title: Stability of G,A triple helices.
abstract: In this work we selected double-stranded DNA sequences capable of forming stable triplexes at 20 or 50 degrees C with corresponding 13mer purine oligonucleotides. This selection was obtained by a double aptamer approach where both the starting sequences of the oligonucleotides and the target DNA duplex were random. The results of selection were confirmed by a cold exchange method and the influence of the position of a 'mismatch' on the stability of the triplex was documented in several cases. The selected sequences obey two rules: (i) they have a high G content; (ii) for a given G content the stability of the resulting triplex is higher if the G residues lie in stretches. The computer simulation of the Mg2+, Na+and Cl-environment around three triplexes by a density scaled Monte Carlo method provides an interpretation of the experimental observations. The Mg2+cations are statistically close to the G N7 and relatively far from the A N7. The presence of an A repels the Mg2+from adjacent G residues. Therefore, the triplexes are stabilized when the Mg2+can form a continuous spine on G N7.
authors.affiliation: CNRS UMR 8532, Institut Gustave-Roussy, 94805 Villejuif, France.
authors.forename: A
authors.initials: A
authors.lastname: Debin
authors.forename: C
authors.initials: C
authors.lastname: Laboulais
authors.forename: M
authors.initials: M
authors.lastname: Ouali
authors.forename: C
authors.initials: C
authors.lastname: Malvy
authors.forename: M
authors.initials: M
authors.lastname: Le Bret
authors.forename: F
authors.initials: F
authors.lastname: Svinarchuk
mesh_terms: D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA