Impact of the Supramolecular Organisation of Pyrene – Quinoline Conjugates on their Interaction with ds – DNA

Abstract

Two novel pyrene-quinoline conjugates differing in the linker flexibility between aryls were prepared. In comparison with referent pyrene derivative, both conjugates showed intramolecular pyrene-quinoline stacking in aqueous medium, much more efficient for rigid conjugate. Consequently, only rigid conjugate showed excimer fluorescence with exceptionally strong bathochromic shift (+ 55 nm) of emission maximum in respect to referent pyrene analogue and flexible conjugate. All studied compounds showed similar, 10 µmol dm −3 affinity toward ds-DNA, characterised in general by fluorescence quenching. The flexible conjugate showed at large excess of DNA over dye formation of pyrene-quinoline excimer, while rigid conjugate retained excimer emission throughout all DNA concentrations. Lack of significant thermal stabilisation of ds-DNA by studied compounds and minor changes in CD spectrum of DNA supported non-specific agglomeration of both conjugates and referent pyrene analogue within hydrophobic DNA grooves as the dominant binding mode.

Flexibility and Preorganization of Fluorescent Nucleobase-Pyrene Conjugates Control DNA and RNA Recognition

“…If the effect can be attributed to the same mechanism here that would suggest intramolecular stacking interactions between pyrene and qAN1 within one qAN1-pyr2 molecule, resulting in exciplex-type emission. Another possible reason for the appearance of the λ max at approximately 500 nm is pyrene-excimer emission [ 18 , 19 , 21 ], which is caused by two or more aromatically stacked pyrenes, thus presuming intermolecular interactions of two or more qAN1-pyr2 molecules.…”

“…Pyrene is also prone to form exciplex in combination with other chromophores. For instance, we recently reported the formation of a pyrene–quinoline exciplex with an emission maximum that was 60 nm bathochromically shifted compared to the common pyrene emission [ 21 ].…”

Impact of the Histidine-Triazole and Tryptophan-Pyrene Exchange in the WHW Peptide: Cu(II) Binding, DNA/RNA Interactions and Bioactivity

“…All these differences imply that the pyrenes of 6 and 7 are involved in aromatic stacking interactions [31]. In particular, strong emission of 6 and 7 at about 480-500 nm could be attributed to either (a) pyrene excimer emission resulting from intermolecular stacking of the two pyrenes [31][32][33][34][35] or (b) pyrene exciplex emission [35,45], in which a heterodimeric exciplex of pyrene and Trp is intramolecularly formed. Since the emission of 6 and 7 was proportional to their concentration (Supplementary Information Figures S14 and S15), that supports option (b); an intramolecularly formed exciplex formation between pyrene and Trp, eventually also including a triazole ring.…”

“…The ct-DNA was additionally sonicated and filtered through a 0.45 mm filter to obtain mostly short (ca. 100 base pairs) rod-like B-helical DNA fragments [45]. Polynucleotide concentration was determined spectroscopically [46] as the concentration of phosphates (corresponds to c(nucleobase)).…”

Phenanthridine-pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

“…Further, pyrene-guanidiniocarbonyl-pyrrole discriminated DNA and RNA by different spectroscopic (namely, induced circular dichroism signal and fluorescent signal) response [ 8 ]. Also, we recently reported pyrene-quinoline hybrid molecule that formed exciplex [9], as well as conjugates formed of pyrene and amino acid-fluorescent nucleobase derivative qAN1, differing in length and flexibility between fluorophores [ 10 ]. Both conjugates strongly interacted with ds-DNA/RNA grooves with similar affinity but opposite fluorescence response, due to pre-organization.…”