title: Centromeric Alpha-Satellite DNA Adopts Dimeric i-Motif Structures Capped by AT Hoogsteen Base Pairs.
abstract: Human centromeric alpha-satellite DNA is composed of tandem arrays of two types of 171 bp monomers; type A and type B. The differences between these types are concentrated in a 17 bp region of the monomer called the A/B box. Here, we have determined the solution structure of the C-rich strand of the two main variants of the human alpha-satellite A box. We show that, under acidic conditions, the C-rich strands of two A boxes self-recognize and form a head-to-tail dimeric i-motif stabilized by four intercalated hemi-protonated C:C(+) base pairs. Interestingly, the stack of C:C(+) base pairs is capped by T:T and Hoogsteen A:T base pairs. The two main variants of the A box adopt a similar three-dimensional structure, although the residues involved in the formation of the i-motif core are different in each case. Together with previous studies showing that the B box (known as the CENP-B box) also forms dimeric i-motif structures, our finding of this non-canonical structure in the A box shows that centromeric alpha satellites in all human chromosomes are able to form i-motifs, which consequently raises the possibility that these structures may play a role in the structural organization of the centromere.
authors.affiliation: Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain).|Centro de Biología Molecular, "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid (Spain).
authors.forename: Miguel
authors.initials: M
authors.lastname: Garavís
authors.affiliation: Departament de Química Orgànica and IBUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona (Spain).
authors.forename: Núria
authors.initials: N
authors.lastname: Escaja
authors.affiliation: Univ. Bordeaux, ARNA Laboratory, IECB, 2 rue Robert Escarpit 33600 Pessac (France).|Inserm, ARNA Laboratory, 146 Rue Leo Saignat, 33000 Bordeaux (France).
authors.forename: Valérie
authors.initials: V
authors.lastname: Gabelica
authors.affiliation: Centro de Biología Molecular, "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid (Spain).
authors.forename: Alfredo
authors.initials: A
authors.lastname: Villasante
authors.affiliation: Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain). cgonzalez@iqfr.csic.es.
authors.forename: Carlos
authors.initials: C
authors.lastname: González
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D002503:Centromere / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000378:metabolism; D006801:Humans; D007364:Intercalating Agents / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation
chemical_list: D004268:DNA-Binding Proteins; D007364:Intercalating Agents
keywords: DNA recognition; DNA structures; helical structures; nucleic acids; structural biology