroxypicolinic
acid/ammonium acetate matrix. No internal mass calibration was used in this case, which would be
required for more accurate mass measurement
(Figure 11.18) appears as multiply charged peaks. The observed masses correspond to the oligonucleotide in
which some of the phosphates are protonated. In some cases the replacement of a proton by sodium or potas-
sium ions can be observed. The actual mass can be calculated from the accurate mass of any of the multiply
charged species. For example [M-4H]^4 (1198) has an accurate mass of 1198.4396, and since the observed
masses correspond to m/z, the moleculer mass of the oligonucleotide is 4 1198.43964793.7584
4H(4 1.008)4797.7904. The theoretically calculated mass is 4797.8091.
Electrospray ionization has emerged as a tool for studying non-covalent complexes and has enabled the
measurement of spectra of intact viruses and whole ribosomes (Figure 11.19).50,51It is possible to measure
directly the mass of a macromolecular complex as long as the binding interactions that support complex
formation are maintained during its transit from solution micro-droplets into the gas phase. Nanoflow ESI^52
is a miniaturized version of ESI that facilitates this desolvation process because of the reduced size of droplets
it generates compared with conventional ESI.
11.7 Molecular Modelling and Dynamics
Despite the remarkable developments in experimental techniques to determine the molecular structure of
nucleic acids, there remain many instances in which such information is not available. Certain nucleic acid
structures (e.g.the triple helix) have proved remarkably difficult to crystallize, while the homogenous and
repetitive nature of other structures makes NMR structure determination difficult or ambiguous. Molecular
modelling can provide a method to predict the structure of such nucleic acids and also to study transient