Triplex formation is a promising strategy for realizing artificially controlling of gene expression, reversible assembly of nanomaterials and DNA nanomachine and single-walled nanotubes (SWNTs) have been widely used as gene and drug delivery vector or as ‘building blocks’ in nano-/microelectronic devices. CGC+ triplex is not as stable as TAT triplex. The poor stability of CGC+ triplex limits its use in vitro and in vivo. There is no ligand that has been reported to selectively stabilize CGC+ triplets rather than TAT. Here, we report that SWNTs can cause d(CT)•d(AG) duplex disproportionation into triplex d(C+T)•d(AG)•d(CT) and single-strand d(AG) under physiological conditions. SWNTs can reduce the stringency of conditions for CGC+ triplex formation studied by UV–vis, CD, DNA melting, light scattering and atomic force microscopy. Further studies indicate that electrostatic interaction is crucial for d(CT)•d(AG) repartition into triplex d(C+T)•d(AG)•d(CT). Our findings may facilitate utilization of SWNTs–DNA complex in artificially controlling of gene expression, nanomaterials assembly and biosensing.