Structural polymorphism and dynamism in the DNA segment GATCTTCCCCCCGGAA: NMR investigations of hairpin, dumbbell, nicked duplex, parallel strands, and i-Motif

Abstract

Structure and dynamism in a DNA segment d-GATCTTCCCCCCGGAA have been investigated by nuclear magnetic resonance (NMR) spectroscopy. At neutral pH, the molecule exists largely as a dumbbell, formed by the association of two hairpins with sticky ends. A small percentage of hairpin is also detectable. The stem of the dumbbell, which is 12 base pairs long, has two nicks separated by 4 base pairs. The three-dimensional structures of the dumbbell and also of a 12-mer duplex, the sequence of which is identical to that of the stem of the dumbbell, have been determined by NMR in conjunction with restrained molecular dynamics calculations. It is observed that the presence of nicks causes minor changes in the structure of the duplex. Fraying at the nicks is much less than at the ends of a regular duplex. The loop shows very few nuclear Overhauser effects, which is a reflection on the greater dynamism in its structure. At lower pH, the molecule undergoes a transition to an i-motif type of structure with two parallel stranded duplexes involving C-C⁺ pairing, interdigitating each other. The structure is highly stable, with a melting temperature >60 °C.