The DNA molecule, the carrier of genetic information, can adopt several different structural forms. In addition to the Watson-Crick structure, B-DNA, this molecule can also form other secondary structures, including G-quadruplexes and i-motifs. These two types of structures are predominantly found in the promoter regions of genes, where they participate in gene regulation processes.
In this thesis, I focused on the formation of an i-motif from the DNA sequence 5'-CCTTTCCTTT/2-AP/CCTTTCC-3', modified with 2-aminopurine (2-AP). I-motifs typically form from cytosine-rich sequences under conditions that enable the protonation of certain cytosines, allowing the formation of C-C$^+$ base pairs and the subsequent folding of the DNA strand into a secondary structure called an i-motif. I monitored the formation of the i-motif using various spectroscopic methods. The conditions for i-motif formation were created by gradually lowering the pH of the solution through the addition of hydrochloric acid (HCl).
The experiments performed demonstrate that the modification of the DNA sequence, in which adenine is replaced with 2-AP, does not affect its ability to form an i-motif. Thermal denaturation, like that observed in i-motifs formed from unmodified sequences, is an irreversible process. An important conclusion is that this modification allows the monitoring of i-motif formation using fluorescence spectroscopy via the emission of 2-AP.
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