Solution structure of the Tetrahymena telomeric repeat d(T2G4)4 G-tetraplex

Background: Telomeres in eukaryotic organisms are protein–DNA complexes which are essential for the protection and replication of chromosomal termini. The telomeric DNA of Tetrahymena consists of T 2 G 4 repeats, and models have been previously proposed for the intramolecular folded structure of the d(T 2 G 4 ) 4 sequence based on chemical footprinting and cross-linking data. Ahigh-resolution solution structure of this sequence would allow comparison with the structures of related G–tetraplexes. Results The solution structure of the Na + –stabilized d(T 2 G 4 ) 4 sequence has been determined using a combined NMR–molecular dynamics approach. The sequence folds intramolecularly into a right-handed G–tetraplex containing three stacked G-tetrads connected by linker segments consisting of a G-T-T-G lateral loop, a central T-T-G lateral loop and a T-T segment that spans the groove through a double chain reversal. Te latter T–T connectivity aligns adjacent G-G-G segments in parallel and introduces a new G-tetraplex folding topology with unprecedented combinations of strand directionalities and groove widths, as well as guanine syn/anti distributions along individual strands and around individual G-tetrads. Conclusion The four repeat Tetrahymena and human G-tetraplexes, which differ by a single guanine for adenine substitution, exhibit strikingly different folding topologies. The observed structural polymorphism establishes that G-tetraplexes can adopt topologies which project distinctly different groove dimensions, G-tetrad base edges and linker segments for recognition by, and interactions with, other nucleic acids and proteins.