Aptamer-Based K+ Sensor: Process of Aptamer Transforming into G

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Aptamer-Based K Sensor: Process of Aptamer Transforming into G-Quadruplex Dongju Zhang, Juan Han, Yunchao Li, Louzhen Fan, and Xiaohong Li J. Phys. Chem. B, Just Accepted Manuscript • DOI: 10.1021/acs.jpcb.6b05002 • Publication Date (Web): 20 Jun 2016 Downloaded from http://pubs.acs.org on June 23, 2016

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The Journal of Physical Chemistry

Aptamer-based K+ Sensor: Process of Aptamer Transforming into G-quadruplex Dongju Zhang, Juan Han, Yunchao Li, Louzhen Fan, Xiaohong Li* Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China Email：[email protected] Telephone：+86-10-58802741

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Abstract G-rich aptamers have been widely applied to develop various sensors for detecting proteins, small molecules and cations, which is based on the target-induced conformational transfer from single strand to G-quadruplex. However, the transforming process is unclear. Here, with PW17 as an aptamer example, the forming process of G-quadruplex induced by K+ is investigated by circular dichroism spectroscopy, electrospray ionization mass spectroscopy, and native gel electrophoresis. The results demonstrate that PW17 undergoes a conformational transforming process from loose and unstable to compact and stable G-quadruplex, which is strictly K+ concentration-dependent. The process contains three stages: (1) K+ (< 0.5 mM) could induce PW17 forming a loose and unstable G-quadruplex; (2) the compact and stable K+-stabilized G-quadruplex is almost formed when K+ is equal to or larger than 7 mM; (3) when K+ is ranged from 0.5 mM to 7 mM, the transformation of K+-stabilized PW17 from loose and unstable to compact and stable is occurred. Interestingly, dimeric G-quadruplex through 5’-5’ stacking is involved in the forming process until completely formed at 40 mM K+. Moreover, the total process is thermodynamically controlled. With PW17 as a sensing probe and PPIX as a fluorescent probe for detection of K+, three linear fluorescent ranges are observed, which is corresponding to the three forming stages of G-quadruplex. Clarifying the forming process provides a representative example to deeply understand and further design aptamer-based biosensers and logic devices.


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Introduction Guanine-rich DNA sequences (G2+NxG2+NxG2+NxG2+) containing two or more G tracts and loop regions (Nx, typically 1-7 nucleotides) have the potential to form G-quadruplex structures, which are stabilized by Hoogsteen H-bonds1 and central cations such as K+.2 G-quadruplexes have drawn increasing attention, as the potential G-quadruplex-forming sequences are widespread in the human telomere region and the promoter regions of numerous oncogenes. The formed G-quadruplex motif is found to play important roles in gene transcription and regulation.3 Because of their functional importance, a large number of G-quadruplex stabilizers have been developed to regulate the expression levels of these oncogenes to realize the anticancer and anti-HIV.4 In addition, the thermodynamic

and folding kinetic

study, structure and stability of

G-quadruplex have been widely explored,5-7 which is very useful for understanding the biological roles and drug targeting. On the other hand, some guanine-rich DNA sequences named as aptamers are screened in vitro by the SELEX (systematic evolution of ligands by exponential enrichment) approach.8 The selected aptamers have specific and high binding affinity for a variety of targets including metal cations,9 small organic molecules,9 and proteins.9 Subsequently, relying on a variety of electrochemical and optical signal readout methods, aptamer-based biosensors are widely developed.4,

6-14

For example, some functional aptamers, such as

c-MYC, PW17, AGRO100, T30695, PS2.M and TBA, are selected to detect K+,15-19 respectively, which is based on a fact that K+ could induce the aptamer forming G-quadruplex. Integrated with a fluorescent, colorimetric or electrochemical probe, K+ concentration ranged from nM to µM or mM levels is linearly dependent with signal readout, and the highly sensitive and selective detection of K+ is achieved.20-23 However, the detection is easily interfered by co-existing ions.24 Until now, only a few aptamer-based sensors could detect K+ in the presence of excess Na+.18 Under this situation, clarifying the forming



