A. Bromine foot printing of HC35,
(B) HC27 and
(C) CmidT oligonucleotides at pH 6.5. The cytosine runs (I-V) are shown along side of the bromine foot printing pattern. The solid lines along the sequencing lanes depict the four cytosine runs that are involved in the i-motif structure. The dotted line along the fifth run (V) depicts the cytosine run that is not involved in the formation of the i-motif.
D. A schematic representation of the cytosines within the HC27 oligonucleotide that react to bromine. Open (white), closed (black) and half or quarter filled (white/ black) circles correspond to the reactivity of each cytosine to protection, non-protection and partial-protection to bromination, respectively.
E. The 3:3:3, 4:4:3 and 3:4:2 i-motif folding models derived from these experiments. The cytosines that were mutated to thymines in the CmidT oligo are flagged with asterisks alongside the schematic representation of HC27 bromination sites and the model of HIF-1α 3:3:3 i-motif.
