Abstract
Rare earth elements (REEs), including scandium, yttrium and lanthanides, are strategic resources with unique electric, luminescent and magnetic properties. However, owing to their highly similar physiochemical properties, the identification and separation of all REEs are challenging. Here a Mycobacterium smegmatis porin A nanopore is engineered to contain a nitrilotriacetic acid ligand at its pore constriction. By the further introduction of a secondary ligand Nα,Nα-bis(carboxymethyl)-L-lysine hydrate (ANTA), a dual-ligand sensing strategy was established. A unique property of this strategy is that a variety of REE(III) ions report characteristic blockage features containing three-level transitions, which are critical in discriminating different REE(III)s. The nanopore events of REE(III)s also demonstrate a clear periodicity, suggesting the observation of the lanthanide contraction effect at a single-molecule regime. Assisted by machine learning, all 16 naturally occurring REE(III)s have been identified by the nanopore with high accuracy. This sensing strategy is further applied in analysing bastnaesite samples, suggesting its potential use in geological exploration.
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Data availability
The source data underlying the main text figures (Figs. 1–5) and extended data figures are provided as source data files. All raw data used to train the machine learning model are shared on figshare. Follow the link https://doi.org/10.6084/m9.figshare.25679331.v1 for download. Source data are provided with this paper.
Code availability
The custom machine learning code and all raw data used to train, evaluate and test the machine learning model, which is referred to as REE classifier, are shared on figshare. Follow the link https://doi.org/10.6084/m9.figshare.25679331.v1 for download.
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Acknowledgements
S.H. acknowledges the National Key R&D Program of China (grant numbers 2022YFA1304602 and 2023YFF1205900), the National Natural Science Foundation of China (grant numbers 22225405 and 223B2402), the Fundamental Research Funds for the Central Universities (grant number 020514380336) and the Excellent Research Program of Nanjing University (grant number ZYJH004).
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S.H., W.S., Y.X. and K.W. conceived the project. S.Z. prepared the MspA nanopores. W.S., Y.X., T.L., B.C. and L.Y. performed the measurements. W.S. and K.W. prepared the supplementary videos. P.Z. set up the instruments. S.H. and W.S. wrote the paper. S.H. supervised the project.
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W.S. and S.H. have filed patents describing the dual-ligand strategy for rare earth analysis (patent number CN2024118640843). The other authors declare no other competing interests.
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Extended data
Extended Data Fig. 1 The definition of event parameters.
A representative trace containing La3+ sensing events is demonstrated. The trace was acquired with MspA-NTA using the mono-ligand strategy as described in Methods. A + 100 mV bias was continually applied. \({I}_{{NTA}}\) is the open pore current and \({I}_{{REE}}\) is the residual current caused by REE(III) blockade. \({ \% I}_{{REE}}\) is derived from (\({I}_{{REE}}\)-\({I}_{{NTA}}\))/\({I}_{{NTA}}\). \({Std}\) represents the standard deviations of the blockage level. Typically, the \(\% {I}_{{REE}}\) measures between 0.1 and 0.6, which is noticeably smaller than that produced during translocation of nucleic acids22 or trapping of proteins58, with relative blockage levels between 0.3 and 0.9.
Extended Data Fig. 2 Single molecule sensing of La3+, Ce3+, Pr3+, Nd3+, Sm3+, Eu3+, Gd3+ and Tb3+.
The measurements were carried out using MspA-NTA using the mono-ligand strategy. A + 100 mV bias was continually applied. In separate measurements, LaCl3·6H₂O, CeCl3·6H₂O, PrCl3·6H₂O, NdCl3·6H₂O, SmCl3·6H₂O, EuCl3·6H₂O, GdCl3·6H₂O, TbCl3·6H₂O were respectively added to trans with a final concentration of 4 μM. (a, c, e, g, i, k, m, o) Representative traces acquired with La3+ (a), Ce3+ (c), Pr3+ (e), Nd3+ (g), Sm3+ (i), Eu3+ (k), Gd3+ (m) or Tb3+ (o) as the sole analyte. The reported events were respectively marked with sky-blue (La3+), red (Ce3+), blue (Pr3+), green (Nd3+), light purple (Sm3+), yellow (Eu3+), cyan (Gd3+) or brown (Tb3+) bars beneath the corresponding trace. (b, d, f, h, j, l, n, p) The corresponding scatter plots of \({ \% I}_{{REE}}\) versus \({Std}\) respectively derived from results of La3+ (b), Ce3+ (d), Pr3+ (f), Nd3+ (h), Sm3+ (j), Eu3+ (l), Gd3+ (n) or Tb3+ (p) sensing. Each scatter plot contains 50 events.
Extended Data Fig. 3 Single molecule sensing of Sc3+, Dy3+, Ho3+, Y3+, Er3+, Tm3+, Yb3+ and Lu3+.
