The calculated NH NH distances in the strands are much shorter in the α-sheet, consistent with the strong dNN NOEs observed for both α1 and α3, and the observed breaks in the patterns reveal vulnerabilities in the structures and provide direction for improved designs.
Except for the N-terminal residues of the CAN domain, which did not exhibit long-range interactions, the intra-CAN NOEs observed in all the NOE data were fully consistent with the X-ray structure of the mature CAN hexamer.
The backbone assignment was confirmed with a 15N-edited NOESY experiment through the characteristic NOEs observed in helices and β-sheets expected from the 3D crystallographic structure (1HD2 PDB entry [25]).
Most of the intermolecular NOEs observed involve protons on the DB[ a, l]P residue and the modified DNA strand.
The short α2 helix, for example, is rotated by ~120° and translated by ~6 Å in the crystal structure, violating several long-range NOEs observed in solution.
The 1, N-εdG H6 etheno proton was close to the complementary strand compared to the 1, N-εdG H7 etheno proton, consistent with the greater number of NOEs observed for the H6 proton versus the H7 etheno proton.
