Fluorescent "Texas-sized" macrocyclic receptors for the recognition and detection of nucleotides in water

Xin Zhang Zhihao Lu Tianci Ren Junxiang Tang Shuo Li Chenghao Zhu Lijun Mao Da Ma

Citation:  Xin Zhang, Zhihao Lu, Tianci Ren, Junxiang Tang, Shuo Li, Chenghao Zhu, Lijun Mao, Da Ma. Fluorescent "Texas-sized" macrocyclic receptors for the recognition and detection of nucleotides in water[J]. Chinese Chemical Letters, 2025, 36(11): 110946. doi: 10.1016/j.cclet.2025.110946 shu

Fluorescent "Texas-sized" macrocyclic receptors for the recognition and detection of nucleotides in water

English

  • Nucleotides are the fundamental building blocks of DNA and RNA, and involved in various biological processes [13]. Nucleotides participate in energy metabolism, cell signaling, enzyme regulation, and other critical functions [46]. The sensing of adenine triphosphate (ATP) and other nucleotide are of great importance to understand key biological and pathological process [712]. Fluorescent sensors and probes are crucial tools for in situ and real time monitoring of nucleotides [1319]. Artificial anion receptors have been developed for the recognition of nucleotides [2029]. Supramolecular sensors and probes are promising analytical tools for the detection of nucleotides [3033]. Nevertheless, the design and synthesis of anion receptors in aqueous media remain challenging due to factors such as the sensitivity to pH, solvent effects and hydrophobicity [3438].

    The "Texas-sized" macrocyclic receptors, first reported by Sessler and colleagues, represent a class of cationic supramolecular receptors distinguished by their large central cavities, modular syntheses and great anion recognition property [39]. These features make them valuable as artificial receptors for electron-rich molecules [4042]. In our previous work, a non-fluorescent tetra-cationic imidazolyl macrocycle was applied to the recognition of carboxylate anions in organic solvents [4344]]. Here, we report the modular syntheses of water-soluble "Texas-sized" macrocyclic receptor incorporated with fluorescent building blocks. The fluorescent anion receptors are found to be high affinity hosts towards ATP and other suitable nucleotides. It is discovered that these macrocyclic receptors could be used for the fluorescence detection of nucleotides in water.

    Nonfluorescent macrocycle 1 and fluorescent macrocycles 23 are synthesized and investigated (Fig. 1). Macrocycle 1, in the form of hexafluorophosphate salts, was synthesized from pyridine-based precursors and 4, 7-bis(bromomethyl)−2, 1, 3-benzothiadiazole. These hexafluorophosphate salts were converted to their chloride forms with high yield through anion exchange with tetraethylammonium chloride. Macrocycles 2 and 3 were synthesized using a similar protocol, which were incorporated with naphthyl and naphthyridinyl moieties, respectively. These macrocycles exhibited good solubility in water and were fully characterized by 1H NMR, 13C NMR, and X-ray crystallographic analysis (Supporting information).

    Figure 1

    Figure 1.  (a) Chemical structures of the macrocycles 13. (b) Chemical structures of nucleotides and nucleobases.

    Single crystals of macrocycle 1, suitable for X-ray analysis, were obtained through slow vapor diffusion of isopropyl ether into a methanol solution of 1 at room temperature. X-ray diffraction study on the single crystal confirm the cyclic structure and the presence of a well-defined cavity (Figs. S1 and S2 in Supporting information). Macrocycle 1 crystallized in the triclinic space group P-1, exhibiting a complete chair conformation of the macrocyclic core (Table S1 in Supporting information). Measurements of the cavity's length and width reveal an almost 1:1 ratio. Notably, the four imidazolium C–H bonds and the nitrogen atoms of the pyridine direct towards the macrocycle's cavity. The bridging benzothiadiazole subunits in 1 are vertical to the 2, 6-di(1H-imidazol-1-yl)pyridine moieties, oriented in opposite directions away from the cavity, as illustrated in Fig. 2. Based on our results here and combined with our previous research work, these structural features suggest that macrocycle 1 may act as anion receptor. Furthermore, neighbouring one-dimensional arrays of 1 form a two-dimensional nanotubular layer through lattice translation, with a repeat distance of 6.22 Å (Fig. 2a).

