Stabilization of DNA Duplexes and Hairpins by Charge-Transfer Interactions Using DAN:NDI Pairs

Electron-rich1,5-dialkoxynaphthalene (DAN) and electron-deficient1,8,4,5-naphthalenetetracarboxylic diimide (NDI) are known to interactthrough the formation of charge-transfer complexes. The introductionof DAN and NDI into various DNA duplexes and hairpins was investigatedby ultraviolet (UV) melting curve analysis. The positioning of theDAN:NDI pair was found to strongly influence the stability of DNAduplex and hairpins. In particular, while the introduction of oneDAN/NDI pair in front of each other in the center of a DNA duplexled to a decrease of the thermal stability (Delta Tm - 6 degrees C),the addition of a second pair restored or even increased the stability.In contrast, the introduction of DAN:NDI pairs at the end of a duplexalways induced a strong stabilization (Delta Tm up to +20 degrees C).Finally, a DAN:NDI pair positioned in the loop of a hairpin induceda stronger stabilization than a T4 loop (Delta Tm + 10 degrees C).Based on charge-transfer interactions, the strong stabilizations observedallow the preparation of highly stabilized DNA nanostructures openingthe way to numerous applications in nanotechnology.