Supporting Information for

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1 Supporting Information for Oscillatory Reaction Induced Periodic C-Quadruplex DNA Gating of Artificial Ion Channels Jian Wang, Ruochen Fang, Jue Hou, Huacheng Zhang, *, Ye Tian, *, Huanting Wang, and Lei Jiang, Key Laboratory of Bio-inspired Materials and Interface Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing , People s Republic of China Department of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia Beijing National Laboratory for Molecular Sciences, Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing , People s Republic of China Key Laboratory of Organic Optoelectronics and Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing , People s Republic of China * (H. Zhang): zhanghc@mail.ipc.ac.cn * (Y. Tian): tianyely@iccas.ac.cn S1

2 Figure S1. Geometry of single bullet-shaped nanochannel fabricated by etching the ion-tracked polyethylene terephthalate (PET) membrane for about 3 min. a, Scanning electron microscopy (SEM) image of the cross section of a bullet-shaped nanochannel, scale bar 1 μm. b, Distribution of the tip diameter (d t ) of the nanochannel is nm. The mean d t = 33.2 ± 3.7 nm. The inset is SEM image of the small tip side, scale bar 100 nm. c, Distribution of the base diameter is nm with mean d b = ± 19.5 nm. The inset is SEM image of the large base side, and the scale bar is 100 nm. Figure S2. Influence of the etching time on the size of the bullet-shaped nanochannel. a, Tip and base diameters increase with increasing the etching time. When the etching time increases from 150 to 270 s, the average tip diameters of the nanochannels increase from 25.9 ± 3.7 to 98.5 ± 9.6 nm, while the base diameters increase from ± 15.1 to ± 31.0 nm. b, Size ratios of the base and tip diameters of the nanochannels (ratio = d b /d t ) fabricated under different etching times, which demonstrates the base sides of the nanochannels was about 6 times larger than the tip sides. S2

3 Figure S3. Graft C4-DNA molecules onto the inner surface of the single nanochannel by a two-step modification method. Step 1: Carboxyl groups on the nanochannel surface were activated in 4 ml phosphate-buffered saline (PBS, ph 7.4) solution containing 60 mg 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (EDC) and 12 mg N-Hydroxysulfosuccinimide sodium salt (NHSS) for 1 h. Step 2: the film was reacted for 2 h with a solution of 1 µm DNA in PBS buffer (ph 7.4). S3

4 Figure S4. XPS and contact angle results of the PET membrane before and after modification by C4-DNA molecules. a, XPS spectra of the PET film before and after C4 DNA modification. It is clear that there is an obvious peak near 400 ev after modification, which shows a typical N 1s XPS peak, thus it simply indicates DNA molecules are successfully immobilized on the surface of the PET film. b, Contact angles of the PET membrane are of 85.2 ± 0.7, 72.0 ± 1.1, and 62.2 ± 1.9, respectively. The insets are the corresponding photographs of water droplet shape on the PET film. All these changes of wettability in PET film corresponded to the change of chemical composition. XPS measurement. X-ray photoelectron spectroscopy (XPS) was performed on the Thermo Scientific ESCALab 250Xi using 200 W monochromated Al Kα radiation. The 500 µm X-ray spot was used for XPS analysis. The base pressure in the analysis chamber was about mbar. Typically the hydrocarbon C1s line at ev from adventitious carbon is used for energy referencing. The analysis software was used as provided by the instrument s manufacturer. Because no other new element was introduced after every step of modification, the peak of nitrogen (N 1s) was used to reflect the modification process. Contact angles. Contact angles were measured by an OCA 20 instrument (DataPhysics, Germany) at room temperature and saturated humidity. MilliQ water (18.2 MΩ) was employed as the source for the CA measurement. In each measurement, a 2-μL droplet of water was dispensed onto the substrates under investigation. The CA values were obtained from the averages of five drops at different locations. The PET film for contact angle measurements was treated under the same conditions as the single nanochannel. Table S1. The XPS data of the PET membrane before modification Name Start BE Peak BE End BE Height CPS FWHM ev Area (P) CPS.eV At. % C1s, ev O1s, ev Table S2. The XPS data of the PET membrane after C4 DNA modification Name Start BE Peak BE End BE Height CPS FWHM ev Area (P) CPS.eV At. % C1s, ev O1s, ev N1s, ev S4

