Formation of G-Quadruplexes in Poly-G Sequences: Structure of a Propeller-Type Parallel-Stranded G-Quadruplex Formed by a G₁₅ Stretch

Abstract

Poly-G sequences are found in different genomes including human and have the potential to form higher-order structures with various applications. Previously, long poly-G sequences were thought to lead to multiple possible ways of G-quadruplex folding, rendering their structural characterization challenging. Here we investigate the structure of G-quadruplexes formed by poly-G sequences d(TTG(n)T), where n = 12 to 19. Our data show the presence of multiple and/or higher-order G-quadruplex structures in most sequences. Strikingly, NMR spectra of the TTG₁₅T sequence containing a stretch of 15 continuous guanines are exceptionally well-resolved and indicate the formation of a well-defined G-quadruplex structure. The NMR solution structure of this sequence revealed a propeller-type parallel-stranded G-quadruplex containing three G-tetrad layers and three single-guanine propeller loops. The same structure can potentially form anywhere along a long G(n) stretch, making it unique for molecular recognition by other cellular molecules.

Translation initiation events on structured eukaryotic mRNAs generate gene expression noise

“…On the other hand, it has been demonstrated previously that a poly(G) sequence (G 18 ) blocks the 5΄-3΄ exonuclease activity of Xrn1, thus leading to the accumulation of deadenylated and decapped mRNAs (40,41; Supplementary Figure S2). Recent work has shown that a continuous sequence of guanines in DNA manifests proton NMR spectra indicative of higher order structure once the number of Gs reaches 12 or more (forming G-quadruplexes, four-stranded helical structures held together by a guanine core; 42). In this study, we have used one poly(G) sequence that is shorter (G 10 ) than this threshold length, and one that is longer (G 14 ).…”

“…Poly(G) stretches occur quite widely in diverse genomes in a range of locations (for example in promoters, telomeres and 5΄UTRs; 42,58). The G 14 motif selected for use in this study is likely to have an intermediate propensity to form a stable G-quadruplex structure (42), consistent with its ability to inhibit translation initiation in yeast by approximately 90% (Table 1; Supplementary Figure S1).…”

Oligomer formation and G-quadruplex binding by purified murine Rif1 protein, a key organizer of higher-order chromatin architecture

“…Interaction of muRif1 with characteristic subsets of G4 DNA ~ There are several well known G4 oligonucleotides that have been structurally characterized (38)(39)(40)(41)(42)(43)(44)(45)(46). We used ten of them for EMSA with purified muRif1 (Supplementary Fig.…”

Rif1 binds to G quadruplexes and suppresses replication over long distances

“…The DNAbinding domain of mammalian Rif1 has been reported to bind to structured DNAs including forked DNA, flap DNA and cruciform structures 31,32 . Therefore, we prepared various structured DNAs and used them in competition assays with the G 24 DNA, which is known to form a parallel-type G-quadruplex structure 33 . In the presence of Rif1 protein, the G-quadruplex G 24 DNA was specifically mobility shifted (Fig.…”