The nature of stabilization of the tandem DNA duplex pTGGAGCTG (pCAGC + (Phn-NH-(CH2)3-NH)pTCCA) based on the UV-, CD-, and two-dimensional NMR spectroscopy data

Properties and three-dimensional structure of the tandem DNA duplex pTGGAGCTG.(pCAGC+(PhnL)pTCCA) in aqueous solution, where L is an amino linker and Phn is an N-(2-hydroxyethyl)phenazinium residue, were studied spectrophotometrically and by two-dimensional 1H NMR spectroscopy (COSY and NOESY). When a tandem complex involving a Phn residue-bearing oligonucleotide is formed, the dye aromatic system intercalates into the double helix at the nick site and takes part in two stacking interactions: a strong one (3.5-4 A) with the T5-A12 base pair of its own duplex moiety and a weak one (4-5 A) with the C4-G13 pair of the adjoining duplex (mainly with the C4 base). This arrangement of the dye residue, providing a cross-interaction of the phenazinium moiety with the base pairs of the adjacent duplex structures, results in the stabilization of the whole tandem complex.