In the present project, we propose to use multi-nuclear magnetic resonance spectroscopy to investigate the interaction of EcoRI endonuclease with the synthetic oligonucleotide CGCGAATTCGCG which contains the EcoRI recognition sequence. The main objective of this investigation is to elucidate the molecular mechanism(s) responsible for the specific recognition of the DNA sequence d(GAATTC) by the EcoRI restriction endonuclease. To achieve this objective, we specifically propose: (i) to characterize the conformation and the dynamics of the DNA fragment when complexed with the EcoRI endonuclease; (ii) to identify the groups on the DNA molecule which are involved in the intermolecular contacts and hydrogen bonds with EcoRI endonuclease within the complex, and (iii) to ascertain the effects of sequence variations in the oligonucleotide CGCGAATTCGCG (both at the EcoRI recognition site and at the sequences flanking the EcoRI recognition site) upon the conformation and the dynamics of the DNA molecule and upon the intermolecular interactions between DNA and EcoRI endonuclease involved in the specific recognition.
