An overview on the interaction of phenazinium dye phenosafranine to RNA triple and double helices
Ankur Bikash Pradhan, Hasnat Karim Mondal, Lucy Haque, Sutanwi Bhuiya, Suman Das
International Journal of Biological Macromolecules
Triple helical nucleic acids or triplex are formed from the combination of three oligonucleotides. In the double stranded form the base pairs are joined through Watson–Crick base pairing while the third strand of the triplex is joined through Hoogsteen base pairing. The Hoogsteen base paired strands are less stable compare to the Watson–Crick strands. Thus stabilization of the Hoogsteen strand gains importance due to the implication of stable triplexes in various biological processes. For this reason here we have monitored the effect of phenosafranine, a phenazinium dye on the structure of poly(U).poly(A)*poly(U) triplex. Our data revealed that the dye has higher binding affinity to the RNA triplex (K′ = 3.7 × 105 M−1) compared to the parent duplex (K′ = 1.9 × 105 M−1) form. Through a series of spectroscopic and viscometric study we have found that the dye binds to triplex or duplex through the mechanism of intercalation and it stabilizes the Watson–Crick strand while the Hoogsteen strand remains unaffected.
Circular dichroism, Biochemistry