Analysis of noncovalent complexes between human telomeric DNA and polyamides containing N-methylpyrrole and N-methylimidazole by using electrospray ionization mass spectrometry.

Electrospray ionization mass spectrometry (ESI-MS) was used to investigate noncovalent complexes formed between four novel polyamides containing N-methylpyrrole (Py) and N-methylimidazole (Im), and human telomeric DNA. Of the four polyamides investigated, PyPyPygammaImImImbetaDp (3) had the highest binding affinity towards the duplex d(TTAGGGTTAGGG/CCCTAACCCTAA) (D1). Results of competition analysis showed that the polyamides had binding affinities with D1 in the order PyPyPygammaImImImbetaDp (3)>PyPyPyPygammaPyImImPybetaDp (4)>PyPyPybetaImImImbetaDp (2)>ImImImbetaDp (1). MS/MS spectra confirmed that binding between D1 and the hairpin polyamides is more stable than that with the three-ring polyamides. By contrast, in the case of single-stranded d(TTAGGGTTAGGG)(D2), the binding order changes to ImImImbetaDp (1)>PyPyPygammaImImImbetaDp (3)>PyPyPybetaImImImbetaDp (2).