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process of G-quadruplex is beneficial to deeply understand the bio-sensing mechanism. However, the process of K+ inducing G-rich aptamer forming G-quadruplex is remained unknown. In addition, K+ is always used to induce G-rich aptamer forming G-quadruplex, which works as a probe for sensing targets.9,25-29 However, the basis of selecting proper K+ concentration is unclear. In this paper, with PW17 as an example, the transforming process from aptamer to G-quadruplex induced by K+ is qualitatively investigated. We find K+ induces PW17 undergoing the conformation transfer from loose and unstable to compact and stable, which is strictly K+-concentration dependent. The results demonstrate: (1) K+ (< 0.5 mM) could induce PW17 forming a loose and unstable G-quadruplex; (2) the compact and stable K+-stabilized PW17 is formed when K+ is equal to or larger than 5 mM; (3) when K+ is ranged from 0.5 mM to 5 mM, the transformation of K+-stabilized PW17 from loose and unstable into compact and stable is occurred. Interestingly, the transforming process is not only accompanied with the formation of dimeric G-quadruplex until the dimer is completely formed at 40 mM K+, and also thermodynamically controlled. With PW17 as a sensing probe and PPIX as a fluorescent probe for detecting K+, three linear fluorescent ranges are observed, which is corresponding to the three forming stages of G-quadruplex. Clarifying the forming process provides a representative example to deeply understand the formation of G-quadruplex, and also provide a clue to reasonably design aptamer-based biosensors and logic devices.

Experimental Section Chemicals and materials The purified oligo-nucleotide was obtained from Sangon Biotech (Shanghai) Co., Ltd. The applied DNA sequences were given below: PW17:

5’-GGGTAGGGCGGGTTGGG-3’

TT-PW17:

5’-TTGGGTAGGGCGGGTTGGG-3’

PW17-TT:

5’-TTGGGTAGGGCGGGTTGGG-TT-3’


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Tris (Tris - (hydroxymethyl)aminomethane), HAc and KClO4·3H2O were purchased from Sigma-Aldrich (St. Louis, MO) and used without further purification. The stock solution of 100 µM PW17 was prepared in 10 mM Tris ̶ HAc buffer (pH = 8.0), and heated at 90 oC for 10 min, then gradually cooled to room temperature before use. The solution of KClO4 was prepared in 10 mM Tris ̶ HAc buffer (pH 8.0). Deionized water (18.2 MΩ cm resistivity) from a Millipore Milli-Q system was used throughout this work.

Circular Dichroism Circular Dichroism (CD) spectra of 4 µM PW17 in the Tris-HAc buffer (pH 8.0) were collected by a Chirascan (Applied Photophysics Ltd) at room temperature. The optical chamber (1 cm path length, 800µL volume) was deoxygenated with dry purified nitrogen (99.99%) before use and the nitrogen atmosphere was kept during experiments. Two scans from 220 to 340nm at 0.5 nm intervals were accumulated and averaged. The background of the buffer solution was subtracted from the CD data.

Electrospray Ionization Mass Spectroscopy (ESI-MS) All ESI mass spectra were obtained With a Finnigan LCQ Deca XP Plus ion rap mass spectrometer (San Jose, CA).The electrospray source conditions were 2.5 kV spray voltage and 120°C capillary temperature. The obtained results are analysed by promass software.

Gel Electrophoresis K+-stabilized G-quadruplex were characterized in electrophoresis experiments, performed at 105 V on native gels containing 20% polyacrylamide (acrylamide : bis–acrylamide = 29 : 1) in TB buffer (89 mM Tris–borate, pH = 8.3) supplemented with KClO4. Gels were silver stained.

