Stability of Chimeric DNA/RNA Cytosine Tetrads: Implications for i-Motif Formation by RNA

UV melting curves of mono- and di-2‘-hydroxylated cytosine tetrads were recorded. The substitution of one DNA residue by RNA decreased the melting temperature ( T m ) by roughly 6.5 °C. In sequences with two RNA residues, strong positional effects were observed. Juxtaposition of the two d -ribose sugars in the tetrad incurred an additional loss of 6 °C in tetrad stability and decreased the T m by 19 °C from that of the parent compound, d(TCCCCC) 4 . The effect of increasing the number of cytosines on tetrad stability was also measured. Addition (or removal) of one cytosine-protonated cytosine base-pair from the tetrad increased (or decreased) the T m by roughly 9 °C. Thus, the penalty of adding an RNA residue is equal to or greater than the benefit of the additional base-pair. This implies that the stability of RNA cytosine tetrads should not rise with increasing length and that thermal transitions previously observed in poly(rC) correspond to duplex structures.