TY - JOUR A1 - Jana, Poulami A1 - Å upljika, Filip A1 - Schmuck, Carsten A1 - Piantanida, Ivo T1 - Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator JF - Beilstein Journal of Organic Chemistry PY - 2020/// VL - 16 SP - 2201 EP - 2211 SN - 1860-5397 DO - 10.3762/bjoc.16.185 PB - Beilstein-Institut JA - Beilstein J. Org. Chem. UR - https://doi.org/10.3762/bjoc.16.185 KW - AFM KW - circular dichroism KW - DNA/RNA recognition KW - fluorescence KW - guanidinio-carbonyl-pyrrole KW - naphthalene diimide N2 - A novel naphthalene diimde analogue (NDI) equipped at the imide positions with two guanidinio-carbonyl-pyrrole (GCP) pendant arms interacted significantly stronger with ds-DNA at pH 5 than at pH 7, due to reversible protonation of the GCP arms. This was consequence of a pH-switchable threading intercalation into ds-DNAs only at pH 5, while at neutral conditions (pH 7) NDI-GCP2 switched to the DNA minor groove binding. Intriguingly, NDI-GCP2 was at both pH values studied bound to the ds-RNA major groove, still showing a higher affinity and thermal denaturation effect at pH 5 due to GCP protonation. At excess over the DNA/RNA conjugate NDI-GCP2 showed also aggregation along the ds-polynucleotide and AFM and DLS demonstrated that NDI-GCP2 has pronounced ds-DNA condensation ability. ER -