Visualizing transient Watson–Crick-like mispairs in DNA and RNA duplexes

Rare tautomeric and anionic nucleobases are believed to have fundamental biological roles, but their prevalence and functional importance has remained elusive because they exist transiently, in low abundance, and involve subtle movements of protons that are difficult to visualize. Using NMR relaxation dispersion, we show here that wobble dG•dT and rG•rU mispairs in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-populated Watson–Crick-like mispairs that are stabilized by rare enolic or anionic bases. These mispairs can evade Watson–Crick fidelity checkpoints and form with probabilities (10 −3 to 10 −5 ) that strongly imply a universal role in replication and translation errors. Our results indicate that rare tautomeric and anionic bases are widespread in nucleic acids, expanding their structural and functional complexity beyond that attainable with canonical bases. dG•dT and rG•rU ‘wobble’ mispairs in DNA and RNA transiently form base pairs with Watson–Crick geometry via tautomerization and ionization with probabilities that correlate with misincorporation probabilities during replication and translation. The dynamic structure of DNA visualized The conventional, hydrogen-bonded view of DNA is a static representation that does not reflect the actual dynamics of this molecule. In fact, DNA is constantly sampling transient alterations in the nucleobases that have been difficult to quantify and visualize. Hashim Al-Hashimi and colleagues have used NMR to characterize these fleeting forms. Their data indicate that such forms are present at levels that are high enough to influence the fidelity of replication and translation. Specifically, they find that noncanonical dG·T and rG·U 'wobble' mispairs in DNA and RNA duplexes morph transiently into canonical Watson–Crick-like mispairs that are stabilized by rare enol tautomeric and anionic bases.