THE TRINUCLEOTIDE REPEAT SEQUENCE D(CGG)(15) FORMS A HEAT-STABLE HAIRPIN CONTAINING G(SYN)CENTER-DOT-G(ANTI) BASE-PAIRS

TO investigate potential structures of d(CGG/CCG)(n) that might relate to their biological function and association with tripler repeat expa nsion diseases (TREDs), electrophoretic mobility, chemical modificatio n, and P1 nuclease studies were performed with a single-stranded (ss) oligonucleotide containing (CGG)(15) [ss(CGG)(15)]. The results sugges t that ss(CGG)(15) forms a hairpin with the following features: (i) a stem containing G(syn). G(anti) base pairs; (ii) at greater than or eq ual to 200 mM K+, CGG repeats on the 5' portion of the stem base-paire d to GCG repeats on the 3' side (referred to as the (b) alignment); an d (iii) heat stability (T-m 75 degrees C in low ionic strength). At le ss than or equal to 100 mM K+, dimethyl sulfate reactions indicated th at the hairpin in the (b) alignment was in equilibrium with another st ructure, presumably a hairpin in the alternative (a) alignment (CGG re peats on the 5' portion of the stem base paired to CGG repeats on the 3' portion of the stem). Molecular dynamics simulations suggested that the loop region of the (a) alignment contained two guanines stacked o n top of one another. The same guanines in the (b) alignment were base -paired in a syn-anti arrangement. We propose that the stability of th e loop partially determines the stem alignment.