Modesto Orozco, Life Sciences Director of the Barcelona Supercomputing Centre and responsible of the Molecular Modelling and Bioinformatics group at the Institute for Research in Biomedicine (IRB Barcelona), and Guillem Portella, a postdoc researcher in his group, have described for the first time the folding process of a small DNA hairpin in water at an atom-by-atom resolution.
The work has far-reaching implications, not only because it represents a milestone in the study of the folding of nucleic acids, but also because it is of great importance for the design of oligonucleotide drugs, such as those based on RNA-interference.
It has long been understood that the structure of a protein determines how it functions, but attempts to date attempts to observe structural changes at an atomic resolution have been hampered by the ultra-fast nature of the folding process. In addition, the amount of data involved makes it very difficult to build computer models of protein folding.
The unexpected finding is that the folding process appears to be a competition between different fast-folding and slow-folding routes. Microscopic details determine in a (seemingly) random fashion which route is explored. This investigation was made possible by the enormous computing power of the MareNostrum supercomputer at the Barcelona Supercomputing Centre, the most powerful computer in Spain.