Research ArticleChemistry

Triggered reversible substitution of adaptive constitutional dynamic networks dictates programmed catalytic functions

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Science Advances  10 May 2019:
Vol. 5, no. 5, eaav5564
DOI: 10.1126/sciadv.aav5564
  • Fig. 1 Substitution mechanism.

    Schematic cyclic and reversible triggered intersubstitution of three CDNs. Each of the CDNs includes four different constituents and a dormant structure that does not participate in the respective equilibrated CDN. In the presence of trigger T1, T2, or T3, the respective dormant structure is activated, and one of the CDN constituents is locked, resulting in the intersubstitution of one network by another CDN. By applying the appropriate counter trigger T1′, T2′, or T3′, the parent CDN is regenerated.

  • Fig. 2 Cyclic and reversible triggered intersubstitution of three DNA-based CDNs.

    Schematic design and mode of the operation of the cyclic and reversible triggered intersubstitution of nucleic acid–based CDNs using the strand displacement mechanism. Inset: Schematic readout of the performance of the CDNs by the application of nine different Mg2+ ion–dependent DNAzymes as reporter units.

  • Fig. 3 Triggered substitution of CDN “X” by CDN “Y” and back.

    (A) Time-dependent fluorescence changes corresponding to the constituents and accompanying dormant structures associated with the triggered transition of CDN “X” to CDN “Y” and back: (i) before the application of any triggers; (ii) after subjecting CDN “X” to trigger T1 and the transition to CDN “Y”; (iii) after application of the counter trigger T1′ on the resulting CDN “Y” and the recovery of CDN “X.” The time-dependent fluorescence changes stimulated by the DNAzyme reporter units associated with the constituents were translated into concentrations (Table 1 and fig. S2) using the respective calibration curves (fig. S1). (B) Electrophoretic separation of the constituents and accompanying dormant structures associated with CDN “X” and CDN “Y” for the quantitative evaluation of the compositions of the respective CDNs.

  • Fig. 4 Emerging catalytic functions guided by the interconverting CDNs.

    Programmed cyclic and reversible catalytic functions triggered by the intersubstituted CDNs. The three interexchangeable CDNs are subjected to a set of hairpin substrates H1 to H6. Each of the triggered, intersubstituted CDNs selects selectively the respective hairpin substrates from the hairpin pool, resulting in the guided formation of the respective catalytic DNAzymes. CDN “X” cleaves hairpins H1 and H2 to yield DNAzyme 1 (Mg2+ ion–dependent DNAzyme). CDN “Y” cleaves hairpins H3 and H4 to yield DNAzyme 2 (hemin/G-quadruplex DNAzyme). CDN “Z” cleaves hairpins H5 and H6, and the cleaved products self-assemble, in the presence of the added strand P, into DNAzyme 3 (Pb2+ ion–dependent DNAzyme).

  • Fig. 5 Catalytic activities of the emerging DNAzymes.

    (A to C) Time-dependent fluorescence changes corresponding to the emerging catalytic functions: (A) DNAzyme 1, (B) DNAzyme 2, and (C) DNAzyme 3, upon the cyclic and reversible triggered intersubstitution between CDNs “X,” “Y,” and “Z.” Panels I, IV, and VII show the transition of CDN “X” to CDN “Y” and back: (i) CDN “X” before the addition of trigger T1; (ii) after subjecting CDN “X” to T1 and the transition to CDN “Y”; (iii) after applying the counter trigger T1′ to the resulting CDN “Y” and the reequilibration of CDN “X.” Panels II, V, and VIII show the substitution of CDN “X” by CDN “Z” and back: (i) CDN “X” before the addition of trigger T2; (ii) after the treatment of CDN “X” with T2 and the equilibration of CDN “Z”; (iii) after subjecting the resulting CDN “Z” to the counter trigger T2′ and the reequilibration of CDN “X.” Panels III, VI, and IX show the transition of CDNs “Z” to “Y” and back: (i) CDN “Z” before the application of trigger T3; (ii) after the T3-induced transition of CDN “Z” to CDN “Y”; (iii) after applying the counter trigger T3′ to the resulting CDN “Y” and the regeneration of CDN “Z.”

  • Table 1 Concentrations of the equilibrated constituents in the different CDN systems.

    (i) CDN “X” before the addition of T1. (ii) CDN “Y” generated by the addition of T1 to CDN “X.” (iii) CDN “X” before the addition of T2. (iv) After subjecting CDN “X” to T2 and the transition to CDN “Y.” (v) CDN “Z” before the interaction with T3. (vi) After the addition of T3 and the T3-triggered substitution of CDN “Z” by CDN “Y.”

