pH-Modulated Watson-Crick duplex-quadruplex equilibria of guanine-rich and cytosine-rich DNA sequences 140 base pairs upstream of the c-kit transcription initiation site.
Guanine-rich regions of DNA are sequences capable of forming G-quadruplex structures. The formation of a G-quadruplex structure in a region 140 base pairs (bp) upstream of the c-kit transcription initiation site was recently proposed (Fernando et al., Biochemistry, 2006, 45, 7854). In the present study, the acid-base equilibria and the thermally induced unfolding of the structures formed by a guanine-rich region and by its complementary cytosine-rich strand in c-kit were studied by means of circular dichroism and molecular absorption spectroscopies. In addition, competition between the Watson-Crick duplex and the isolated structures was studied as a function of pH value and temperature. Multivariate data analysis methods based on both hard and soft modeling were used to allow accurate quantification of the various acid-base species present in the mixtures. Results showed that the G-quadruplex and i-motif coexist with the Watson-Crick duplex over the pH range from 3.0 to 6.5, approximately, under the experimental conditions tested in this study. At pH 7.0, the duplex is practically the only species present.
Bucek
Pavel
P
Department of Analytical Chemistry, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain.
Jaumot
Joaquim
J
Aviñó
Anna
A
Eritja
Ramon
R
Gargallo
Raimundo
R
D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D054856:G-Quadruplexes; D020862:GC Rich Sequence; D006863:Hydrogen-Ion Concentration; D019009:Proto-Oncogene Proteins c-kit / Q000235:genetics*; D012996:Solutions; D024363:Transcription Initiation Site
D012996:Solutions; D004247:DNA; D019009:Proto-Oncogene Proteins c-kit