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The synthesis, photophysical, and electrochemical properties of selectively mono-, bis- and tris-dimethylamino- and trimethylammonium-substituted bis-triarylborane bithiophene chromophores are presented along with the water solubility and singlet oxygen sensitizing efficiency of the cationic compounds Cat1+ , Cat2+ , Cat(i)2+ , and Cat3+ . Comparison with the mono-triarylboranes reveals the large influence of the bridging unit on the properties of the bis-triarylboranes, especially those of the cationic compounds. Based on these preliminary investigations, the interactions of Cat1+ , Cat2+ , Cat(i)2+ , and Cat3+ with DNA, RNA, and DNApore were investigated in buffered solutions. The same compounds were investigated for their ability to enter and localize within organelles of human lung carcinoma (A549) and normal lung (WI38) cells showing that not only the number of charges but also their distribution over the chromophore influences interactions and staining properties.

A series of 3 dicationic monomethine cyanine dyes was synthesized in moderate yields, applying structural alternations with respect to both the peripheral carrier of additional possitive charge - cyclic amine (pyrrolidine or pyridine) and the introduction of a halogen atom (fluorine or chlorine) at position 6 of the benzothiazole moiety. Structural elucidation of the target fluorophores was achieved employing a combination of 1D, 2D-NMR spectroscopy and ESI mass spectrometry in both positive and negative mode. One of the main goals of current investigation was to examine the impact of the introduced steric and electronic properties on interactions with various DNA and RNA. The cyanine dyes induced the triplex formation of consecutive rA/dA-containing nucleic acid helices. In particular, the chlorinated cyanine 3 stabilized all three triplex helices (dAdTdT, rAdTdT, rArUrU) much stronger than corresponding duplex nucleic acid forms (dAdT, rAdT, rArU). The same derivative, showed a strong tendency for H-aggregate formation in the presence of rA chain in single-stranded, double-stranded, or triple-stranded forms. The three monomethines exerted a significant effect on all tumour cell lines’ viability, especially towards HeLa and A549 cell lines (5–6 μM). Colocalization studies revealed that fluorophores 2 and 3 preferentially accumulate in mitochondria, which, in addition to their proven influence on cell viability, makes them promising therapeutic leads.

New monomethine, unsymmetrical styryl dyes consisting of benzothiazole and N-methylpiperazine or N-phenylpiperazine scaffolds were synthesized, and their binding affinities for different ds-polynucleotides and G-quadruplex were studied. Substitution of piperazine unit with methyl or phenyl group strongly influenced their binding modes, binding affinities, spectroscopic responses and antiproliferative activities. Compounds with N-methylpiperazine substituents showed a significant preference for AT-DNA polynucleotides and demonstrated AT-minor groove binding, which manifested in strong fluorescence increase, significant double helix stabilization, and positive induced circular dichroism spectra. These compounds formed complexes with G-quadruplex by π-π stacking interactions of dye with the top or bottom G-tetrad. Bulkier compounds with N-phenylpiperazine function are probably bound to ds-polynucleotide by partial intercalation between base pairs. On the other hand, they showed stronger stabilization of G-quadruplex compared to methyl-substituted compounds. Fluorimetric titrations pointed to possible mixed stoichiometry’s: 1:1 complex with π-π stacking interactions of dye on the top or bottom G- tetrad and 1:2 complex with dye positioned between two G-quadruplex molecules. Bulkier dyes with N-phenylpiperazine fragments demonstrated micromolar and submicromolar antiproliferative activity that was especially pronounced for leukaemia and lymphoma. Flow cytometric assay shows dose- and time-dependent increase in SubG0/G1 phase. Furthermore, the compounds enter the cells readily and accumulate in the mitochondrial space, co-localize with the standard mitochondrial markers.

