Over recent years it become clear that the sequence dependent structural mechanics properties of DNA play an important role in most of its biological functions.
Studies of such properties have been hindered by the absence of sufficient experimental data to enable any predictions to be made concerning the behaviour of long sequences. Similarly, despite progress in modelling the properties of DNA oligomers in aqeous solution, theoritical studies have been hampered by the considerable number of sequences which have to be studied.
We have recently made one step towards a theoritical solution to predicting the local properties of DNA. By introducing the notion of a variable base sequence within an all-atom representation of DNA (an approach termed ADAPT) we have made it possible to calculate the structural properties of very long sequences and also to generate sequences which exhibit chosen structural properties in a way similar to the experimental SELEX approach.
The present study takes this work one step further by extending ADAPT to enable mechanical properties to be studied.