A novel structure observed in d-GAATTCCCGAATTC by 2D NMR

Sequential resonance assignments of the non exchangeable base and sugar protons in d-GAATTCCCGAATTC have been obtained using two dimensional NMR experiments at 500 MHz. The chemical shifts and the NOEs have been used to determine the structure in the base-pair mismatch region which is located in the central portion of the molecule. It is observed that the molecule adopts a novel unsymmetrical loop structure in this section which is characterised by sugar geometries which are significantly different compared to the rest of the molecular. The base-paired portion of the molecule conforms to a right handed B-DNA type of structure.