Figure 7:

In this reaction mechanism, a magnesium ion quenches the negatively charged backbone phosphate group and simultaneously coordinates the reaction of the 1M7 ligand with the nucleotide through a bridging water molecule. A thick grey arrow shows the dipole moment going through the 1M7 molecule, which points from the partially anionic oxygen bound to the reacting carbon toward the partially cationic ring nitrogen. If bound to an ideally positioned magnesium ion, a coordinating water molecule may weakly hydrogen bond to the partially anionic oxygen on the 1M7 molecule and facilitate increased sampling of SHAPE-reactive space. The magnesium ion may anchor 1M7 in a reactive orientation so that the reactive carbon collides with the 2’-hydroxyl oxygen until the reaction occurs. If the negatively charged phosphodiester backbone is not quenched, the polarized 1M7 molecule would be more likely to sample the reactive space in an unfavorable (nonreactive) orientation. An arced arrow shows the movement of electrons from the 2’-hydroxyl oxygen to form a bond with the reactive carbon. In this picture, the magnesium ion behaves as a kinetic catalyst by providing a means for SHAPE ligands to more frequently sample the reactive space in a favorable orientation, and it acts as a weak chemical catalyst by pulling electrons from the partially negative oxygen through the hydrogen bond with water and increasing the reactivity of the carbon.