Unusual structures of TTTA repeats in icaC gene of Staphylococcus aureus

• TTTA repeat expansions affect the biofilm matrix of Staphylococcus aureus.
• A sequence containing three TTTA repeats can form two dumbbell conformers.
• Fast exchange of the two conformers results in an averaged 2-nt mini-loop structure.
• The occurrence of these structures in nascent strands can lead to repeat expansion.
• The mini-loop and dumbbell account for one and two repeat expansions, respectively.

One and two TTTA repeat expansions have been found in the coding region of icaC gene of Staphylococcus aureus variants which influence the expression of IcaC protein and alter the phenotype. Yet, the mechanism of these small-size TTTA repeat expansions remains unclear. In this study, we performed high-resolution nuclear magnetic resonance spectroscopic studies on TTTA repeats. Our results show that a DNA sequence containing three TTTA repeats can fold into dumbbell structures with a 3′ or 5′-overhang. Exchange of these dumbbells makes the sequence behave like a 2-nt TT mini-loop at 25 °C. The occurrence of these mini-loop and dumbbell structures in the nascent strand during DNA replication provides possible mechanistic pathways which account for one and two repeat expansions.