Hairpin and parallel quartet structures for telomeric sequences

Abstract

The role of thymine residues in the formation of G-quartet structures for telomeric sequences has been investigated using model oligonucleotides of the type d(G4TnG4), with n = 1-4. Sequences d(G4T3G4) and d(G4T4G4) adopt a G-quartet structure formed by hairpin dimerization in 70 mM NaCl as judged by a characteristic circular dichroism signature with a 295 nm positive and 265 nm negative bands while d(G4TG4) adopts a parallel G-quartet structure like d(G12) which exhibits a strong positive band at 260 nm and a negative band at 240 nm. The sequence d(G4T2G4) exhibits a mixture of both conformations. The stability of hairpin G-quartet structures decreases with decrease in the number of intervening thymine residues. Potassium permanganate, a single strand specific probe has been used to establish the presence of loops composed of T residues in the hairpin G quartet structures formed by the oligonucleotides d(G4TnG4) with n = 2-4 in 70 mM NaCl. The formation of hairpin G quartet structure for the above sequences is further supported by the enhanced electrophoretic mobility observed on non-denaturing polyacrylamide gels. Human telomeric sequence d(TTAGGG)4 which showed enhanced electrophoretic mobility like Tetrahymena telomeric sequence d(T2G4)4 also exhibited a characteristic CD spectrum for a folded-back G-quartet structure. A detailed model for G-quartet structure involving hairpin dimer with alternating syn-anti-syn-anti conformation for the guanine residues both along the chain as well as around the G tetrad with at least two thymine residues in the loop is proposed. Intermolecular association of short telomeric sequences reported here provides a possible model for chromosomal pairing.

Roles of flanking sequences in the binding between unimolecular parallel-stranded G-quadruplexes and ligands

“…UV-melting experiments show that all sequences exhibit an invert transition at 295 nm (as shown in Supporting Information), which is a typical characterization of G-quadruplex denaturation [50], inferring that all DNA samples were folded into specific G-quadruplex motifs. Furthermore, the CD spectra of all sequences present a positive CD signal around 265 nm and a negative one at 240 nm (as shown in Supporting Information), which are typical parallel-stranded G-quadruplex features [51]. It is confirmed that all DNA samples with same core sequence folded into similar expected parallel-stranded G-quadruplex motifs.…”

The Human Telomere Sequence, (TTAGGG)4, in the Absence and Presence of Cosolutes: A Spectroscopic Investigation

“…As the percentage of PEG increases to 20%, the shoulder at 292 nm gradually fades away and the peak at 272 nm intensifies. These spectra have characteristics similar to a fully parallel stranded structure [45]. Further, these spectra are strikingly similar to those reported by us for DNA oligomers of sequence (CCCCTTTTGGGGT 1-4 GGGG ) which self-assemble into high molecular weight species of multiple molecularties in the presence of Mg 2+ [46,47].…”

Anti-bovine Prion protein RNA aptamer containing tandem GGA repeat interacts both with recombinant bovine prion protein and its β isoform with high affinity

“…It is known that a parallel G-quadruplex gives a positive CD peak at 260 nm, while an antiparallel G-quadruplex gives a positive CD peak at 295 nm either with or without a positive CD peak at 260 nm in the presence of monovalent cations. 27,28 A peak was observed at 260 nm of CD and the peak intensity increased as the concentration of K + ions increased, with maximum peak intensity at 10 mM KCl (Fig. 3A).…”