    Figure 2

    Figure 2.  (a) Single-crystal X-ray structures of 1. All the solvent molecules have been omitted for clarity. From left to right: side view, side view of the 2D nanotubular layer. The atom-to-atom distances are shown here. (b) From left to right: top view of 2, the π···π interactions found in packing mode of 2. (c) From left to right: top view of 3, the C−H···π interactions found in packing mode of 3.

    Using the same method, we successfully obtained single crystal X-ray structures of macrocycles 2 and 3 (Tables S2 and S3 in Supporting information). The crystal structures reveal that both 2 and 3 exhibited chair conformations similar to that of 1 (Figs. S3-S6 in Supporting information). Notably, the cavities of 2 (10.02 Å × 8.01 Å) and 3 (10.11 Å × 8.09 Å) are significantly larger than that of 1 (7.95 Å × 7.91 Å), as shown in Fig. 2. Additionally, π···π interactions and C−H···π interactions are present in the crystal structures of 2 and 3 (Figs. 2b and c). The presence of positive charges and acidic C–H sites in the structures of hosts 2 and 3 further enhanced their potential as supramolecular hosts for the recognition of anionic biomolecules.

    To investigate the host-guest interaction between "Texas-sized" macrocyclic receptors and nucleotides, we conducted 1H NMR spectroscopic analyses. Mixing a 1.0 mmol/L solution of ATP with one molar equivalent of macrocycle 1 in D₂O resulted in obvious chemical shift changes (Fig. S7 in Supporting information). The protons Ha-Hg of ATP exhibited upfield shifts (Δδ = 0.42–0.91 ppm), and the protons H3 and H5H7 of 1 also showed upfield shifts (Δδ = 0.02–0.74 ppm). Notably, H7 was split into multiple peaks, likely due to the ribose moiety of ATP disrupting the symmetry of the macrocycle. These findings indicated host-guest complexation between ATP and 1 in D₂O. Furthermore, two-dimensional nuclear Overhauser enhancement (2D-NOE) spectroscopic analysis revealed cross-peaks between the Hb of the adenine moiety in ATP and H7 of 1, suggesting that the adenine moiety is positioned closer to the benzothiadiazole unit within the cavity of 1 (Fig. S8 in Supporting information). Consistent with the above expectation, theoretical calculations indicate that the short distances (< 5 Å) between the Hb of ATP and the H7 of 1 are taken as evidence for the adenine moietyis is closer to the cavity of 1 (Fig. S63 in Supporting information). In order to evaluate the binding affinities between macrocycle 1 and ATP, we performed Job plot experiment based on ¹H NMR spectra (Figs. S23 and S24 in Supporting information). The results indicated a binding stoichiometry of 1:1. The association constant (Ka) was calculated to be (2.74 ± 0.2) × 10⁶ L/mol in H₂O using the standard curve fitting methods (Figs. S25 and S26 in Supporting information).

    The interactions between macrocycle 1 and various anionic nucleotides were assessed, confirming 1:1 binding stoichiometries (Figs. S9-S17 and S27-S62 in Supporting information). Notably, mixing a 1 mmol/L solution of nucleobases (A, U, T, C or G) with one molar equivalent of 1 in solution gave rise to no obvious chemical shift change (Figs. S18-S22 in Supporting information). This finding is interpreted in terms of there being little or no complexation between either nucleobases and 1 in DMSO‑d6. Altogether, phosphate anions they may play an important role in the machinery devoted to host recognition. The association constants for these complexes were summarized in Table 1. A comparison of the association constants for three nucleotides (ATP, ADP, AMP) with 1 revealed that these values were significantly influenced by the number of phosphate groups, with tighter binding observed as the number of phosphates increases. For example, the association constant between 1 and ATP is 6.7 and 8.7 times higher than those for ADP and AMP, respectively. Moreover, the association constant between 1 and GTP is 238.2 times greater than that for CTP, indicating that the type of nucleobase also affects binding affinities with 1. The influence of nucleotide bases could be attributed to the difference in their electron density and hydrophobicity. Adenine and guanine possess larger ring systems, which contributes to the hydrophobicity and hydrogen bonding-driven bindings.

