Simulation of (125)I-based radioprobing experiments to study DNA quadruplex structure and topology.
OBJECTIVE
Certain guanine-rich DNA sequences have the capacity to fold into four-stranded structures stabilized by the stacking of square planar arrangements of four hydrogen-bonded guanine bases. However both the overall topology of folding and the more detailed three dimensional structure of these quadruplexes is difficult to determine or predict, and they can be polymorphic, altering radically depending on environmental conditions. Radioprobing experiments, in which Auger electrons emitted during the decay of a (125)I-containing base induce strand cleavage in a distance- and structure-dependent manner, have provided possible means of determining these details. Here we have used a combination of computer simulation methods to study the information obtained by one such experiment, reported in 2004.


METHODS
Models were constructed of three quadruplex topologies considered in the experiment, and one other topology proposed more recently. Molecular Dynamics simulations were used to equilibrate these structures and monitor how they evolved over several nanoseconds in solution. Snapshots from the trajectories were then subjected to Monte Carlo track structure prediction, from which theoretical cleavage patterns have been extracted.


RESULTS
The four topologies were found to yield quite different cleavage patterns, which allow the presence of particular conformations in an experiment to be predicted.


CONCLUSIONS
Radioprobing, which is usable in biologically relevant environments, is sensitive enough to distinguish with some confidence between alternative folding topologies in a DNA structure. Monte Carlo track structure simulation can reinforce or question conclusions drawn from experiment, and Molecular Dynamics used with various restraints provides a practical means of guiding a model towards one that yields cleavage patterns closer to those found experimentally.
Girard
Peter M
PM
Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK.
Nikjoo
Hooshang
H
Laughton
Charles
C
D003198:Computer Simulation; D004247:DNA / Q000737:chemistry / Q000528:radiation effects*; D053837:DNA Cleavage / Q000528:radiation effects; D004583:Electrons; D054856:G-Quadruplexes / Q000528:radiation effects*; D006147:Guanine / Q000737:chemistry; D007457:Iodine Radioisotopes / Q000737:chemistry*; D008958:Models, Molecular; D009010:Monte Carlo Method
D007457:Iodine Radioisotopes; D006147:Guanine; D004247:DNA