An unrestrained MD simulation of the FMN–RNA aptamer complex

Aptamers are nucleic acid molecules selected in vitro to bind small molecules, peptides, proteins or even other nucleic acids with high affinity and specificity. They offer a unique opportunity to extend our knowledge on the basic principles of nucleic acid architecture and ligand recognition. Despite their probable absence in organisms, RNA aptamers are likely to play an important role in molecular diagnostics and therapeutic applications [1]. Flavin mononucleotide (FMN) is a cofactor that mediates redox reactions when bound as a prosthetic group to flavoproteins. Furthermore, recent studies have shown that FMN is able to photocleave RNA specifically at G U base pairs embedded within a helical stack [2]. Recently, the structure of the FMN–RNA aptamer complex has been determined by NMR spectroscopy [3]. Here, we present an unrestrained 1.7 ns molecular dynamics (MD) simulation of the complete FMN–RNA aptamer to probe its structural and dynamical features in aqueous solution.