Lead is unusually effective in sequence-specific folding of DNA

Abstract

DNA quadruplex structures based on the guanine quartet are typically stabilized by monovalent cations such as K+, Na+, or NH3+. Certain divalent cations can also induce quadruplex formation, such as Sr2+. Here we show that Pb2+ binds with unusually high affinity to the thrombin binding aptamer, d(GGTTGGTGTGGTTGG), inducing a unimolecular folded structure. At micromolar concentrations the binding is stoichiometric, and a single lead cation suffices to fold the aptamer. The lead-induced changes in UV and CD spectra are characteristic of folded quadruplexes, although the long wavelength CD maximum occurs at 312 nm rather than the typical value of 293 nm. The one-dimensional exchangeable proton NMR spectrum shows resonances expected for imino protons involved in guanine quartet base-pairing. Furthermore, two-dimensional NMR experiments reveal NOE contacts typically seen in folded structures formed by guanine quartets, such as the K+ form of the thrombin aptamer. Only sequences capable of forming guanine quartets appear to bind Pb+2 tightly and change conformation. This sequence-specific, tight DNA binding may be relevant to possible genotoxic effects of lead in the environment.