Open Access: Nucleic Acids Research 2006, 34, 206 - 216

Resolution of a structural competition involving dimeric G-quadruplex and its C-rich complementary strand

Joaquim Jaumot, Ramón Eritja, Romà Tauler and Raimundo Gargallo

Abstract

The resolution of the dimeric intermolecular G-quadruplex / duplex competition of the telomeric DNA sequence 5’-TAG-GGT-TAG-GGT-3’ and of its complementary 5’-ACC-CTA-ACC-CTA-3’ is reported. To achieve this goal, melting experiments of both sequences and of the mixtures of these sequences were monitored by molecular absorption, molecular fluorescence, and circular dichroism spectroscopies. Molecular fluorescence measurements were carried out using molecular beacons technology, in which the 5’-TAG-GGT-TAG-GGT-3’ sequence was labelled with a fluorophore and a quencher at the ends of the strand. Mathematical analysis of experimental spectroscopic data was performed by means of Multivariate Curve Resolution, allowing the calculation of concentration profiles and pure spectra of all resolved structures (dimeric antiparallel and parallel G-quadruplexes, Watson-Crick duplex and single strands) present in solution. Our results show that parallel G-quadruplex is more stable than antiparallel G-quadruplex. When the complementary C-rich strand is present, a mixture of both G-quadruplex structures and Watson-Crick duplex is observed, the duplex being the major species. In addition to melting temperatures, equilibrium constants for the parallel / antiparallel G-quadruplex equilibrium and for the G-quadruplex / duplex equilibrium were determined from the concentration profiles.

Keywords

G-quadruplex, duplex competition, parallel, antiparallel, molecular beacon, Multivariate Curve Resolution

MCR-ALS analysis of the spectroscopic data recorded during the four melting experiments. a) Resolved concentration profiles for the melting of the SC sequence. b) Resolved concentration profiles for the melting of the SG sequence. c) Resolved concentration profiles for the mixture 1:1 SG:SC. d) Resolved concentration profiles for the mixture 2:1 SG:SC. Cyan: ordered SC strand, Magenta: disordered SC strand, Green: parallel SG G-quadruplex, Blue: antiparallel SG G-quadruplex, red: disordered SG strand, yellow: SG·SC duplex.