Structure of a single-cytidine hairpin loop formed by the DNA triplet GCA

Abstract

In certain contexts the DNA triplet GGA, when juxtaposed on opposite strands of a DNA duplex, shows the unusual property of pairing with itself in an antiparallel orientation to form the (GGA)2 motif. In this motif the central guanines do not pair but intercalate and stack between sheared G.A pairs. Similar studies with GCA triplets reveal that they do not form analogous paired (GCA)2 motifs but instead strongly promote formation of a hairpin, the structure of which is now reported here. The GCA hairpin loop consists of a single cytidine residue closed by a sheared G.A pair and this structure is discussed in the context of triplet expansions in triplet-repeat diseases.

A single G-to-C change causes human centromere TGGAA repeats to fold back into hairpins.

“…5 B and C. The loop structure in this hairpin is thus virtually identical to our previous GCA loop structure determined in a hairpin containing a simpler stem sequence devoid of (GGA)2 motifs (8). Although the "double-stranded" (GGA)2 motif in the stem and the (GCA)-turn motif in the loop have quite different geometries and quite different backbone traces, they share sugar 04'-base stacking as a common structural feature.…”

“…1 A and B indicate that qualitatively the stem of this hairpin contains a structural motif very similar to that of the (GGA)2 motifs in the antiparallel satellite III (GTGGAAT-GGAAC)2 duplex (3, 4)-i.e., 4G is intercalated between 14G and the sheared 3Go15A pair, and conversely 14G is intercalated between 4G and the sheared 13Go5A pair. On the other hand, the 8G-9C-1OA loop appears to be qualitatively very similar to the single-residue GCA hairpin loop that we reported recently (8). A schematic representation of this hairpin is presented in Fig.…”

“…Since TGCAA is the most frequent variant among TGGAA repeats (2), especially in the centromeric repeats immediately adjacent to and contiguous with human a satellite DNA (31), we reasoned that this variant pentamer might function to "turn the corner" at the loop end of such putative hairpins. Our reasons for suspecting this were the extremely "tight turn" loops (containing only one residue in the loop) formed by the triplet GCA (8). The present structure confirms that these suspicions were well founded in that the GTGGAATGCAATGGAAC heptadecamer indeed forms an extremely stable hairpin (Tm = 63°C) in which the GCA triplet forms a tight-turn loop of one cytidine closed by a sheared G°A pair, and the first and last TGGAA pentamers form an antiparallel "duplex" containing the intercalative GGGG stack motif.…”

“…The most frequent among these variants is TGCAA-i.e., the central GGA triplet [which forms the self-paired (GGA)2 motifl is changed to GCA. Interestingly, we recently found that the triplet GCA is a very strong hairpin promoter (8,9). Among the four GNA triplets in a d(NAATGNAATG) sequence context, GGA predominantly forms bimolecular duplexes containing a (GGA)2 motif, as described previously (3,4), while GCA forms a unimolecular hairpin (8,9) and GAA and GTA form a mixture of mostly hairpin in equilibrium with a minor (GNA)2 duplex form (9).…”

“…Interestingly, we recently found that the triplet GCA is a very strong hairpin promoter (8,9). Among the four GNA triplets in a d(NAATGNAATG) sequence context, GGA predominantly forms bimolecular duplexes containing a (GGA)2 motif, as described previously (3,4), while GCA forms a unimolecular hairpin (8,9) and GAA and GTA form a mixture of mostly hairpin in equilibrium with a minor (GNA)2 duplex form (9). If (TGGAA), repeats self-pair to form antiparallel (GGA)2 motifs in vivo, we reasoned that occasional TGCAA pentamers interspersed among (TG-GAA), repeats might promote folding back of the chain on itself by forming GCA-turn loops, and thus modulate centromere folding.…”