Synthesis and fluorescence properties of 3,6-diaminocarbazole-modified pyrrolidinyl peptide nucleic acid

Abstract

This work aims to explore a new clickable carbazole-based fluorescent label, its incorporation into pyrrolidinyl peptide nucleic acid (acpcPNA), and the interactions between the labeled PNA probe and DNA by fluorescence spectrophotometry and molecular dynamics simulation. A carbazole derivative, namely 3,6-diaminocarbazole (DAC), was synthesized and incorporated into the internal and terminal positions of azide-modified acpcPNA via a sequential reductive alkylation and click reaction previously developed by our group. The DAC-modified acpcPNA can form a stable hybrid with complementary DNA with somewhat lower stability compared to unmodified acpcPNA. Most importantly, the DAC-modified acpcPNA exhibits a remarkable fluorescence increase in the presence of DNA (up to 35.5 fold with complementary DNA). Non-complementary as well as single mismatched DNA targets gave a smaller fluorescence increase (1.1 to 18.6 fold), and the discrimination could be further improved by increasing the temperature to dissociate the mismatched hybrids. Molecular dynamic simulations revealed that the DAC interacts with adjacent nucleobases in single stranded PNA, resulting in quenching of the fluorescence signal. When the PNA formed a hybrid with DNA, the DAC was pushed away from the duplex, resulting in a fluorescence increase. Thus, the DAC-labeled acpcPNA is a potential candidate as a self-reporting probe for determination of DNA sequences.