    Table 1

    Table 1.  Summary of the association constants Ka (L/mol) between macrocycles 13 and nucleotides as inferred from fluorescence spectra analyses carried out in H2O.
    DownLoad: CSV
    1 2 3
    ATP (2.74 ± 0.2) × 106 (2.05 ± 0.9) × 106 (7.97 ± 0.5) × 105
    CTP (4.05 ± 0.1) × 104 (3.12 ± 0.2) × 104 (6.77 ± 0.1) × 104
    (1.32 ± 0.02) × 104
    GTP (9.65 ± 0.6) × 106 (1.97 ± 0.8) × 106 (2.83 ± 0.2) × 105
    UTP (1.33 ± 0.05) × 104 (4.45 ± 0.2) × 104 (3.19 ± 0.3) × 104
    (1.52 ± 0.02) × 103
    ADP (4.05 ± 0.1) × 105 (2.89 ± 0.1) × 105 (1.03 ± 0.03) × 105
    AMP (4.04 ± 0.09) × 104 (3.13 ± 0.08) × 104 (2.69 ± 0.01) × 104
    dAMP (2.20 ± 0.02) × 104 (1.99 ± 0.05) × 104 (1.31 ± 0.01) × 104
    dTMP (1.09 ± 0.01) × 104 (2.12 ± 0.1) × 104 (1.75 ± 0.05) × 103
    (3.65 ± 0.03) × 103
    dCMP (8.69 ± 0.1) × 103 (3.25 ± 0.2) × 103 (8.14 ± 0.3) × 102
    dGMP (3.64 ± 0.1) × 104 (1.81 ± 0.03) × 105 (2.58 ± 0.06) × 104

    We failed to obtain a single crystal for the supramolecular complex. As an alternative method, density functional theory (DFT) calculation was employed to obtain further insight into the molecular recognition (Figs. S63-S72 in Supporting information). The complexes composed of macrocycle 1 and nucleotides were optimized at the B3LYP-D3/6–31+G(d) level of theory, where the phosphate group located into the "chair-like" cavity of 1 (Fig. 3a), in line with the 1H NMR and 2D NOESY results. In the simulated structures, non-covalent interaction including hydrogen bonds and electrostatic interactions existed between 1 and nucleotides (Fig. 3b). Additionally, molecular surface electrostatic potential (ESP) analysis indicated that electron-deficient host 1 was able to act as an electron receptor to interact with negatively charged and electron-rich nucleotides (Figs. 3c and d).

    Figure 3

    Figure 3.  (a) Energy-minimized structure of 1·ATP at the B3LYP-D3/6–31+G(d) level of theory. (b) Hydrogen bonds in 1·ATP. (c) Molecular surface electrostatic potential of 1·ATP. (d) IGMH analyses of 1·ATP.

    Compared to macrocycle 1, hosts 2 and 3 exhibited significant fluorescence enhancement, positioning them as potential fluorescent probes for anion sensing. The association constants between macrocycles 2 and 3 and ten different nucleotides were investigated using fluorescence spectroscopic titrations (Figs. S75 –S114 in Supporting information). The calculated association constants for macrocycles 23 were listed in Table 1. A similar guest selectivity was observed as that for macrocycle 1. The association constants for macrocycles 2 and 3 with nucleotides (ATP, ADP, and AMP) decreased gradually with a reduction in the number of phosphates. Notably, macrocycle 2 formed a host-guest complex with three guest anions (CTP, UTP, and dTMP) in solution consistent with a 1:2 binding model, which suggests that the formation of a 1:2 host-guest complexations (Figs. S82, S86, and S90 in Supporting information). These two macrocycles also demonstrated higher binding affinity towards ATP and GTP compared to CTP and UTP, which indicated the nucleotide base played a major role in the binding. Based on the above observations, the selective binding may likely be driven by π-π stacking, hydrogen bonding and electrostatic interaction.