The measurements were carried out using MspA-NTA using mono-ligand strategy. A + 100 mV bias was continually applied. In separate measurements, ScCl3·6H₂O, DyCl3·6H₂O, HoCl3·6H₂O, YCl3·6H₂O, ErCl3·6H₂O, TmCl3·6H₂O, YbCl3·6H₂O, LuCl3·6H₂O were respectively added to trans with a final concentration of 4 μM. (a, c, e, g, i, k, m, o) Representative traces acquired with Sc3+ (a), Dy3+ (c), Ho3+ (e), Y3+ (g), Er3+ (i), Tm3+ (k), Yb3+ (m) or Lu3+ (o). In (a), the trace segment acquired with Sc3+ was enlarged to show details. The reported events were respectively marked with burgundy (Sc3+), dark blue (Dy3+), orange (Ho3+), purple (Y3+), light blue (Er3+), light green (Tm3+), light pink (Yb3+) or light orange (Lu3+) bars beneath the corresponding trace. (b, d, f, h, j, l, n, p) The corresponding scatter plots of \(\% {I}_{{REE}}\) versus \({Std}\) respectively generated by results of Sc3+ (a), Dy3+ (c), Ho3+ (e), Y3+ (g), Er3+ (i), Tm3+ (k), Yb3+ (m) or Lu3+ (o) sensing. Each scatter plot contains 50 events.
Extended Data Fig. 4 Nanopore measurement with sequential addition of different REE(III)s.
The measurements were carried out using mono-ligand strategy in a buffer of 1.5 M KCl, 100 mM MOPS, pH 7.0. MspA-NTA was used as the sensor. During a continuous nanopore measurement using the same pore, LaCl3·6H₂O, CeCl3·6H₂O, PrCl3·6H₂O and NdCl3·6H₂O were sequentially added to trans with a final concentration of 4 μM for each component. A + 100 mV bias was continually applied. (a) A representative trace acquired in the presence of La3+. Only La3+ events were observed. (b) The event scatter plot of \(\% {I}_{{REE}}\) versus \({Std}\) generated by results acquired as described in a. 147 events were used to generate the scatter plot. (c) A representative trace acquired after further addition of Ce3+. Ce3+ events, appearing as deeper blockade events, were then observed. (d) The event scatter plot of \({ \% I}_{{REE}}\) versus \({Std}\) generated by results acquired as described in c. 158 events were used to generate the plot. (e) A representative trace acquired after further addition of Pr3+. Pr3+ events appear as further deeper blockage events. (f) The event scatter plot of \({ \% I}_{{REE}}\) versus \({Std}\) generated by results as described in e. 185 events were used to generate the plot. (g) A representative trace acquired after further addition of Nd3+. Nd3+ events report the largest blockage amplitude. (h) The event scatter plot of \({ \% I}_{{REE}}\) versus \({Std}\) generated by results acquired as described in g. 169 events were used to generate the plot.
Extended Data Fig. 5 Representative dual-ligand events of different REE(III)s.
The measurements were carried out in a buffer of 1.5 M KCl, 100 mM MOPS, pH 7.0. A + 100 mV bias was continually applied.
Extended Data Fig. 6 Single and triple level events.
A sole REE(III) is first chelated by the stationary ligand installed to the pore constriction, causing the conversion from state (i) to state (ii). Afterwards, reversible switching between state (ii) and state (iii) is happening due to further binding of the mobile ligand (ANTA) to the bound REE(III) and its dissociation from it. This dynamic switching behavior generates clearly observable nanopore events, which are also defined as dual-ligand events. For different REE(III), distinct event features were reported. Generally, two types of events were observed. For La3+, Ce3+, Pr3+, or Nd3+, the events contain only a single blockage level. Whereas, for Sc3+, Y3+, Sm3+, Eu3+, Gd3+, Tb3+, Dy3+, Ho3+, Er3+, Tm3+, Yb3+ or Lu3+, the events contain three blockage levels.
Extended Data Fig. 7 Definition of τL1.
(a) The flow diagram demonstrating the derivation of the τL1. Only nanopore events with three-level transitions are selected for further analysis described here. Otherwise, the corresponding τL1 is assigned as 0. Among all three blockage levels, the lowest level is defined as level 1, as marked on the trace. The dwell time of each level 1 segment (tL1) within a single event is collected for histogram plotting. The histogram plot of tL1 is fit to a single exponential curve according to the equation y = a*exp(−x/τ\()\), from which the mean dwell time of level 1 (τL1) is derived. (b) The statistics of τL1. Each dual-ligand event with three-level transitions reports a single τL1 value.
Extended Data Fig. 8 The demonstration of lg(τoff) acquired from dual-ligand events of REE(III).
