Pyrene–cyanine conjugates as multipurpose fluorescent probes for non-covalent recognition of ds-DNA, RNA and proteins

Abstract

One molecule-dual fluorescence response: pyrene emission highly selective for BSA protein and “switch-on” of cyanine fluorescence selective for DNA.

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

“…Since till now various NDI derivatives were applied for binding and sensing different types of DNA/RNA constructs, including G-quartets [ 55 – 57 ], and other, more complex sequences, the herein presented amino acid–NDI conjugates may in future also be investigated for such applications, either directly or incorporated in peptidoid constructs. Indeed, the colourful and fluorescent NDIs 3a and 3b are ideal for use in peptide-backbone constructed multichromophores targeting FRET-based sensing [ 14 , 26 , 58 ]. For the application of here presented results in bioanalytical sciences or biologically relevant studies it will be necessary to further modify the presented compounds and precisely collect information about their sensitivity to particular target, read-out accuracy, limits of detection, and selectivity at biorelevant conditions.…”

“…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].…”

Bis-Pyrene Photo-Switch Open- and Closed-Form Differently Bind to ds-DNA, ds-RNA and Serum Albumin and Reveal Light-Induced Bioactivity

“…As targeted biomacromolecules, we have chosen ds-DNA/RNA of various secondary structure ( Table S1, Supplementary Materials ), thus differing in properties of binding sites (minor or major grooves and eventually intercalation): namely, we previously showed interesting applications of pyrene fluorophore by relying on its interactions with the DNA or RNA grooves [ 30 ] or combined with switch on and off of pyrene excimer [ 6 , 7 , 8 ]. In addition, since some pyrene analogues tended to prefer proteins over ds-DNA [ 31 ], we studied interactions of new compounds with the representative protein, i.e., bovine serum albumin (BSA), the most abundant protein in blood plasma responsible for the transport of many small molecules [ 32 , 33 ], which is characterized by up to eight different binding sites [ 34 ].…”

Polycationic Monomeric and Homodimeric Asymmetric Monomethine Cyanine Dyes with Hydroxypropyl Functionality—Strong Affinity Nucleic Acids Binders

“…There is a challenging task to design and synthesize a small molecule capable of strong binding combined with specific recognition of a certain structure type (e.g., AT-rich sequence or GC-rich sequence, DNA or RNA, single-stranded or double-stranded helix, a different type of helix, like A, B, Z, etc.) and also a specific binding response [6,7]. A combination of different functionalities and structural building blocks within the same ligand molecule could result in an enhanced number of non-covalent interactions, increased affinity and selective recognition of specific DNA/RNA structure.…”