The Phenanthridine-modified Tyrosine Dipeptide

Abstract

Dipeptide 4 containing two unnatural amino acids, a modified tyrosine and a phenanthridine derivative, was synthesized. Binding of the dipeptide to a series of polynucleotides including ct-DNA, poly A - poly U, poly (dAdT)2, poly dG - poly dC and poly (dGdC)2 was investigated by thermal denaturation experiments, fluorescence spectroscopy and circular dichroism. Thermal denaturation experiments indicated that dipeptide 4 at pH 5.0, when phenanthridine is protonated, stabilizes ds-DNA, whereas it destabilizes ds-RNA. At pH 7.0, when the phenanthridine is not protonated, effects of 4 to the polynucleotide melting temperatures are negligible. At pH 5.0, dipeptide 4 stabilized DNA double helices, and the changes in the CD spectra suggest different modes of binding to ds-DNA, most likely the intercalation to poly dG- poly dC and non-specific binding in grooves of other DNA polynucleotides. At variance to ds-DNA, addition of 4 destabilized ds-RNA against thermal denaturation and CD results suggest that addition of 4 probably induced dissociation of ds-RNA into ss-RNA strands due to preferred binding to ss-RNA. Thus, 4 is among very rare small molecules that stabilize ds-DNA but destabilize ds-RNA. However, fluorescence titrations with all polynucleotides at both pH values gave similar binding affinity (log Ka ≈ 5), indicating nonselective binding. Preliminary photochemical experiments suggest that dipeptide 4 reacts in the photochemical reaction, which affects polynucleotides chirality, presumably via quinone methide intermediates that alkylate DNA.

Dipeptides Containing Pyrene and Modified Photochemically Reactive Tyrosine: Noncovalent and Covalent Binding to Polynucleotides

“…The same group also developed a series of modified peptides with incorporated aminonaphthalimide as a fluorophore [26]. Furthermore, the binding of a series of fluorophore-modified oligopeptides to polynucleotides has been investigated [27][28][29], where the binding units were phenantridines [27], pyrenes [28], naphthalenedimide [30], guanidinocarbonylpyrroles [27] or coumarins [31].…”

“…We have recently developed a series of oligopeptides that bind noncovalently to polynucleotides and induce a fluorescence response owing to the phenantridine [31] or ditryptophan unit [32]. In addition, these oligopeptides contained a photochemically reactive modified tyrosine [33], which upon irradiation underwent deamination forming quinone methide (QM) intermediates, allowing for the covalent attachment of the fluorescence label to the polynucleotides.…”

Photochemical Reactivity of Naphthol-Naphthalimide Conjugates and Their Biological Activity

“…However, for the ultimate application of QM precursors in biological systems, it is important to develop molecules that can generate QMs upon excitation with visible light [34], as well as to increase their reaction selectivity with biological targets, which can be facilitated via the substitution of QM precursors to DNA binding units [10]. In that context, we have explored the application of QM precursors attached to phenanthridine [35]. Further modifications are required, since in these examples QMs were generated by UV light, precluding their application in living cells.…”