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Solution equilibria of cytosine- and guanine-rich sequences near the promoter region of the n-myc gene that contain stable hairpins within lateral loops

AuthorsBenabou, Sanae; Ferreira, Rubén ; Aviñó, Anna ; González, Carlos ; Lyonnais, Sébastien; Solà, Maria ; Eritja Casadellà, Ramón ; Jaumot, Joaquim ; Gargallo, Raimundo
KeywordsG-quadruplex i-Motif
Multivariate analysis
Quadruplex/duplex competition
Issue DateJan-2014
CitationBiochimica et Biophysica Acta - General Subjects 1840(1): 41-52 (2014)
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.
[General significance] 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. © 2013 Elsevier B.V.
Publisher version (URL)http://dx.doi.org/10.1016/j.bbagen.2013.08.028
Identifiersissn: 0304-4165
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