CD Melting Experiments



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CD melting measurements were performed at 264 nm for 1 µM K+-stabilized PW17 from 20 oC to 90 oC, with a heating rate of 0.5 oC /min.

Results and Discussion The forming process of G-quadruplex induced by K+ It is reported that K+ could induce PW17 forming parallel G-quadruplex.2 When PW17 as a probe is selected for sensing metal ions,30 telomerases,31 DNA,11 Escherichia coli,32 and even to design logic gates,2,33 different K+ concentration such as 0.1 Mm,34 2 mM,2 10 mM,10,34 20 mM,19 40 mM,35 50 mM11 or 100 mM32 is utilized to form G-quadruplex, respectively. Then, how to select proper K+ concentration to induce PW17 forming G-quadruplex? It is unclear. As shown in Figure. 1a, circular dichroism (CD) spectra demonstrate that 4 µM PW17 in 10 mM Tris-Ac buffer (pH = 8.0) is randomly dispersed, and exhibits relatively low intensity with a positive peak at 257 nm and a negative peak at 240 nm.2 Upon adding K+ ranged from 0.2 mM to 5 mM, the positive peak is red-shifted to 264 nm and gradually increased, accompanied with a decreased negative peak at 245 nm and a decreased positive peak at 295 nm, which indicates the formation of K+-stabilized G-quadruplex. The ellipticity at 264 nm, which is characteristic of parallel G-quadruplex, is continually increased and saturated at 5 mM as shown in Figure. 1b. Further increasing K+ from 5 mM to 40 mM, even to 100 mM, it is almost unchanged (Figure. S1 in the Supporting Information). The results show that PW17 is gradually folded into a parallel G-quadruplex until saturated at 5 mM K+. When K+ is below 5 mM (such as 0.5 mM), PW17 possibly folds into a loose and unstable G-quadruplex.36-37 Due to the presence of isodichroic points at 250 and 282 nm (Figure. 1a), two-state model (loose and unstable vs. compact and stable) and the transforming behavior are suggested.38 Thus, it could be concluded that K+-stabilized PW17 undergoes a conformation transfer from loose and unstable to compact and stable, which is strictly K+-concentration dependent.


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Next, the effect of K+ on the forming process is further investigated through electrospray ionization mass spectroscopy (ESI-MS) as shown in Figure 2.39 A distinct mass peak at m/z = 5404 is observed and gradually decreased and almost disappeared, which is corresponding to PW17 with no K+ binding or loose and unstable G-quadruplex (M[PW17+H]+). Meanwhile, a new mass peak at m/z = 5482 is starting to appear at 0.5 mM K+, and further increased from 0.5 mM to 40 mM K+. The 78 (m/z) deviation from M[PW17+H]+ indicates the formation of stable [PW17+2K]+. Another



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small peak at m/z = 5442 is appeared when K+ is ranged from 1 mM to 2 mM. The 38 (m/z) deviation from M[PW17+H]+ indicates the formation of [PW17+K]+. The results mean that the process of forming K+-stabilized PW17 ([PW17+2K]+) from [PW17+H]+ undergoes a [PW17+K]+ transition state. For the cases of 0.1 mM and 0.2 mM K+, the formed G-quadruplex exists as [PW17+H]+, which is indicative of a loose and unstable G-quadruplex. For the case of 0.5 mM K+, most of G-quadruplex exists as [PW17+H]+ and only a few exists as [PW17+2K]+, which means that the compact and stable K+-stabilized PW17 is starting to form at 0.5 mM K+. Subsequently, the amount of [PW17+2K]+ is gradually enhanced as K+ is increased from 0.5 mM to 6 mM. Meanwhile, the ratio of [PW17+H]+ is accordingly decreased. Further increasing K+ from 7 mM to 40 mM, the amount of [PW17+2K]+ is kept unchanged, and the amount of [PW17+H]+ is almost omitted. Integrated with CD results, we can conclude: (1) K+ (< 0.5 mM) could induce PW17 forming a loose and unstable G-quadruplex; (2) the compact and stable K+-stabilized PW17 is almost formed when K+ is equal to or larger than 7 mM; (3) when K+ is ranged from 0.5 mM to 7 mM, the transformation of K+-stabilized PW17 from loose and unstable into compact and stable is occurred.


