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Nucleic Acids Research 2006 34(1):206-216; doi:10.1093/nar/gkj421
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Published online 5 January 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

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

Joaquim Jaumot, Ramon Eritja1, Romà Tauler2 and Raimundo Gargallo*

Department of Analytical Chemistry, University of Barcelona Diagonal 647, Barcelona, E-08028 Spain 1Department of Structural Biology, IBMB-CSIC Jordi Girona 18-26, Barcelona, E-08034 Spain 2Department of Environmental Chemistry, IIQAB-CSIC Jordi Girona 18-26, Barcelona, E-08034 Spain

*To whom correspondence should be addressed. Tel: +34 934034445; Fax: +34 934021233; Email: raimon{at}apolo.qui.ub.es

Received July 26, 2005. Revised November 28, 2005. Accepted December 14, 2005.

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.


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