5 Figure S5. Ion transport properties of the single nanochannel before and after modification by C4 DNA measured in 0.1 M KCl solution of ph 9. a, I-V properties of the nanochannel before and after modification. Inset schemes are used to indicate the surface property changes of the nanochannel before and after modification. b, Ion current rectification ratio of the nanochannel before and after modification (ICR ratio = I +0.4V / I -0.4V ). Before modification, the PET nanochannel is negatively charged due to deprotonation of the carboxyl groups on the channel inner surface under high ph condition, and pka of the carboxyl group is about As a result, the negatively charged nanochannel shows asymmetric I-V curve with ICR ratio of ~2.7. After modification, however, the carboxyl groups are coated by C4-DNA molecules, and the surface charge density of the nanochannel dramatically decreases because the DNA molecule can only be slightly charged under basic condition. Therefore, the ICR effect of the nanochannel reduced after modification. S5

6 Figure S6. ph-gating property of the C4-DNA-modified nanochannel measured in 0.1 M KCl solutions at various ph values. a, I-V properties of the nanochannel under different ph conditions. b, Representation of the transmembrane ionic current at 0.4 V as a function of ph value. The insets illustrate the gate-like ph-responsive change in the effective pore size of the nanochannel. c, Uncontinuous ion current change of the nanochannel by manual changing of ph 4 and M KCl solutions. The time for manual changing electrolyte solution is about 1 min. S6

7 Figure S7. Molecular structure of the C4 DNA. The oligonucleotide sequence (5' to 3') of C4 DNA is 5'-(NH 2 )-(CH 2 ) 6 -AAAAAAAAAA CCC TAA CCC TAA CCC TAA CCC (Bodipy493/503)-3'. The DNA strand contains both negatively charged phosphates and protonatable bases. S7

8 Figure S8. Experimental setup for the oscillatory nanochannel system. a, The plexiglass cells ( mm, with a cylindrical storage tank of 40 mm in diameter and 45 mm in depth). b, The ph and ion current oscillations measurement apparatus. Figure S9. ph oscillations of the oscillating reaction solution. Figure S10. Autonomously open and close the nanochannel by the chemical oscillator. a, Scheme of the autonomous gating process of the oscillatory nanochannel system measured in the oscillating reaction solution. b, Original experimental current-time curve (black line) of the oscillatory nanochannel system measured by the picoammeter. Red line is smoothed current-time curve, which is used in Figure 3c. S8

9 Figure S11. Ionic current oscillations of the C4 DNA-modified nanochannel recorded at 2 V. a, ph oscillation of the reaction solution at 35. b, Ion current oscillation of the C4-DNA-modified nanochannel at 2V. The system possess a wide range of ph values (ca. 3.5 to ca. 6.8), and the period time and full amplitude of the ion current-oscillation are approximately 1600 s and 1.5 na, respectively. S9

10 Figure S12. Influence of the ion concentration, temperature, ph, and peristaltic pump on the ionic current variation of the oscillatory system. a, ph and ionic current oscillations of a reproduced oscillatory nanochannel system. b, ph, temperature, redox potential, and ion conductivity changes of the oscillating reaction solution. c, Comparison of the experimental ionic current oscillation (black line) and theoretical ionic current oscillation (violet line) induced by the ion-conductivity and temperature variations of the reaction solution. d, Influence of the peristaltic pumps on the ionic current noise of the nanochannel system. As the nanochannel is bullet-shaped, its average radius profile could be theoretically described by equation S1. 2, 3 r x r r r x ( ) b b t exp( ) (S1) h where r t = r(x = 0) = 13 nm, r b = r(x = L) = 81 nm, L is length of the nanochannel corresponding to membrane thickness (about 12 μm), and h is a geometrical parameter characterizing the curvature of the nanochannel profile, 4 named as curvature radius, which is defined as 600 nm in accordance with previous works. 3, 4 Theoretical average resistance (R) of the uncharged bullet-shaped nanochannel can be calculated by equation S2. R th 1 k 0 L dx x rb rb rt exp( ) h 2 where k is the specific ion conductivity of the reaction solution, k of the continuously-fed reaction solution was varied as show in Figure S12b (voilet line). Theoretical ionic current (I th ) of the nanochannel is calculated by I th = U/R th. Therefore, the theoretical ion current of the the nanochannel induced by ion-conductivity variation in the continuously-fed reaction solution could be calculated by equation S3. The calculated resultwas shown in Figure S12c (violet line). k I U / R ku / th th dx =0.46 k( na) 2 x exp( ) 1000 S10 (S2) (S3)

