Spectrometric study of the folding process of i-motif-forming DNA sequences upstream of the c-kit transcription initiation site

Abstract

The c-kit oncogene shows a cytosine-rich DNA region upstream of the transcription initiation site which forms an i-motif structure at slightly acidic pH values (Bucek et al. [5]). In the present study, the pH-induced formation of i-motif – forming sequences 5′-CCC CTC CCT CGC GCC CGC CCG-3′ (ckitC1, native), 5′-CCC TTC CCT TGT GCC CGC CCG-3′ (ckitC2) and 5′-CCCTT CCC TTTTT CCC T CCC T-3′ (ckitC3) was studied by spectroscopic techniques, such as UV molecular absorption and circular dichroism (CD), in tandem with two multivariate data analysis methods, the hard modelling-based matrix method and the soft modelling-based MCR-ALS approach. Use of the hard chemical modelling enabled us to propose the equilibrium model, which describes spectral changes as functions of solution acidity. Additionally, the intrinsic protonation constant, K in, and the cooperativity parameters, ω c, and ω a, were calculated from the fitting procedure of the coupled CD and molecular absorption spectra. In the case of ckitC2 and ckitC3, the hard model correctly reproduced the spectral variations observed experimentally. The results indicated that folding was accompanied by a cooperative process, i.e. the enhancement of protonated structure stability upon protonation. In contrast, unfolding was accompanied by an anticooperative process. Finally, folding of the native sequence, ckitC1, seemed to follow a more complex mechanism.