Formation of an interlocked quadruplex dimer by d(GGGT)

A tetranucleotide sequence d(GGGT) has been shown to self-assemble into an interlocking quadruplex dimer. UV-melting studies indicated the existence of two species that each showed distinct quadruplex melting transitions, a low-T-m species, Q(l), and a high-T-m species, Q(h). Conditions were controlled to favor the formation of either Q(l) or Q(h). Q(l) and Q(h) each showed circular dichroism spectra characteristic of parallel quadruplexes. Negative ion nano-electrospray ionization mass spectrometry confirmed that Q(l) was a tetrameric complex, d(GGGT)(4), and Q(h) was an octameric complex, d(GGGT)(8). High-resolution H-1 NMR spectroscopy evidenced that d(GGGT)(4) was a C-4-symmetric parallel tetramolecular quadruplex. The H-1 NMR spectrum of d(GGGT)8 was consistent with a structure formed by the dimerization of a parallel, slipped tetramolecular quadruplex that has its diagonal strands staggered by one base. This slippage results in two guanine bases at the 5' end of the quadruplex being presented diagonally that are not involved in tetrads. Two such slipped quadruplexes dimerize via these free G-bases at the 5' ends by forming an extra G-tetrad. Each slipped quadruplex contributes two guanine bases to this extra G-tetrad. The formation of a novel GTGT tetrad is also observed at both the 3' ends of the interlocked quadruplex dimer.