Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA

Abstract

Two novel unnatural amino acids, prepared by linking a dicationic purple-coloured and fluorescent naphthalene diimide (NDI) at core position to amino acid side chains of variable length, strongly interacted with ds-DNA/RNA by threading intercalation. Different from a reference NDI dye with identical visible range absorbance (520–540 nm) and Stokes shifts in emission (+60 nm, quantum yield > 0.2), only these amino acid–NDI conjugates showed selective fluorimetric response for GC-DNA in respect to AT(U)-polynucleotides. The DNA/RNA binding-induced circular dichroism (ICD) response of NDI at 450–550 nm strongly depended on the length and rigidity of the linker to the amino acid unit, which controls the orientation of the NDI unit inside within the intercalative binding site. The ICD selectivity also depends on the type of polynucleotide, thus the studied NDI dyes act as dual fluorimetric/ICD probes for sensing the difference between here used GC-DNA, AT-DNA and AU-RNA.

Cascade Energy Transfer in Biopolymer-Templated Multi-Chromophoric Assemblies: Ratiometric Temperature Sensing

“…In the case of DNA-based co-assemblies, only weak induced CD (ICD) bands were observed (Figure S11a–c). This indicated that presumably only a fraction of PIm N molecules underwent intercalation or groove binding, whereas the rest of the molecules were bound as multivalent aggregates to DNA through electrostatic interactions. , Similarly, the absence of ICD in the heparin co-assembles confirmed the multivalent surface interaction of the aggregates with heparin (Figure S11d–f). Further experiments were performed to investigate the other aspects connected to the co-assembly formation.…”

“…Herein, we chose two negatively charged biopolymers heparin and ds DNA as biomolecular scaffolds to fabricate FRET systems with multi-stimuli responsiveness. Heparin is the most negatively charged dense biopolymer and routinely used as an anticoagulant in clinical applications , whereas DNA bears the genetic information of the living systems. , In the presence of these biopolyanions, cationic pyrene appended imidazolium amphiphiles ( PIm N , N = 8, 10, and 12, the number of carbon atoms present in the attached n -alkyl segments, Figure ) which were in the self-assembled state in aqueous media and formed electrostatically driven co-assemblies (the self-assemblies are hereafter designated as SA N , whereas the heparin and DNA-based co-assemblies would be referred as HCA N and DCA N , respectively. N denotes the number of carbon atoms in the alkyl segment).…”