Advances in Cyanine - Amino Acid Conjugates and Peptides for Sensing of DNA, RNA and Protein Structures

Abstract

Small molecule spectrophotometric probes for DNA/RNA and proteins are of the utmost importance for diagnostics in biochemical and biomedical research. Both, naturally occurring and synthetic probes, often include peptide sequence responsible for the selectivity toward the particular target; however, commercially available dyes are restricted to single point attachment to the peptide (having one reactive group). Here presented are our recent advances in the development of novel amino acidfluorophore probes, with the unique characteristic of free N- and C-terminus available for incorporation at any peptide backbone position. Intriguingly, already monomeric amino acid-fluorophores showed recognition among various DNA/RNA, whereby steric impact and contribution of halogens is systematically studied. Moreover, some dyes revealed intracellular mitochondria specificity. Further, several hetero-dimeric chromophore systems were prepared, demonstrating that synergistic effect can lead to simultaneous DNA, RNA and protein fluorimetric recognition, combined with enzyme inhibition. Also, homodimeric cyanines equipped with chlorine revealed intriguing DNA/RNA selectivity in respect to well-known parent TOTO and YOYO dyes.

Peptide–Fluorophore Hydrogel as a Signal Boosting Approach in Rapid Detection of Cancer DNA

“…Among a broad range of available fluorophores, we used Cy3.5, AlexaFluor547, and anthracene (AC), as shown in Figure C. The rationale behind the choice of these fluorophores was their high quantum yield and confirmed interactions with biomolecules. , Azide functionalities were incorporated into the fluorophores to provide an ability of covalent conjugation to a control probe, described below. However, having an azide is not critical for hydrogel formation and can be omitted. , …”

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

“…With this concept in mind, Piantanida and co-workers recently developed several series of fluorophore-amino acid conjugates, thereby making use of the availability of C-and N-terminal amino acid residues for peptide-bond formation. Also, several short multichromophoric peptide constructs were prepared and studied with regard to their interactions with DNA/RNA [11][12][13][14][15][16].…”