| Abstract
| - The c-kit gene encodes a receptor tyrosine kinase, whose engagement by its ligand triggerssignals leading to cell proliferation. c-kit activity is elevated in gastrointestinal stromal tumors (GISTs),and its therapeutic inhibition by small molecules such as imatinib is clinically validated. We identified aputative quadruplex forming 21-nucleotide sequence upstream of the c-kit transcription initiation site(c-kit21), on the G-rich strand, which occupies a site required for core promoter activity. Here, we showby nuclear magnetic resonance (NMR), circular dichroism (CD), and ultraviolet (UV) spectroscopic methodsthat c-kit21 forms quadruplexes under physiological conditions. Mutational analysis of c-kit21 has providedinsights into its structural polymorphism. In particular, one mutated form appears to form a single quadruplexspecies that adopts a parallel conformation. The quadruplex-forming sequence shows a high level ofsequence conservation across human, mouse, rat, and chimpanzee. The small variation in sequence betweenthe quadruplex in human/chimpanzee as compared to the rat/mouse was examined more closely bybiophysical methods. Despite a variation in the sequence and length of loop 2, the quadruplexes showedboth comparable CD spectra, indicative of parallel quadruplexes, and also similar thermal-stability profiles,suggesting conservation of biophysical characteristics. Collectively, the evidence suggests that thisquadruplex is a serious target for a detailed functional investigation at the cell-biology level.
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