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Figure 2. ESI-MS of PW17 in the presence of 0, 0.1 mM, 0.2 mM, 0.5 mM, 1 mM, 1.5 mM, 2 mM, 5 mM, 6 mM, 7mM, 8mM, 9 mM, 10 mM and 40 mM K+.

It is also noted that such a transformation is accompanied with the formation of dimeric G-quadruplex, which is observed by native gel electrophoresis. It was reported that 16-mer T30177 and 18-mer TT-T30177 form a dimeric and monomeric G-quadruplex in the presence of K+, respectively,5 which are selected as a dimeric and a monomeric marker, respectively (Figure. S2 in the Supporting Information). As shown in Figure 3, the first and second lanes in every gel electrophoresis photograph (from 1 to 6) are corresponding to a dimeric and a monomeric marker, and the third lane is corresponding to PW17 in the presence of K+ from 0.1 mM to 40 mM. For the case of 0.1 mM K+, there is only one tailed band, which migrates similarly to that of the monomeric marker. For the case of 0.5 mM K+, there are two smeared bands: the



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slower band migrates similarly to that of the dimeric marker; the faster band is close to that of the monomeric marker, which means the formed unstable G-quadruplex contains more than one structure.40 For the cases of 2 mM and 5 mM K+, the slower and faster bands become clearer, which is indicative of the formation of more stable monomeric and dimeric G-quadruplex.5,40-41 The results demonstrates that PW17 folds into a relatively loose G-quadruplex containing dimer and monomer. Upon increasing K+ from 5 mM to 40 mM, the slower and faster bands become much clearer, and the faster bands are gradually disappeared, which means the compact and stable monomeric G-quadruplex gradually forms more compact and stable dimeric G-quadruplex. Further increasing K+ to 100 mM, the gel electrophoresis is kept unchanged. The results show that a compact dimeric G-quadruplex is finally formed when K+ concentration is equal to or larger than 40 mM. Thus, it is concluded that dimeric G-quadruplex is involved in the forming process whether the structure is loose or compact. Through adding two thymines at 3’-terminal and 5’-terminal, respectively, PW17-TT (3’-terminal) and TT-PW17 (5’-terminal) are selected for native gel electrophoresis (Figure S3 in the Supporting Information). PW17-TT migrates as fast as the dimeric G-quadruplex, and TT-PW17 migrates at a similar rate as the monomeric G-quadruplex. The results show K+-stabilized PW17 forms dimeric G-quadruplex through 5’-5’ stacking.

Figure 3. Gel electrophoresis analysis of PW17 in the presence of K+: (1) 0.1 mM; (2) 0.5 mM; (3) 2 mM; (4) 5 mM; (6) 40 mM. Dimeric G-quadruplex is 16-mer T30177, and monomeric G-quadruplex is 18-mer TT-T30177.

Finally, the K+-dependent G-quadruplex formation is rationalized. CD melting experiments performed at 264 nm are used to investigate the stability of formed G-quadruplex as shown in Figure 4. When K+ is ranged from 2 mM to 40 mM, Tm is gradually increased from 39 oC (2 mM K+) to 50 oC (5 mM K+), 63 oC (10 mM K+), and


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75 oC (40 mM K+), respectively. For the case of 0.5 mM K+, K+-stabilized PW17 is too unstable to accurately measure its melting temperature (Tm) (Figure S4 in the Supporting Information).36 For the case of 100 mM K+, Tm is too high to be measured.36 Tm is summarized (Table S1 in the Supporting Information), and corresponding thermodynamic parameter ∆G is calculated through van’t Hoff analysis.36 ∆G is accordingly decreased from -8.38 kJ/mol (2 mM K+) to -10.49 kJ/mol (5 mM K+), -12.30 kJ/mol (10 mM K+), and -20.76 kJ/mol (40 mM K+). Based on the Tm and ∆G results, the stability of K+-stabilized PW17 gradually enhances, which could thermodynamically account for the forming process of K+-dependent G-quadruplex from unstable to stable.

