Nucleic Acids Research Advance Access published online on April 22, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm111
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Structural Biology |
Guanines are a quartet's best friend: impact of base substitutions on the kinetics and stability of tetramolecular quadruplexes
1Laboratoire de Biophysique, Muséum National d’Histoire Naturelle USM503, INSERM U565, CNRS UMR 5153, 43 rue Cuvier, 75231 Paris cedex 05, France and 2Laboratoire de Spectrométrie de Masse, Université de Liège, Institut de Chimie, Bat. B6c, B-4000 Liège, Belgium
*To whom correspondence should be addressed. Tel: +33-1 40 79 36 89; Fax: +33-1 40 79 37 05; Email: mergny{at}mnhn.fr
Received December 22, 2006. Revised February 6, 2007. Accepted February 7, 2007.
Parallel tetramolecular quadruplexes may be formed with short oligodeoxynucleotides bearing a block of three or more guanines. We analyze the properties of sequence variants of parallel quadruplexes in which each guanine of the central block was systematically substituted with a different base. Twelve types of substitutions were assessed in more than 100 different sequences. We conducted a comparative kinetic analysis of all tetramers. Electrospray mass spectrometry was used to count the number of inner cations, which is an indicator of the number of effective tetrads. In general, the presence of a single substitution has a strong deleterious impact on quadruplex stability, resulting in reduced quadruplex lifetime/thermal stability and in decreased association rate constants. We demonstrate extremely large differences in the association rate constants of these quadruplexes depending on modification position and type. These results demonstrate that most guanine substitutions are deleterious to tetramolecular quadruplex structure. Despite the presence of well-defined non-guanine base quartets in a number of NMR and X-ray structures, our data suggest that most non-guanine quartets do not participate favorably in structural stability, and that these quartets are formed only by virtue of the docking platform provided by neighboring G-quartets. Two notable exceptions were found with 8-bromo-guanine (X) and 6-methyl-isoxanthopterin (P) substitutions, which accelerate quadruplex formation by a factor of 10 when present at the 5' end. The thermodynamic and kinetic data compiled here are highly valuable for the design of DNA quadruplex assemblies with tunable association/dissociation properties.
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