During nanopore measurement using MspA-NTA, REE(III) was added to the trans side with a final concentration of 40 μM. Simultaneously, ANTA was added to cis with a final concentration of 40 μM. A + 100 mV bias was continually applied. (a) The plot of \({\mathrm{lg}(\tau }_{{off}})\) derived from dual-ligand events of REE(III) compared with their ionic radius. Clearly, the \({\mathrm{lg}(\tau }_{{off}})\) decreases with the increase of the ionic radius of REE(III). (b) The classification of REE(III) based on \({\mathrm{lg}(\tau }_{{off}})\). According to the plot, the REE can be classified to three groups as marked with different color shadings. This classification result is consistent with the definition of light REE (LREE), middle REE (MREE) and heavy REE (HREE)13. Here, LREE consists of La, Ce, Pr and Nd. MREE includes Sm, Eu, Gd, Tb and Dy. HREE includes Y, Ho, Er, Tm, Yb and Lu. Three independent measurements (N = 3) were performed for each analyte type to form the statistics. Data are presented as mean values ± SD. The error bars represent standard deviation values. All detailed results discussed above are also listed in Supplementary Table 8.
Extended Data Fig. 9 Nanopore analysis of a standard sample containing Ce3+, Nd3+, Sm3+ and Y3+.
(a) A continuous trace acquired with the standard sample containing Ce3+, Nd3+, Sm3+ and Y3+. 2.7 mg CeCl3·6H2O, NdCl3·6H2O, SmCl3·6H2O and 2.3 mg YCl3·6H2O were dissolved in 30 mL ultrapure water to reach the same concentration of 0.25 mM. Then, 2 μL above described sample was added to the trans chamber. ANTA was added to the cis chamber with a final concentration of 40 µM. A + 100 mV bias was applied. All nanopore events were predicted by the previously trained Ensemble model and labeled accordingly. (b) The 3D events scatter plots of \({ \% I}_{b}\), \({std}\) and \({\tau }_{L1}\) generated by results acquired with (a). 278 events were included. The events demonstrated were acquired from a 60 min continuous recording. The z-axis is linear from 0 to 0.02 ms and logarithmic from 0.3 to 100 ms. (c) Comparison of the reported concentration of Ce, Nd, Sm and Y, respectively derived from results of ICP-MS and the dual ligand strategy. The true value is also listed as a reference. The measured values of this work were determined and calibrated according to that described in Methods. During the quantitative analysis using ICP-MS and this work, three independent measurements (N = 3) were respectively performed to form the statistics. Data are presented as mean values ± SD. The error bars represent standard deviation values.
Supplementary information
Supplementary Information
Materials, Supplementary Tables 1–10 and Figs. 1–45.
Supplementary Video 1
A cartoon demonstration of the dual-ligand strategy. This demonstration serves to illustrate the sensing mechanism of the dual-ligand strategy. It however only represents an artistic overview of the technology.
Supplementary Video 2
The demonstration of the three-level event features. All measurements were performed using MspA-NTA using the dual-ligand strategy in a buffer of 1.5 M KCl, 100 mM MOPS, pH 7.0. A +100 mV bias was continually applied. Er3+, Tm3+, Yb3+ and Lu3+ were simultaneously added to trans with a final concentration of 40 μM for each component. Simultaneously, ANTA was also added to cis with a final concentration of 40 μM. The values of τL1 were derived from each dual-ligand event. According to this demonstration, it is clear that the τL1 value is critical in the discrimination of different REE(III)s.
Supplementary Video 3
Simultaneous sensing of seven types of REE(III). All measurements were performed using MspA-NTA using the dual-ligand strategy in a buffer of 1.5 M KCl, 100 mM MOPS, pH 7.0. A +100 mV bias was continually applied. REE(III)s, including La3+, Ce3+, Pr3+, Nd3+, Sm3+, Dy3+ and Er3+, were simultaneously added to trans with a final concentration of 40 μM for each component. Simultaneously, ANTA was added to cis with a final concentration of 40 μM. Characteristic dual-ligand events of different REE(III)s were clearly observed. With a trained machine learning algorithm, each dual-ligand event was automatically identified and labelled with La3+, Ce3+, Pr3+, Nd3+, Sm3+, Dy3+ and Er3+, respectively.
Supplementary Video 4
Identification of REE(III) from bastnaesite. All measurements were performed using MspA-NTA using the dual-ligand strategy in a buffer of 1.5 M KCl, 100 mM MOPS, pH 7.0. A +100 mV bias was continually applied. Crushed bastnaesite (2 μl) was added to the trans chamber. Simultaneously, ANTA was added to the cis chamber with a final concentration of 40 μM. Characteristic dual-ligand events of different REE(III)s were clearly observed. With a trained machine learning algorithm, each dual-ligand event was automatically identified and labelled, respectively.
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Sun, W., Xiao, Y., Wang, K. et al. Nanopore discrimination of rare earth elements. Nat. Nanotechnol. 20, 523–531 (2025). https://doi.org/10.1038/s41565-025-01864-w
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DOI: https://doi.org/10.1038/s41565-025-01864-w
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