SOLUTION STRUCTURES OF THE INDIVIDUAL SINGLE STRANDS OF THE FRAGILE-XDNA TRIPLETS (GCC)(N)CENTER-DOT(GGC)(N)

Three-dimensional structures of the fragile X triplet repeats (GCC)(n) and (GGC)(n) are derived by using one-dimensional/two-dimensional NMR . Under a wide range of solution conditions (10-150 mM NaCl, pH 6-7) ( GCC)(5-7) strands form exclusively slipped hairpins with a 3' overhang ing C. The slipped hairpins of (GCC)(n) strands show the following str uctural characteristics: (i) maximization of Watson-Crick G . C pairs; (ii) formation of C . C mispairs at the CpG steps in the stem; (iii) C2'-endo, anti conformations for all the nucleotides. The ability of ( GCC)(n) strands to form hairpin structures more readily than complemen tary (GGC)(n) strands suggests preferential slippage during replicatio n and subsequent expansion of the (GCC)(n) strands. In addition, the C . C mispairs at the CpG site of (GCC)(n) hairpins account for their e xceptional substrate efficiencies for human methyltransferase. Gel ele ctrophoresis data show that (GGC)(n) strands form both hairpin and mis matched duplex structures in 10-150 mM NaCl (pH 6-7) for n < 10, but f or n greater than or equal to 11 hairpin structures are exclusively pr esent. However, (GGC)(n) strands remain predominantly in the duplex st ate for n = 4-11 under NMR solution conditions, which require DNA conc entrations 100- to 1000-fold higher than in gel electrophoresis. NMR a nalyses of [(GGC)(n)](2) duplexes for n = 4-6 show the presence of Wat son-Crick G . C and mismatched G(anti). G(syn) pairs. The mismatches a djacent to the CpG step introduce local structural flexibility in thes e duplexes, Similar structural properties are also expected in the ste m of the hairpins formed by (GGC)(n) strands.