The synthesis, photophysical, and electrochemical properties of selectively mono‐, bis‐ and tris‐dimethylamino‐ and trimethylammonium‐substituted bis‐triarylborane bithiophene chromophores are presented along with the water solubility and singlet oxygen sensitizing efficiency of the cationic compounds Cat1+ , Cat2+ , Cat(i)2+ , and Cat3+ . Comparison with the mono‐triarylboranes reveals the large influence of the bridging unit on the properties of the bis‐triarylboranes, especially those of the cationic compounds. Based on these preliminary investigations, the interactions of Cat1+ , Cat2+ , Cat(i)2+ , and Cat3+ with DNA, RNA, and DNApore were investigated in buffered solutions. The same compounds were investigated for their ability to enter and localize within organelles of human lung carcinoma (A549) and normal lung (WI38) cells showing that not only the number of charges but also their distribution over the chromophore influences interactions and staining properties., Four selectively mono ‐, bis ‐ and tris ‐trimethylammonium‐substituted, bithiophene‐bridged bis‐triarylboranes were synthesized and their potential biological applications were investigated including live cell imaging and photo‐induced cell death. It is demonstrated that their photophysical and electrochemical properties and their interactions with DNAs, RNA and cells, are strongly influenced by the number and distribution of charges within the compounds.

New analogs of the commercial asymmetric monomethine cyanine dyes thiazole orange (TO) and thiazole orange homodimer (TOTO) with hydroxypropyl functionality were synthesized and their properties in the presence of different nucleic acids were studied. The novel compounds showed strong, micromolar and submicromolar affinities to all examined DNA ds-polynucleotides and poly rA–poly rU. The compounds studied showed selectivity towards GC-DNA base pairs over AT-DNA, which included both binding affinity and a strong fluorescence response. CD titrations showed aggregation along the polynucleotide with well-defined supramolecular chirality. The single dipyridinium-bridged dimer showed intercalation at low dye-DNA/RNA ratios. All new cyanine dyes showed potent micromolar antiproliferative activity against cancer cell lines, making them promising theranostic agents.

Interactions of two newly synthesized and six previously reported benzoxanthene lignans (BXLs), analogues of rare natural products, with DNA/RNA, G-quadruplex and HSA were evaluated by a set of spectrophotometric methods. Presence/absence of methoxy and hydroxy groups on the benzoxanthene core and minor modifications at C-1/C-2 side pendants – presence/absence of phenyl ring and presence/absence of methoxy and hydroxy groups on phenyl ring – influenced the fluorescence changes and the binding strength to double- stranded (ds-) and G-quadruplex structures. In general, compounds without phenyl ring showed stronger fluorescence changes upon binding than phenyl-substituted BXLs. On the other hand, BXLs with an unsubstituted phenyl ring showed the best stabilization effects of G-quadruplex. Circular dichroism spectroscopy results suggest mixed binding mode, groove binding and partial intercalation, to ds-DNA/RNA and end- stacking to top or bottom G-tetrads as the main binding modes of BXLs to those targets. All compounds exhibited micromolar binding affinities toward HSA and an increased protein thermal stability. Moderate to strong antiradical scavenging activity was observed for all BXLs with hydroxy groups at C-6, C-9 and C-10 positions of the benzoxanthene core, except for derivative bearing methoxy groups at these positions. BXLs with unsubstituted or low-substituted phenyl ring and one derivative without phenyl ring showed strong growth inhibition of Gram- positive Staphylococcus aureus. All compounds showed moderate to strong tumor cell growth- inhibitory activity and cytotoxicity.

A new group of multifunctional ligands for DNA and RNA were prepared, comprising phenanthridinium and triazolyluracil connected by various aliphatic or peptide linkers. The peptide linker conjugates showed at least one order of magnitude higher affinity in comparison to aliphatic analogues, which was attributed to peptide-specific hydrophobic and hydrogen bonding interactions within DNA/RNA binding sites. Particularly, a peptide linker conjugate with lysine residue showed selectivity toward poly rA–poly rU, as well as toward poly U, both characterized by strong affinity and a selective fluorescence response. Negligible cytotoxicity of compounds additionally supported their possible applications as fluorimetric probes in laboratory use.

