Structural and Thermodynamic Studies of the i-Motif of DNA: Sequence Context Effects

The telomere, located at the end of eukaryotic chromosomes, consists of tandem repeating nucleic acid bases. The G rich strand, with a (TTAGGG) repeat, of the human telomere has a C-rich complimentary stand (a CCCTAA repeat). Former investigations performed on a DNA oligomer possessing the G-rich repeat indicated that it folds into what is known as the G-quadruplex, where the GGG segments form tetrads, and the TTA segments are loops that join the tetrads together. While under acidic conditions, the C-rich strand has also been shown to form a unique structure known as the i-motif. Investigated here is the conformations formed from synthetic DNA oligomers of general sequence (CCCXXX)4, where X= A and/or T, when in the presence of K+ buffer ranging in pH from 7.0 to 5.0. Circular dichroism (CD) spectra were determined at different solution pH and temperatures to investigate the pH and temperature dependence of the folding of these sequences into i-motifs.