    Fluorescent macrocyclic receptors 2 and 3 were used for the sensing of ATP. As shown in Fig. 4a and Fig. S75 (Supporting information), the addition of ATP resulted in the fluorescent quenching of macrocycles, which could be attributed to the photoinduced electron transfer (PET) from 3 to ATP based on the formation of the host-guest complex. There were linear regions at 0–12 µmol/L for macrocycle 2 and 0–10 µmol/L for macrocycle 3 on the fluorescence intensity-ATP concentration correlation curves (Fig. 4b and Fig. S119 in Supporting information). Macrocycles 23 also show fluorescence responses to other nucleotides (Figs. S116 and S118 in Supporting information). Overall, the fluorescence response was correlated with the binding affinity. As shown in Fig. 4c, in the range 1–60 µmol/L, the ATP curve showed a rapid decrease as the concentration increased, whereas the fluorescence intensity for both ADP and AMP displayed a relatively slow decreasing trend, indicating a high selectively for ATP sensing in this concentration range. Notably, in the range of 0–50 µmol/L, the binding of 2 with guest anions (CTP, UTP) increases the fluorescence intensity in the solution, while the binding with ATP and GTP decreases the fluorescence intensity (Fig. 4d). This is a large enough difference to be able to discriminate these analytes of ATP and GTP. A good nucleotide recognition results were also observed when replacing 2 with 3 (Figs. 4e and f). Macrocycles 2–3 showed fluorescence intensity change to ATP, while their fluorescence intensity barely changed other common biological analytes (Figs. S120 and S121 in Supporting information). The detection limits (LOD) of 2 and 3 for the ATP were calculated to be 0.29 µmol/L and 0.04 µmol/L, respectively, indicating that 3 could sensitively recognize ATP (Figs. S122-S127 in Supporting information). Further optimization of macrocycle structures may lead to the discovery of fluorescent sensors for molecular recognition of nucleotides and their detection.

    Figure 4

    Figure 4.  (a) The fluorescence intensity response of host 3 (10 µmol/L) to ATP at varied concentrations. (b) ATP concentration-dependent fluorescence intensity change of 3 at 353 nm. Excitation wavelength: 331 nm. (c) Plots of fluorescence intensity against ATP, ADP, and AMP concentrations in the range of 0–0.1 mmol/L in the presence of host 2. (d) Plots of fluorescence intensity against ATP, CTP, GTP and UTP concentrations in the range 0–0.05 mmol/L in the presence of host 2. (e) Plots of fluorescence intensity against ATP, ADP, and AMP concentrations in the range 0–0.14 mmol/L in the presence of host 3. (f) Plots of fluorescence intensity against ATP, CTP, GTP and UTP concentrations in the range 0–0.2 mmol/L in the presence of host 3.

    In summary, we have successfully synthesized three new tetracationic imidazolium-based macrocycles 13 via a modular SN2 nucleophilic substitution reaction. These macrocycles are characterized by X-ray diffraction in single crystals or NMR spectroscopy in solution. X-ray crystallographic analysis undoubtedly confirm their cyclic structures and chair conformations. Their unique architecture, featuring positive charges and acidic C–H sites, enables effective binding with ten nucleotides in aqueous solutions, as confirmed by 1H NMR, 2D NOESY, fluorescence titrations, and DFT calculations. The association constants for the macrocycles with the same anion are similar, while the number of phosphates and the type of nucleobase influenced these constants. Additionally, macrocycles 2 and 3 exhibit enhanced fluorescence and distinct correlations between fluorescence intensity and concentration for UTP, CTP, and dTMP, positioning them as promising candidates for the selective sensing of nucleotide anions.

