Triplex formation at physiological pH: comparative studies on DNA triplexes containing 5-Me-dC tethered at N⁴ with spermine and tetraethyleneoxyamine

Abstract

Oligodeoxynucleotides with spermine conjugation at C4 of 5-Me-dC (sp-ODN) exhibit triple helix formation with complementary Watson-Crick duplexes, and were optimally stable at physiological pH 7.3 and low salt concentration. This was attributed to a favored reassociation of the polycationic third strand with the anionic DNA duplex. To gain further insights into the factors that contribute to the enhancement of triplex stability and for engineering improved triplex systems, the spermine appendage at C4 of 5-Me-dC was replaced with 1,11-diamino-3,6,9-trioxaundecane to create teg-ODNs. From the triple helix forming abilities of these modified ODNs studied by hysteresis behaviour and the effect of salts on triplex stability, it is demonstrated here that teg-ODNs stabilise triplexes through hydrophobic desolvation while sp-ODNs stabilise triplexes by charge effects. The results imply that factors in addition to base stacking effects and interstrand hydrogen bonds are significantly involved in modulation of triplex stability by base modified oligonucleotides.