G-DNA: a twice-folded DNA structure adopted by single-stranded oligo(dG) and its implications for telomeres.

Abstract

Our dimethyl sulfate modification experiments suggest that (dG). stretches within single-stranded DNA fragments, which represent the simplest model for telomeric sequences, adopt a complex intrastrand structure other than a simple hairpin. We present a molecular model for the DNA structure that conforms to dimethyl sulfate methylation data. The principal element of this G-DNA structure is a quadruple helix formed by pairwise antiparallel segments of the twicefolded (dG). stretch. This quadruple core has two wide and two narrow grooves connected by three loop-shaped segments. The strong stacking interactions of the neighboring guanine tetrads and the large number of hydrogen bonds formed can be the primary reasons that such structures are favored over a common hairpin for long (dG pPG27, which contain (dG),-(dC)" inserts at the Pst I site of pUC18 with n = 37 and 27, respectively. It has been found (11) that, after the short insert-containing restriction fragments have been denatured, the (dG),-and (dC)Q-containing strands renature much more slowly than do those of arbitrary sequence. In addition, the (dG)n strand has an abnormally high mobility in polyacrylamide gel electrophoresis (PAGE) (11). These data argue in favor of the existence within (dG),-containing single-stranded fragments of an intrastrand structure (G structure) stabilized by formation of hydrogen bonds between guanines. In this paper we describe the results of methylation experiments on the oligo(dG)-containing frag- (14). However, the G-structure methylation pattern for longer stretches-(dG)27 and (dG)37-is more complicated (Fig. 1). Clear maxima and minima of modification are seen against the background of general diminution of peak amplitude associated with overmodification (more than one dimethyl sulfate modification per fragment). The maxima between extremities are positioned at one-quarter, one-half, and three-quarters of the way along the insert. This suggests that the (dG), strand is bent in three places, with three exposed and methylated loops. The fact that all four segments flanking the loops are simultaneously protected against methylation at their N7 positions can only mean (15) that these loci are shielded by formation of Hoogsteen-like hydrogen-bonded tetrads (16,17) like that shown in Fig. 2. But in any event, the similarity of disposition of maxima and minima for the (dG)27 and (dG)37 oligomers shows that these two share a common structure, whatever §Present address:

Single strand targeted triplex-formation. Destabilization of guanine quadruplex structures by foldback triplex-forming oligonucleotides

“…These G-rich tracts form self-association complexes involving other than Watson-Crick hydrogen bonding patterns. Both solution (12) and solid state (13) studies have revealed that these sequences can form stable-structures with Hoogsteen-type hydrogen bonded guanine tetrads (G4), not only by intermolecular association of four different strands (14), but also by intermolecular association oftwo hairpins (15) or even by intramolecular folding of a single-strand (16).…”

Thermodynamics and structure of a DNA tetraplex: a spectroscopic and calorimetric study of the tetramolecular complexes of d(TG3T) and d(TG3T2G3T).

“…This intriguing structural motif was proposed some time ago based on fiber diffraction studies (2)(3)(4) and only recently has been rediscovered. This rekindled interest has been fueled, in part, by the recognition that telomeres, the 3' single-stranded guanine-rich overhangs found at the termini ofchromosomes, (5)(6)(7)(8) may form G-DNA type structures of potential biological significance (1,(9)(10)(11)(12)(13)(14). In addition to their presence in telomeres, where they may play a role in maintaining the stability and integrity of chromosomes (8), guanine-rich regions also are found within recombination and mutation hot spots (15)(16)(17)(18)(19) and in gene regulatory regions (20)(21)(22)(23)(24).…”

“…Guanine-rich regions can form G-tetrad-containing structures monomolecularly via intramolecular folding (11,13,14,25), bimolecularly by association of two hairpins (11,12,25,26), or tetramolecularly by alignment of four separate strands (10,(27)(28)(29)(30)(31)(32)(33)(34)(35). An examination of the literature reveals examples of tetrad-containing structures from each of these three classes, including, in some cases, superstructures formed by their aggregation (31,33).…”

Quadruplex structure of d(G3T4G3) stabilized by K+ or Na+ is an asymmetric hairpin dimer.

“…Earlier reports have also appeared describing parallel four-stranded structures for poly(G) and poly(I) (12). In the last 5 years, several telomeric sequences have been studied using physical and structural methods (13)(14)(15)(16)(17)(18). Henderson et al (15) have examined a variety of sequences with enhanced electrophoretic mobility that exhibited low-field exchangeable protons in the NMR spectra, indicating the presence of GIG base pairing.…”