A bis‐triarylborane tetracation (4‐Ar₂B‐3,5‐Me₂C₆H₂)‐C≡C−C≡C‐(3,5‐Me₂C₆H₂‐4‐BAr₂ [Ar=(2,6‐Me₂‐4‐NMe₃‐C₆H₂)⁺] (2⁴⁺) shows distinctly different behaviour in its fluorimetric response than that of our recently published bis‐triarylborane 5‐(4‐Ar₂B‐3,5‐Me₂C₆H₂)‐2,2′‐(C₄H₂S)₂–5′‐(3,5‐Me₂C₆H₂‐4‐BAr₂) (3⁴⁺). Single‐crystal X‐ray diffraction data on the neutral bis‐triarylborane precursor 2 N confirm its rod‐like dumbbell structure, which is shown to be important for DNA/RNA targeting and also for BSA protein binding. Fluorimetric titrations with DNA/RNA/BSA revealed the very strong affinity of 2⁴⁺ and indicated the importance of the properties of the linker connecting the two triarylboranes. Using the butadiyne rather than a bithiophene linker resulted in an opposite emission effect (quenching vs. enhancement), and 2⁴⁺ bound to BSA 100 times stronger than 3⁴⁺. Moreover, 2⁴⁺ interacted strongly with ss‐RNA, and circular dichroism (CD) results suggest ss‐RNA chain‐wrapping around the rod‐like bis‐triarylborane dumbbell structure like a thread around a spindle, a very unusual mode of binding of ss‐RNA with small molecules. Furthermore, 2⁴⁺ yielded strong Raman/SERS signals, allowing DNA or protein detection at ca. 10 nm concentrations. The above observations, combined with low cytotoxicity, efficient human cell uptake and organelle‐selective accumulation make such compounds intriguing novel lead structures for bio‐oriented, dual fluorescence/Raman‐based applications.

A strong impact of fluorophores’ charge and length on the binding mode, intracellular distribution and antiproliferative activity; intriguing theragnostic potential.

The synthesis, photophysical, and electrochemical properties of selectivelymono‐,bis‐ andtris‐dimethylamino‐ and trimethylammonium‐substitutedbis‐triarylborane bithiophene chromophores are presented along with the water solubility and singlet oxygen sensitizing efficiency of the cationic compoundsCat¹⁺,Cat²⁺,Cat(i)²⁺, andCat³⁺. Comparison with themono‐triarylboranes reveals the large influence of the bridging unit on the properties of thebis‐triarylboranes, especially those of the cationic compounds. Based on these preliminary investigations, the interactions ofCat¹⁺,Cat²⁺,Cat(i)²⁺, andCat³⁺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.

We demonstrate here for the first time that a guanidiniocarbonyl-pyrrole (GCP) unit can be applied for the fine recognition of single stranded RNA sequences—an intuitively unexpected result since so far binding of the GCP unit to ds-DNA or ds-RNA relied strongly on minor or major groove interactions, as shown in previous work. Two novel nucleobase–GCP isosteric conjugates differing in the flexibility of GCP unit revealed a fluorimetric recognition of various single stranded RNA, which could be additionally regulated by pH. The more rigid conjugate showed a specific fluorescence increase for poly A only at pH 7, whereby this response could be reversibly switched-off at pH 5. The more flexible derivative revealed selective fluorescence quenching by poly G at pH 7 but no change for poly A, whereas its recognition of poly AH⁺ can be switched-on at pH 5. The computational analysis confirmed the important role of the GCP fragment and its protonation states in the sensing of polynucleotides and revealed that it is affected by the intrinsic dynamical features of conjugates themselves. Both conjugates showed a negligible response to uracil and cytosine ss-RNA as well as ds-RNA at pH 7, and only weak interactions with ds-DNA. Thus, nucleobase–GCP conjugates can be considered as novel lead compounds for the design of ss-RNA or ss-DNA selective fluorimetric probes.

We synthesized a new amino acid-fluorescent nucleobase derivative (qAN1-AA) and from it two new fluorescent nucleobase–fluorophore (pyrene) conjugates, whereby only the analogue with the longer and more flexible linker (qAN1-pyr2) self-folded into intramolecularly stacked qAN1/pyrene conformation, yielding characteristic, 100 nm-red-shifted emission (λ_max = 500 nm). On the contrary, the shorter and more rigid linker resulted in non-stacked conformation (qAN1-pyr1), characterized by the emission of free pyrene at λ_max = 400 nm. Both fluorescent nucleobase–fluorophore (pyrene) conjugates strongly interacted with ds-DNA/RNA grooves with similar affinity but opposite fluorescence response (due to pre-organization), whereas the amino acid-fluorescent base derivative (qAN1-AA) was inactive. However, only intramolecularly self-folded qAN1-pyr2 showed strong fluorescence selectivity toward poly U (Watson–Crick complementary to qAN1 nucleobase) and poly A (reverse Hoogsteen complementary to qAN1 nucleobase), while an opposite emission change was observed for non-complementary poly G and poly C. Non-folded analogue (qAN1-pyr1) showed no ss-RNA selectivity, demonstrating the importance of nucleobase-fluorophore pre-organization.

Three novel pyrene–pyrrolocytosine (PyrrC) conjugates efficiently bind to ds-DNA/RNA grooves. The compounds exhibit DNA/RNA secondary structure-dependent fluorimetric selectivity. The most pronounced differentiation was observed between poly(dAdT)₂ and poly A–poly U. Moreover, the most flexible conjugate showed the specific fluorescence band at 470 nm with poly(dAdT)₂. The different induced circular dichroism (I)CD response of rigid and flexible pyrene–pyrrC conjugates upon A–T(U) binding revealed the fine structural tuning of the pyrene position within the DNA/RNA binding site. The novel conjugates have shown unmatched specific fluorimetric recognition of poly G to date, with respect to other ss-RNA, attributed to the synergistic effect of pyrene intercalation combined with H-bonding recognition of the complementary base pair. The most prominent response for poly G was observed for the most rigid conjugate, having a conveniently pre-organized conformation. All the conjugates efficiently entered into the human cells, showing no cytotoxicity, thus giving rise to promising lead compounds for the further development of cellular or biochemical spectrophotometric probes.