title: The effect of loop residues in four-stranded dimeric structures stabilized by minor groove tetrads.
abstract: Some DNA oligonucleotides can fold back and self-associate forming dimeric structures stabilized by intermolecular base pairs. The resulting antiparallel dimer is a tightly packed four-stranded structure formed by a core of minor groove tetrads connected by short loops of unpaired nucleotides. We have explored the sequential requirements for the loop residues and have found that this family of structures is only stable with one- and two-residue loops, with the stability of the former ones being only marginal. Two-residue loops with purines in the first position give rise to the most stable structures due to their enhanced stacking interaction with the adjacent minor groove tetrad. On the other hand, pyrimidines confer more stability than purines in the second position of the loop.
authors.affiliation: Departament de Química Orgànica, Universitat de Barcelona, C/Martí i Franquès 1-11, 08028 Barcelona, Spain.
authors.forename: Núria
authors.initials: N
authors.lastname: Escaja
authors.forename: Irene
authors.initials: I
authors.lastname: Gómez-Pinto
authors.forename: Júlia
authors.initials: J
authors.lastname: Viladoms
authors.forename: Enrique
authors.initials: E
authors.lastname: Pedroso
authors.forename: Carlos
authors.initials: C
authors.lastname: González
mesh_terms: D019281:Dimerization; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D013696:Temperature
chemical_list: D009841:Oligonucleotides