    The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

    Xin Zhang: Writing – original draft, Investigation, Data curation, Conceptualization. Zhihao Lu: Investigation. Tianci Ren: Investigation. Junxiang Tang: Investigation. Shuo Li: Investigation. Chenghao Zhu: Investigation. Lijun Mao: Writing – original draft, Investigation, Conceptualization. Da Ma: Writing – review & editing, Writing – original draft, Supervision, Project administration, Funding acquisition, Conceptualization.

    The authors are grateful to Zhejiang Provincial Natural Science Foundation of China (Nos. LR24B020003 and LQ24B020003) and Science and Technology Project of Taizhou City (No. 24gyb17) for financial support.

    Supplementary material associated with this article can be found, in the online version, at doi:10.1016/j.cclet.2025.110946.


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  • Figure 1  (a) Chemical structures of the macrocycles 13. (b) Chemical structures of nucleotides and nucleobases.

    Figure 2  (a) Single-crystal X-ray structures of 1. All the solvent molecules have been omitted for clarity. From left to right: side view, side view of the 2D nanotubular layer. The atom-to-atom distances are shown here. (b) From left to right: top view of 2, the π···π interactions found in packing mode of 2. (c) From left to right: top view of 3, the C−H···π interactions found in packing mode of 3.

    Figure 3  (a) Energy-minimized structure of 1·ATP at the B3LYP-D3/6–31+G(d) level of theory. (b) Hydrogen bonds in 1·ATP. (c) Molecular surface electrostatic potential of 1·ATP. (d) IGMH analyses of 1·ATP.

    Figure 4  (a) The fluorescence intensity response of host 3 (10 µmol/L) to ATP at varied concentrations. (b) ATP concentration-dependent fluorescence intensity change of 3 at 353 nm. Excitation wavelength: 331 nm. (c) Plots of fluorescence intensity against ATP, ADP, and AMP concentrations in the range of 0–0.1 mmol/L in the presence of host 2. (d) Plots of fluorescence intensity against ATP, CTP, GTP and UTP concentrations in the range 0–0.05 mmol/L in the presence of host 2. (e) Plots of fluorescence intensity against ATP, ADP, and AMP concentrations in the range 0–0.14 mmol/L in the presence of host 3. (f) Plots of fluorescence intensity against ATP, CTP, GTP and UTP concentrations in the range 0–0.2 mmol/L in the presence of host 3.

    Table 1.  Summary of the association constants Ka (L/mol) between macrocycles 13 and nucleotides as inferred from fluorescence spectra analyses carried out in H2O.

    1 2 3
    ATP (2.74 ± 0.2) × 106 (2.05 ± 0.9) × 106 (7.97 ± 0.5) × 105
    CTP (4.05 ± 0.1) × 104 (3.12 ± 0.2) × 104 (6.77 ± 0.1) × 104
    (1.32 ± 0.02) × 104
    GTP (9.65 ± 0.6) × 106 (1.97 ± 0.8) × 106 (2.83 ± 0.2) × 105
    UTP (1.33 ± 0.05) × 104 (4.45 ± 0.2) × 104 (3.19 ± 0.3) × 104
    (1.52 ± 0.02) × 103
    ADP (4.05 ± 0.1) × 105 (2.89 ± 0.1) × 105 (1.03 ± 0.03) × 105
    AMP (4.04 ± 0.09) × 104 (3.13 ± 0.08) × 104 (2.69 ± 0.01) × 104
    dAMP (2.20 ± 0.02) × 104 (1.99 ± 0.05) × 104 (1.31 ± 0.01) × 104
    dTMP (1.09 ± 0.01) × 104 (2.12 ± 0.1) × 104 (1.75 ± 0.05) × 103
    (3.65 ± 0.03) × 103
    dCMP (8.69 ± 0.1) × 103 (3.25 ± 0.2) × 103 (8.14 ± 0.3) × 102
    dGMP (3.64 ± 0.1) × 104 (1.81 ± 0.03) × 105 (2.58 ± 0.06) × 104
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  • 发布日期:  2025-11-15
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