title: Study of cavity size and nature of bridging units on recognition of nucleotides by cyclophanes.
abstract: We synthesized a few novel cyclophanes CP-1 to CP-4 containing anthracene units linked together through different bridging and spacer groups and have investigated their interactions with various nucleosides and nucleotides. Of these systems, CP-1 and CP-3 showed selectivity for 5'-GTP and 5'-ATP as compared to other nucleotides and nucleosides, whereas negligible selectivity was observed with CP-2 and CP-4. Interestingly, CP-1, CP-2 and CP-3 exhibited significant binding interactions with the fluorescent indicator, 8-hydroxy-1,3,6-pyrene trisulfonate (HPTS), resulting in the formation of non-fluorescent complexes. Titration of these complexes with nucleosides and nucleotides resulted in the displacement of HPTS, leading to the revival of its fluorescence intensity. It was observed that 5'-GTP induced the maximum displacement of HPTS from the complex [CP-1·HPTS] with an overall fluorescence enhancement of ca. 150-fold, while 5'-ATP induced ca. 45-fold. Although the displacement of HPTS from the complexes [CP-2·HPTS] and [CP-3·HPTS] was found to be similar to that of [CP-1·HPTS], these complexes showed lesser selectivity and sensitivity. In contrast, negligible displacement of HPTS was observed from the complex [CP-4·HPTS] under similar conditions. These results indicate that CP-1, having a well-defined cavity and good electron acceptor (viologen), is capable of forming selective and stable complexes. Though CP-2 and CP-3 retain the good electron acceptor (viologen), their reduced aromatic surface and larger cavity, respectively, resulted in lesser sensitivity. In contrast, CP-4 having a large cavity and a poor acceptor (1,2-bis(pyridin-4-yl)ethene) showed negligible selectivity, thereby indicating the importance of cavity size, bridging unit and aromatic surface on biomolecular recognition properties of cyclophanes.
authors.affiliation: Photosciences and Photonics, Chemical Sciences and Technology Division, National Institute for Interdisciplinary Science and Technology (NIIST), CSIR, Trivandrum, 695019, India.
authors.forename: Prakash P
authors.initials: PP
authors.lastname: Neelakandan
authors.forename: Paramjyothi C
authors.initials: PC
authors.lastname: Nandajan
authors.forename: Baby
authors.initials: B
authors.lastname: Subymol
authors.forename: Danaboyina
authors.initials: D
authors.lastname: Ramaiah
mesh_terms: D001952:Bridged-Ring Compounds / Q000737:chemistry*; D004988:Ethers, Cyclic / Q000737:chemistry*; D008958:Models, Molecular; D015394:Molecular Structure; D009711:Nucleotides / Q000032:analysis* / Q000737:chemistry; D010880:Piperidines / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D001952:Bridged-Ring Compounds; D004988:Ethers, Cyclic; D009711:Nucleotides; D010880:Piperidines