It is well established that the presence of terminal unpaired bases (i.e., dangling ends) influences the stability of duplex DNA. The stabilization is a function of location (i.e., 5' vs 3'), the number of unpaired bases and the identities of the unpaired bases. We have been investigating the structures and stabilities of intramolecular DNA quadruplexes related to the human telomere sequence (TTAGGG)4, which has a -TTA- dangling end at the 5'-terminus. The presence of a -TTA- dangling end on the 5' terminus, the 3' terminus or both destabilize the quadruplex relative to the quadruplex with no dangling ends. We are currently investigating the effect of a single dangling base on the stability of an intramolecular quadruplex using spectroscopic and calorimetric approaches. We will present thermodynamic data (?H, ?S and ?G) for the quadruplex to single strand transition as a function of unpaired base location and identity and discuss these results in terms of base stacking effects.

Influence of dangling ends on the stability of intramolecular DNA quadruplexes

245th National Meeting (2013)

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