    SystemConcentration (μM)
    [AA′][AB′][AC′][BA′][BB′][BC′][CA′][CB′][CC′]
    Substitution of CDN “X” by CDN “Y”
    (i)*
    (i)
    0.64
    (0.62)
    0.41
    (0.37)
    0.05
    (—)
    0.41
    (0.36)
    0.57
    (0.61)
    0.06
    (—)
    0.01
    (—)
    0.04
    (—)
    0.98
    (0.99)
    (ii)*
    (ii)
    0.34
    (0.31)
    0.06
    (—)
    0.65
    (0.64)
    0.03
    (—)
    0.99
    (—)§
    0.01
    (—)
    0.6
    (0.61)
    0.05
    (—)
    0.37
    (—)§
    Substitution of CDN “X” by CDN “Z”
    (iii)*
    (iii)
    0.61
    (0.63)
    0.38
    (0.41)
    0.05
    (—)
    0.38
    (0.45)
    0.58
    (0.59)
    0.02
    (—)
    0.01
    (—)
    0.06
    (—)
    1.00
    (0.95)
    (iv)*
    (iv)
    0.98
    (0.97)
    0.06
    (—)
    0.01
    (—)
    0.04
    (—)
    0.46
    (0.45)
    0.51
    (0.47)
    0.05
    (—)
    0.53
    (0.52)
    0.47
    (0.52)
    Substitution of CDN “Z” by CDN “Y”
    (v)*
    (v)
    0.99
    (1.04)
    0.01
    (—)
    0.05
    (—)
    0.04
    (—)
    0.49
    (0.47)
    0.53
    (0.56)
    0.02
    (—)
    0.56
    (0.54)
    0.46
    (0.51)
    (vi)*
    (vi)
    0.32
    (0.29)
    0.06
    (—)
    0.68
    (0.68)
    0.03
    (—)
    0.98
    (—)§
    0.05
    (—)
    0.64
    (0.66)
    0.03
    (—)
    0.32
    (—)§

    *Data provided by the catalytic activities of the respective DNAzyme reporter units and appropriate calibration curves.

    †Data provided by the electrophoretic separation of the constituent mixtures and the quantitative analysis of the separated stained bands (for details, see the Supplementary Materials).

    ‡No detectable bands.

    §Bands cannot be evaluated due to the overlap.

    Supplementary Materials

    • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/5/5/eaav5564/DC1

      Section S1. Guiding rules for the assembly of the CDNs for the triggered interconversion of the CDNs

      Fig. S1. Calibration curves.

      Fig. S2. Concentration changes following the transition of CDN “X” to CDN “Y” and back.

      Fig. S3. Results of the triggered substitution of CDN “X” by CDN “Z” and back.

      Fig. S4. Results of the triggered substitution of CDN “Z” by CDN “Y” and back.

      Fig. S5. Internal equilibration of CDN “X”.

      Fig. S6. Internal equilibration of CDN “Y”.

      Fig. S7. Internal equilibration of CDN “Z”.

      Fig. S8. Detailed design of the emerging catalytic functions.

      Fig. S9. Catalytic rates of the emerging DNAzymes guided by the intersubstituted CDNs.

      Table S1. NUPACK-predicted and experimental concentrations of the constituents and dormant structures associated with CDN “X” and CDN “Y”.

    • Supplementary Materials

      This PDF file includes:

      • Section S1. Guiding rules for the assembly of the CDNs for the triggered interconversion of the CDNs
      • Fig. S1. Calibration curves.
      • Fig. S2. Concentration changes following the transition of CDN “X” to CDN “Y” and back.
      • Fig. S3. Results of the triggered substitution of CDN “X” by CDN “Z” and back.
      • Fig. S4. Results of the triggered substitution of CDN “Z” by CDN “Y” and back.
      • Fig. S5. Internal equilibration of CDN “X”.
      • Fig. S6. Internal equilibration of CDN “Y”.
      • Fig. S7. Internal equilibration of CDN “Z”.
      • Fig. S8. Detailed design of the emerging catalytic functions.
      • Fig. S9. Catalytic rates of the emerging DNAzymes guided by the intersubstituted CDNs.
      • Table S1. NUPACK-predicted and experimental concentrations of the constituents and dormant structures associated with CDN “X” and CDN “Y”.

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