11 Figure S13. Temperature-dependent conformation transition of the C4-DNA molecule characterized by circular dichroism (CD) under different temperatures. Conformational change between i-motif and single-stranded structures at various ph values: a) 3.5, b) 4.5, c) 5.5, d) 6.0, and e) 6.5, respectively. CD results recorded at room temperature demonstrated C4 DNA molecules underwent a ph-response conformational change between i-motif and single-stranded structures. CD experiments of C4 DNA in response to different temperatures at various ph values were performed in phosphate-buffered saline (PBS). CD spectra were measured by a JASCO J-815 CD spectrometer, and wavelength scans were performed between 220 and 320 nm. C4 DNA (3.2 n mols) was dissolved in an alkaline PBS buffer solution (ph 7.4, 1.6 ml) containing NaCl (0.138 M) and KCl ( M), to give a final concentration of 2 µm DNA-PBS buffer solution in a quartz cell. The ph value of the buffer was cycled from 3.5 to 6.5 by alternatively adding 1 M HCl and/or 1 M KOH to obtain the proper solution, and vice versa. As shown in Figure S13a and b, there is no distinct conformation change appears at ph 3.5 or 4.5, which means the conformation of C4 DNA is not responsive to low ph values. An obvious change in the CD spectrum could be observed when the ph value of the environmental solution changed to 5.5 at 45, which indicates the deformation of the i-motif structure at higher ph (5.5) value (Figure S13c). As the ph value increased to 6.0, however, the i-motif conformation began to change at ~35 (Figure S13d). When ph increased to 6.5, the deformation from the four-stranded i-motif to the single-stranded structures could be observed at ~20, indicating a typical completely transformation at high ph (6.5) value (Figure S13e). S11

12 Figure S14. Original experimental current-time curves of the oscillatory nanochannel systems measured by the picoammeter at different temperatures. Red lines were smoothed values used in Figure 4b. Figure S15. Temperature-dependent gating periods and amplitudes of the oscillatory nanochannel system. a, oscillation periods of the ph and ionic current. b, oscillation amplitudes of the ph and ionic current. S12

13 Figure S16. Diameter distributions and SEM images of the bullet-shaped nanochannels fabricated under different etching conditions, and the scale bar is 500 nm. a,b, Tip and base diameters of the nanochannels etched for 150 s. The average d t is 25.9 ± 3.7 nm, while the mean d b is ± 15.1 nm. c,d, Tip and base diameters of the nanochannels etched for 210 s. The average d t is 46.2 ± 6.6 nm, while the mean d b is ± 26.6 nm. e,f, Tip and base diameters of the nanochannels etched for 270 s. The average d t is 98.5 ± 9.6 nm, while the mean d b is ± 31.0 nm. S13

14 Figure S17. Corresponding ph oscillations of the reaction solution for Figure 6. a, ph oscillation for Figure 6a. b, ph oscillation for Figure 6b. c, ph oscillation for Figure 6c. d, ph oscillation for Figure 6d. Figure S18. Original current-time curves for Figure 6. a, Original current-time curve for Figure 6a. b, Original current-time curve for Figure 6b. c, Original current-time curve for Figure 6c. d, Original current-time curve for Figure 6d. S14

15 Figure S19. Influence of the channel size on the gating effect of the oscillatory nanochannel systems. ON-OFF ratio is calculated from ratio = I open /I close. The ON-OFF ratio decreases with increasing the channel size. References (1) Siwy, Z.; Fulinski, A., Fabrication of a Synthetic Nanopore Ion Pump. Phys. Rev. Lett. 2002, 89, (2) Patricio, R.; Pavel Yu, A.; Javier, C.; Salvador, M., Pore Structure and Function of Synthetic Nanopores with Fixed Charges: Tip Shape and Rectification Properties. Nanotechnology 2008, 19, (3) Zhang, H.; Hou, X.; Zeng, L.; Yang, F.; Li, L.; Yan, D.; Tian, Y.; Jiang, L., Bioinspired Artificial Single Ion Pump. J. Am. Chem. Soc. 2013, 135, (4) Pavel Yu, A.; Irina, V. B.; Oleg, L. O.; Patricio, R.; Bozena, A. S., Effect of Nanopore Geometry on Ion Current Rectification. Nanotechnology 2011, 22, S15