Electrospray ionization mass spectrometric analysis of noncovalent complexes between DNA and polyamides containing N-methylpyrrole and N-methylimidazole.
Electrospray ionization mass spectrometry was utilized to investigate the noncovalent complexes between novel polyamides and DNA containing the TCCT sequence. We analyzed the noncovalent binding of the polyamides with the DNA and assessed their relative affinities and stoichiometry. The results confirm that hairpin polyamides have higher binding affinities than three-ring polyamides. The hairpin polyamide (PyPyPyPygammaPyImImPybetaDp) has the highest affinity, and the beta-linked polyamide (PyPyPybetaImImImbetaDp) shows a dominant 1:2 binding stoichiometry. Two groups of competition experiments were undertaken to compare the binding affinities of the duplex DNA with different polyamides directly. The affinity scale thus obtained for the group-1 polyamides is PyPyPyPygammaPyImImPybetaDp > PyPyPybetaImImImbetaDp approximately PyPyPygammaImImImbetaDp >> PyPyPybetaDp > PyImImbetaDp approximately ImImPybetaDp, and the order for the group-2 polyamides is PyPyPygammaImImImbetaDp > PyPyPygammaImImImbetaOEt > PyPyPygammaImImImbetaCOOH.
Zhou
Jiang
J
Department of Chemical Biology, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, P. R. China.
Yuan
Gu
G
D004247:DNA / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry*; D007093:Imidazoles / Q000737:chemistry*; D015394:Molecular Structure; D009757:Nylons / Q000737:chemistry*; D011758:Pyrroles / Q000737:chemistry*; D021241:Spectrometry, Mass, Electrospray Ionization; D013329:Structure-Activity Relationship
D004277:DNA, Single-Stranded; D007093:Imidazoles; D009757:Nylons; D011758:Pyrroles; D004247:DNA; C096654:N-methylpyrrole; C018100:1-methylimidazole