Electron-rich 1,5-dialkoxynaphthalene (DAN) and electron-deficient 1,8,4,5naphthalenetetracarboxylic diimide (NDI) are known to interact through the formation of charge-transfer complexes. The introduction of DAN and NDI into various DNA duplexes and hairpins was investigated by UV melting curve analysis. The positioning of the DAN:NDI pair was found to strongly influence the stability of DNA duplex and hairpins. In particular, while the introduction of one DAN/NDI pair in front of each other in the centre of a DNA duplex led to a decrease of the thermal stability (∆Tm-6 °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 duplex always induced a strong stabilization (∆Tm up to + 20 °C). Finally a DAN:NDI pair positioned in the loop of a hairpin induced a stronger stabilization than a T4-loop (∆Tm + 10 °C). Based on charge-transfer interactions, the strong stabilizations observed allow the preparation of highly stabilized DNA nanostructures opening the way to numerous applications in nanotechnology.