Unusual structures of TTTA repeats in icaC gene of Staphylococcus aureus

Abstract

a b s t r a c tOne 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 0 or 5 0 -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.

New insights into the genetic instability in CCTG repeats

“…Thereby, the mini-dumbbell intermediate provides a possible pathway for the occurrence of two-repeat expansion. This is analogous to our earlier findings that only two TTTA repeats are required to fold into a mini-dumbbell structure [11], which probably accounts for the observed two-repeat expansion in the coding region of icaC gene of Staphylococcus aureus mutants [28].…”

“…Recently, we have shown a mini-dumbbell structure formed by simply two TTTA repeats [11]. This mini-dumbbell comprises two 2-nt TT loops closed by TA base pairs, providing possible mechanistic pathways that account for one and two-repeat expansions.…”

“…Recently, we have shown a mini-dumbbell structure formed by simply two TTTA repeats [11]. This mini-dumbbell comprises two Abbreviations: DM, myotonic dystrophy; DM1, myotonic dystrophy type 1; DM2, myotonic dystrophy type 2; NMR, nuclear magnetic resonance; PAGE, polyacrylamide gel electrophoresis; DSS, 2,2-dimethyl-2-silapentane-5-sulfonic acid; 1D, one-dimensional; 2D, two-dimensional; NOESY, nuclear Overhauser effect spectroscopy; TOCSY, total correlation spectroscopy; HSQC, heteronuclear singlequantum coherence; MMR, mismatch repair Author contributions: P.G.…”

“…The non-B secondary structures such as hairpin [9], dumbbell [10,11], triplex [12] and quadruplex [13] formed by short tandem repeats in the nascent strand during DNA replication have been proposed to be the intermediates which stabilize the slipped strand structures, thus leading to expansion mutations if not repaired [14,15]. For CCTG repeats, solution nuclear magnetic resonance (NMR) spectroscopic studies have revealed two types of non-B structures adopted by sequences containing three and four repeats [10].…”

“…By analyzing the pyrimidine H6 chemical shifts, similar thermodynamic results were also obtained (Supporting Information, S5). By comparing the thermodynamic results of the dumbbell formed by two TTTA repeats [11], the T m of the dumbbell formed by two CCTG repeats was found to be $4°C higher and the DG°w as $0.8 kcal mol À1 lower. Since the type II CT loop has been found to be less stable than TT loop [17], the more stable CCTG mini-dumbbell suggests that the CG loop closing base pairs have a better stabilizing effect than the TA base pairs in the TTTA mini-dumbbell via stacking interactions (i) with the loop residues and (ii) between themselves.…”