Past exam of the chemistry B course of the University of Cambridge / 2024 / Paper 1 / B5 / b / ii / Solution

At ordinary physiological pH, the arginine side chain is predominantly guanidinium. Its N–H groups are donors, and its positive charge can reinforce favorable electrostatic interactions. guanine exposes adjacent O6 and N7 acceptors in the major groove, allowing two guanidinium N–H donors to make a paired interaction without breaking Watson–Crick pairing. The diagram places this arginine contact on the exposed guanine edge, not between the paired bases.

adenine also exposes N7, but at the corresponding neighboring position it has the exocyclic N6 amino donor rather than a carbonyl acceptor. It therefore cannot make the same donor-to-two-acceptors match with guanidinium. A single N7 contact would be less discriminating. The classic structural recognition analysis explicitly proposed paired arginine–guanine contacts in the major groove.^[ref] protein geometry, hydration and phosphate contacts also affect sequence recognition; this local motif explains a preference rather than guaranteeing that every arginine-containing protein recognizes every G–C site.