Molecular Modelling of Intermediate States

Using MD simulations with explicit inclusion of counterions and solvent Stefl et al. investigated the stability of supramolecular intermediates (including 

Despite major differences between the various classes of quadruplexes, some general conclusions may be drawn. For these oligomers, it is clear that  

As a final word, although our understanding of the thermodynamic, kinetic and structural properties of quadruplexes has improved, considerable work lies ahead to fully understand the rules governing their formation and to identify the intermediates state. 

Solution tumbling of a small quadruplex Typical MD simulations 

Half-formation TGfT quadruplex (mM) Half-formation of intramolecular quadruplex (25°C) 

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