(p-Cymene)-ruthenium bioconjugates ML (1) and ML2 (2), bearing phosphane ligands substituted with chiral or non-chiral amino acid esters, L, were synthetized and characterized by instrumental methods (NMR, CD, MS) and DFT calculations (using the wB97xD functional). Cytotoxic activity of complexes 1 and 2 was investigated by using human cervical carcinoma cell line (HeLa) and MTT assay. Four (2pG, 2pA, 2mG and 2mA) out of ten synthesized ruthenium complexes showed significant toxicity, with IC50 values of 5–30 μM. Evaluation of the potential biomolecular targets of bioconjugates 2 by UV–Vis, fluorescence and CD spectroscopy revealed no measurable interaction with DNA, but micromolar affinity for proteins. The cytotoxicity of bioconjugates 2 is in correlation with their BSA binding constants, i. e. bioconjugates with lower IC50 values show higher binding affinities towards BSA. Compound 2mG with value of IC50 16 μM was selected for further biological characterization. The higher level of toxicity towards tumor compared to normal cell lines indicates its selective activity, important characteristic for potential medical use. It was detected 2mG caused increase of cells in the S phase of cell cycle and consequential decrease of cells in G0/G1 phase. Additionally, 2mG caused dose- and time-dependent increase of SubG0/G1 cell population, suggesting its ability to induce programmed cell death. Further investigation determined autophagy as the mode of cell death. The role of GSH in HeLa cells response to investigated organometallic ruthenium complexes was confirmed using specific regulators of GSH synthesis, buthionine sulfoximine and N-acetyl-cysteine. Pre-treatment of cells with ethacrynic acid and probenecid emphasized the role of GSH in detoxification of 2mG compound. The amount of total ruthenium accumulation in the cell did not correlate with toxicity of 2pG, 2pA, 2mG and 2mA, suggesting structure dependent differences in either cell uptake or kinetics of ruthenium complexes detoxification. We speculate that ruthenium complexes bind protein-based biomolecules further triggering cell death. Based on the gained knowledge, the synthesis and development of more tumor-specific ruthenium-based complexes as potential anticancer drugs can be expected.

Copper(II) complexes with cysteine and histidine, amino acids that coordinate copper(II) in human body, were investigated. Cu-His and Cu-Cys complexes were detected in pH range from 5.0 to 9.0 using voltammetric techniques. [CuHis2] complex reduces by two- electron reversible process at  -0.40 V, while [CuCys] complex by one-electron quasireversible process at -0.6 V, revealing strong adsorption at the electrode surface. When both amino acids are present in the solution, new peak appeared at -0.5 V, which corresponded to the [CuHisCys] complex reduction. Formation and characterization of mixed ligand complex was also supported by UV-Vis spectra recorded at fixed histidine and various cysteine concentrations. Formation of [CuHisCys] complex in the solution was detected and stability constant calculated to amount to logKCuHisCys=16.90.3. This study was the first attempt to characterize formation of Cu(II) mixed ligand complexation process with biochemically important amino acids in electron transport and oxygenation reactions in human body.

Cobalt (II) as an important micronutrient for numerous biological processes in marine environment, has been tested in model aqueous solutions with naturally occurring ligands 4-nitrocatecol (4NC) and humic acid (HA) by voltammetry and spectrophotometry. Irreversible, two-electron reduction processes of Co(II)–4NC and Co(II)-HA complexes adsorbed on the mercury drop surface, depending on accumulation time and composition of the solution (cCo, c4NC, cHA and pH), were detected. Complexes Co:L = 1:1 stability constants formed only in the solution, were determined by spectrophotometry and amout to log KCo(II)4NC = 3.98 (pH = 8.2) and log KCo(II)4NC = 5.76 (pH = 6.5), and log KCo(II)HA = 3.80 (pH = 8.2). Co:L = 1:2 complexes Co(II)-(4NC)2 at pH 6.5 and 8.2 and Co(II)-(HA)2 at pH 8.2, formed at the mercury drop electrode surface as hydrophobic specia, were detected only by voltammetric measurements. Conditional stability constants were calculated by the CLE/ACSV method: log KCo(II) (4NC)2 = 21.86 (pH = 8.2), log KCo(II) (4NC)2 = 21.11 (pH = 6.5) and log KCo(II) (HA)2 = 11.32 (pH = 8.2).

