Kinetic hybrid i-motifs: Intercepting DNA with RNA to form a DNA_2-RNA_2 i-motif

摘要

We have constructed and characterized a long-lived hybrid DNA_2-RNA_2 i-motif that is kinetically formed by mixing equivalent amount of C-rich RNA (R) and C-rich DNA (D). Circular dichroism shows that these hybrids are distinct from their parent DNA_4 or RNA_4 i-motif. pH dependent CD and UV thermal melting experiments showed that the complexes were maximally stable at pH 4.5, the pK_a of cytosine, consistent with the complex being held by CH~+-C base pairs. Fluorescence studies confirmed their tetrameric nature and established the relative strand polarities of the RNA and DNA strands in the complex. These showed that in a hybrid D_2R_2 i-motif two DNA strands occupy one narrow groove and the two RNA strands occupy the other. This suggests that even the sugar-sugar interactions are highly specific. Interestingly, this hybrid slowly disproportionates into DNA_4 i-motifs and ssRNA which would be valuable to study intermediates in DNA_4 i-motif formation.