title: Solution equilibria of cytosine- and guanine-rich sequences near the promoter region of the n-myc gene that contain stable hairpins within lateral loops.
abstract: BACKGROUND
  Cytosine- and guanine-rich regions of DNA are capable of forming complex structures named i-motifs and G-quadruplexes, respectively. In the present study the solution equilibria at nearly physiological conditions of a 34-base long cytosine-rich sequence and its complementary guanine-rich strand corresponding to the first intron of the n-myc gene were studied. Both sequences, not yet studied, contain a 12-base tract capable of forming stable hairpins inside the i-motif and G-quadruplex structures, respectively.
  
  
  METHODS
  Spectroscopic, mass spectrometry and separation techniques, as well as multivariate data analysis methods, were used to unravel the species and conformations present.
  
  
  RESULTS
  The cytosine-rich sequence forms two i-motifs that differ in the protonation of bases located in the loops. A stable Watson-Crick hairpin is formed by the bases in the first loop, stabilizing the i-motif structure. The guanine-rich sequence adopts a parallel G-quadruplex structure that is stable throughout the pH range 3-7, despite the protonation of cytosine and adenine bases at lower pH values. The presence of G-quadruplex aggregates was confirmed using separation techniques. When mixed, G-quadruplex and i-motif coexist with the Watson-Crick duplex across a pH range from approximately 3.0 to 6.5.
  
  
  CONCLUSIONS
  Two cytosine- and guanine-rich sequences in n-myc gene may form stable i-motif and G-quadruplex structures even in the presence of long loops. pH modulates the equilibria involving the intramolecular structures and the intermolecular Watson-Crick duplex.
  
  
  CONCLUSIONS
  Watson-Crick hairpins located in the intramolecular G-quadruplexes and i-motifs in the promoter regions of oncogenes could play a role in stabilizing these structures.
authors.affiliation: Solution Equilibria and Chemometrics Group, Department of Analytical Chemistry, University of Barcelona, Diagonal 645, E-08028 Barcelona, Spain.
authors.forename: Sanae
authors.initials: S
authors.lastname: Benabou
authors.forename: Rubén
authors.initials: R
authors.lastname: Ferreira
authors.forename: Anna
authors.initials: A
authors.lastname: Aviñó
authors.forename: Carlos
authors.initials: C
authors.lastname: González
authors.forename: Sébastien
authors.initials: S
authors.lastname: Lyonnais
authors.forename: Maria
authors.initials: M
authors.lastname: Solà
authors.forename: Ramon
authors.initials: R
authors.lastname: Eritja
authors.forename: Joaquim
authors.initials: J
authors.lastname: Jaumot
authors.forename: Raimundo
authors.initials: R
authors.lastname: Gargallo
mesh_terms: D002850:Chromatography, Gel; D002942:Circular Dichroism; D003596:Cytosine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D054856:G-Quadruplexes; D006147:Guanine / Q000737:chemistry*; D008956:Models, Chemical; D011401:Promoter Regions, Genetic; D016271:Proto-Oncogene Proteins c-myc / Q000737:chemistry* / Q000235:genetics*; D012996:Solutions; D021241:Spectrometry, Mass, Electrospray Ionization
chemical_list: D016271:Proto-Oncogene Proteins c-myc; D012996:Solutions; D006147:Guanine; D003596:Cytosine; D004247:DNA
keywords: Chromatography; G-quadruplex; Multivariate analysis; Quadruplex/duplex competition; i-Motif; n-myc