A series of novel hydrazino-based peptidomimetics and analogues comprising N-terminal lysine and C-terminal phenanthridinyl-L-alanine were prepared. The presented results demonstrate the up to now unknown possibility to finely modulate peptide interactions with DNA/RNA by α-hydrazino group insertion and how the different positioning of two α-hydrazino groups in peptides controls binding to various double stranded and single stranded DNA and RNA. All peptidomimetics bind with 1–10 micromolar affinity to ds-DNA/RNA, whereby the binding mode is a combination of electrostatic interactions and hydrophobic interactions within DNA/RNA grooves. Insertion of the α-hydrazino group into the peptide systematically decreased its fluorimetric response to DNA/RNA binding in the order: mono-hydrazino < alternating-hydrazino < sequential-hydrazino group. Binding studies of ss-polynucleotides suggest intercalation of phenanthridine between polynucleotide bases, whereby affinity and fluorimetric response decrease with the number of α-hydrazino groups in the peptide sequence. Particularly interesting was the interaction of two sequential α-hydrazino acids-peptidomimetic with poly rG, characterised by a specific strong increase of CD bands, while all other peptide/ssRNA combinations gave only a CD-band decrease. All mentioned interactions could also be reversibly controlled by adjusting the pH, due to the protonation of the fluorophore.

Two structurally similar bis-phenanthridinium–adenine conjugates (equipped with one or two adenines, respectively), exhibiting strong ds-DNA/RNA groove binding, revealed ratiometric fluorescent recognition of alternating AT-DNA with respect to other ds-DNA/RNA and ss-RNA. Further, CD spectra pattern of adenine–bis-phenanthridinium conjugate/polynucleotide complexes strongly depended on polynucleotide secondary structure. Attached adenine was essential for spectrophotometric recognition response, ds-DNA stabilisation and orientation of compounds regarding chiral DNA helix.

Interactions between DNA/RNA and huge variety of peptides are quite common in nature, controlling vast number of processes. Also, there are several naturally occurring small molecules which contain peptide and DNA intercalator in structure, whereby their biological activity is based on synergistic interactions of both components ; for instance bis-intercalator echinomycin. Versatility of synthetic approaches to short peptides allowed their usage as simple recognition units within the DNA or RNA grooves or as backbone carriers for variety of bioactive substituents attached to amino acid side chains, one of very popular examples being PNAs. Such peptide-backbones were also used for synthesis of novel intercalators and poly-intercalators, many of them showing intriguing novel DNA/RNA interacting properties.

By sterically controlled monomer-dimer equilibrium novel dyes kinetically differentiate between homo-AT and alternating AT-AT polynucleotides and finely probe width and sterical occupation of DNA minor groove by induced CD signals.

The aim of this review is to summarize the most comprehensive results in the field of bis-aromatic compounds targeting DNA and RNA, whereby both aromatic units of small molecule bind to the polynucleotide by the aromatic stacking interactions. The most recent results about structure - DNA/RNA binding affinity, selectivity and biological implications are discussed for bis-intercalators, sterically restricted macrocyclic and threading bis-aromatics and intercalator - nucleobase conjugates.

Novel bis-nucleobase-phenanthridinium conjugates were synthesised and their aqueous solutions spectroscopically characterised. Bis-adenine conjugate revealed in aqueous solutions significantly more pronounced intramolecular aromatic stacking interactions than bis-uracil analogue. In contrast with previously reported poly A recognition by bis-uracil conjugate, recognition of complementary nucleotides and poly U was not observed due to the strong interference of bulk water with hydrogen bonding between nucleobases. The screening of anticancer activity on six human cell lines revealed that tethering of a nucleobase to phenanthridinium moiety diminished antiproliferative potential of phenanthridinium. However, among mono-nucleobase conjugates adenine derivative was found to be the most selective one (MiaPaCa-2, Hep-2).

N-Methyl-8-aminophenathridinium–uracil and –adenine conjugates possessing a nucleobase attached at the phenanthridinium 8-amino group by a trimethylene spacer were prepared in the form of water-soluble hydrogensulfate salts. Spectroscopic characteristics of the conjugates reveal the formation of folded conformations in water characterized by intramolecular aromatic stacking between the phenanthridinium unit and the tethered nucleobase. The conjugates form 1:1 complexes in water with either complementary or non-complementary nucleotides, giving log Ks values between 1 and 2 and showing a lack of any base recognition. Also, the binding studies with single-stranded polynucleotides showed no preference of conjugates to polynucleotides containing complementary nucleobases. At pH 5, the N-methylphenanthridinium–adenine conjugate exhibited preferred binding to double-stranded (ds-) polyAH+, whereas its protonated analogue bound preferably to polyU. The results reveal that the presence of protonated or permanently charged intercalator units in the conjugates dramatically changes their binding preferences for polynucleotides. Copyright © 2003 John Wiley & Sons, Ltd.

