Supramolecular Recognition of Cytidine Phosphate in Nucleotides and RNA Sequences

Abstract

Supramolecular recognition of nucleotides would enable manipulating crucial biochemical pathways like transcription and translation directly and with high precision. Therefore, it offers great promise in medicinal applications, not least in treating cancer or viral infections. This work presents a universal supramolecular approach to target nucleoside phosphates in nucleotides and RNA. The artificial active site in new receptors simultaneously realizes several binding and sensing mechanisms: encapsulation of a nucleobase via dispersion and hydrogen bonding interactions, recognition of the phosphate residue, and a self-reporting feature�"turn-on" fluorescence. Key to the high selectivity is the conscious separation of phosphate-and nucleobase-binding sites by introducing specific spacers in the receptor structure. We have tuned the spacers to achieve high binding affinity and selectivity for cytidine 5′ triphosphate coupled to a record 60-fold fluorescence enhancement. The resulting structures are also the first functional models of poly(rC)-binding protein coordinating specifically to C-rich RNA oligomers, e.g., the 5′-AUCCC(C/U) sequence present in poliovirus type 1 and the human transcriptome. The receptors bind to RNA in human ovarian cells A2780, causing strong cytotoxicity at 800 nM. The performance, self-reporting property, and tunability of our approach open up a promising and unique avenue for sequence-specific RNA binding in cells by using low-molecular-weight artificial receptors.

A box-in-box supramolecular assembly for the highly selective recognition of natural, epigenetically and chemically modified cytosines in water

“…42 On the other hand, they could also be detected as guest molecules, especially for synthetic receptors. For example, naphthyridines 4 and dyes 5 were designed for targeting specific nucleotides or sequences; however, the detection was based on fluorescence signals. Recently, a Mn-MOF was reported to recognize all known purine nucleobases; however, the recognition was only characterized by high-resolution synchrotron powder X-ray diffraction.…”

“…Thus, scientists turned to use synthetic receptors, e.g. , naphthyridines 4 and dyes, 5 which provided a novel approach for targeting specific nucleotides or sequences. However, most of these detection methods depended on fluorescence signals 6,7 which could be influenced by other factors and result in a false decision.…”

“…2 Biomacromolecules, e.g., proteins, 3 were reported to bind specific nucleotides; however, the delivery of macromolecules to the human body remained a significant problem. Thus, scientists turned to use synthetic receptors, e.g., naphthyridines 4 and dyes, 5 which provided a novel approach for targeting specific nucleotides or sequences. However, most of these detection methods depended on fluorescence signals 6,7 which could be influenced by other factors and result in a false decision.…”

“…9 A wide variety of macrocycles were reported, e.g., crown ethers, cyclodextrins, calixarenes, and pillararenes; 9 however, most of them were seldom used for the recognition of nucleobases, because their hydrophobic cavities were not consistent with the hydrophilic nature of nucleobases. Besides these macrocycles, it was interesting to note that cucurbiturils with a large cavity could encapsulate a small hydrophilic molecule, e.g., CB [10]@CB [5], 10 and the "blue box" reported by Stoddart et al could also encapsulate hydrophilic guests, 11 and even form a hierarchical Russian doll; 12 however, macrocycles synthesized for the recognition of nucleobases have not been reported so far.…”

Macrocyclic Conformational Switch Coupled with Pyridinium-Induced PET for Fluorescence Detection of Adenosine Triphosphate

“…6 Incredibly challenging in this regard is the design of synthetic receptors with a turn-on fluorescence response for a desired nucleotide. 7 The receptor must function not only in an aqueous solution but also in a competitive cell environment. 8 The recently explored strategies to visualize nucleotide recognition with a turn-on response include metal-based receptors, 9,10 receptors based on photoinduced electron transfer (PET) processes, 11 aggregation-induced emission, 12,13 excimer−monomer emission, 13−15 FRET, 16 and restriction of internal rotation.…”