A series of novel phenanthridine–nucleobase conjugates were prepared and studied by spectroscopic methods. An analysis of 1H NMR, UV–Vis and fluorescence spectra in aqueous media revealed intramolecular aromatic stacking interactions between the phenanthridinium unit and the nucleobase, due to the conformation of the molecules. Fluorimetric titrations showed that phenanthridinium–nucleobase conjugates 8, 10 and reference phenanthridine compound 12 form 1:1 non-covalent complexes with nucleotides in water with binding constants ranging from 10 to 100 mol−1 dm3. Interestingly, compounds 9 and 11 form intercalative-type 1:1 complexes with the nucleotide aromatic unit inserted between phenanthridinium and covalently attached nucleobase, yielding binding constants of 103–104 mol−1 dm3. Aromatic ππ stacking interactions were found to be dominant in complexes with nucleotides of all compounds studied. Copyright © 2002 John Wiley & Sons, Ltd.

A series of structurally similar bis-phenanthridinium derivatives, some with uracil at different positions, revealed different interactions with various polynucleotides. The uniform binding of mononucleotides to all studied compounds by "cyclobisintercaland" binding type indicated that compound-polynucleotide interaction selectivity was the consequence of polynucleotide secondary structure and not direct nucleobase recognition. Although affinity and fluorimetric response of all studied compounds toward ds-DNA/RNA was similar, the thermal denaturation and ICD signal-based sensing was highly sensitive to polynucleotide basepair composition and secondary structure. In particular, for the specific poly rAH(+)-poly rAH(+) double helix MD parameters are newly developed and used for analysis of its complexes. The highly sensitive orientation of phenanthridinium as well as the role of the uracil substituent, both binding interactions finely tuned by the steric and binding properties of the DNA/RNA-ligand interaction site, offer novel structural information about binding and steric properties of particular DNA-RNA systems.

To explore in greater detail the recently reported rare kinetic differentiation between homo-polymeric and alternating AT-DNA sequences by using sterically restricted phosphonium dyes that form dimers within the DNA minor groove, new analogues were prepared in which the quinolone phosphonium moiety was kept constant, while the size and hydrogen bonding properties of the rest of the molecule were varied. Structure–activity relationship studies revealed that a slight increase in length by an additional methylene unit results in loss of kinetic AT selectivity, but yielded an AT-selective fluorescence response. These DNA/RNA-groove-bound dyes combine very low cytotoxicity with efficient cellular uptake and intriguingly specific fluorescent marking of mitochondria. In contrast to longer analogues, a decrease in length (by methylene unit removal) and rearrangement of positive charge resulted in dyes that had switched to the intercalative binding mode to GC DNA/dsRNA but that still form dimers in the minor groove of AT sequences, consequently yielding a significantly different chiro-optical response. The latter dyes also revealed strongly selective antiproliferative activity toward HeLa cancer cells.

Among series of novel bis-phenanthridinium – nucleobase conjugates, the adenine derivative revealed high (logKs = 6.9 M-1) and selective affinity toward complementary nucleotide (UMP), accompanied by specific change in the UV/Vis spectrum of phenanthridine subunits, differing significantly from changes caused by addition of other nucleotides. High stability and selectivity of adenine-conjugate/UMP non-covalent complex is, according to the molecular modelling studies, correlated to the number of inter- and intramolecular aromatic stacking interactions between phenanthridinium subunits, covalently attached adenine and added UMP, while the selectivity of adenine-conjugate toward UMP in respect to other nucleotides is most likely the consequence of additional hydrogen bonding between UMP and adenine.

Among novel bis-nucleobase–phenanthridinium conjugates bis-uracil analogue 2 stabilized significantly more effective poly-dA–poly-dT and poly-AH+–poly-AH+ than adenine analogue 3 and reference compound 1. For the alternating poly-dAdT–poly-dAdT however, the binding preference is lost, pointing to the importance of specific interactions of uracils of 2 with homopolynucleotides containing consecutive adenines.

Adenine containing conjugates 4 and 5 exhibit specific spectroscopic changes and two orders of magnitude higher affinity toward poly U than uracil conjugates 2 and 3 and the reference compound 1 due to the existence of specific interactions between adenine and uracil, possibly Watson-Crick hydrogen bonding between the bases stacked on the phenanthridinium moiety.