Figure 4. CD melting curves for PW17 in the presence of K+: (a) 2 mM; (b) 5 mM; (c) 10 mM; (d) 40 mM.

Implications for Detection of K+ Based on the results discussed above, with PW17 as a sensing probe and PPIX as a fluorescent probe for detecting K+, the fluorescent intensity is gradually increased when K+ concentration is changed from 10 nM to 100 mM, and three linear fluorescent ranges (vs. K+ concentration: 10 nM ~ 0.5 mM, 0.5 mM ~ 5 mM and 5 mM ~ 100 mM) are observed as shown in Figure 5. The three linear fluorescent ranges are corresponding to three forming stages of G-quadruplex. However, the presence of 10 mM42 or 140 mM Na+18 greatly destroys the linear ranges, which is probably due to the fact that Na+ easily interferes with the formation of K+-stabilized PW17 (Figure S5 in the Supporting Information). The results could explain the fact that most aptamer-based



K+ sensors have been developed, but it is very difficult to selectively determine extracellular K+ concentration due to the large excess of Na+ (up to 140 mM) present in physiological conditions. In order to avoid the interferences from Na+, a complementary strand is selected to totally hybridize with PW17 forming double stranded DNA, which works as a probe for detecting K+ instead of PW17. As shown in Figure S6, the linear relationship between fluorescent readout signal and K+ concentration even in the presence of 10 mM or 140 mM Na+ is greatly improved. 5

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Figure 5. (a): Fluorescence emission spectra of 1 µM PPIX in the Tris-HAc buffer (pH 8.0) buffer containing 1 µM PW17 and different concentrations of K+ (from bottom to top): 0, 10 nM, 50 nM, 100 nM , 1 µM, 10 µM, 100 µM, 500 µM, 1 mM , 5 mM , 10 mM, 40 mM. (b): Dependence of the fluorescence change (F-F0) at 628 nm on K+ concentration (from 10 nM to 100 mM ).


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Conclusion In summary, with PW17 as an aptamer example, the process of K+ inducing PW17 forming G-quadruplex is investigated by CD spectra, ESI-MS and native gel electrophoresis. The results demonstrate: (1) K+ (< 0.5 mM) could induce PW17 forming a loose and unstable G-quadruplex; (2) the compact and stable K+-stabilized G-quadruplex is almost formed when K+ is equal to or larger than 7 mM; (3) when K+ is ranged from 0.5 mM to 7 mM, the transformation of K+-stabilized PW17 from loose and unstable to compact and stable is occurred. Interestingly, dimeric G-quadruplex through 5’-5’ stacking is involved in the forming process whether the structure is loose or compact until completely formed at 40 mM K+. Moreover, the forming process is thermodynamically controlled. Clarifying the process of K+ inducing PW17 to form G-quadruplex provides a representative example to explain the formation of G-quadruplex, which is beneficial to deeply understand the bio-sensing mechanism and reasonably design aptamer-based biosensors and logic devices.

Supporting Information Experimental results of CD spectra of PW17, gel electrophoresis of monomeric and dimeric markers, and primary K+ sensing process. The material is available free of charge via the Internet at http://pubs.acs.org.

Acknowlegements

This work was supported by the Major Research Plan of National Natural Science Foundation of China (21233003) and the Fundamental Research Funds for the Central Universities.



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References (1) M, G.; N, L. M.; Davies, D. R. Helix formation by guanylic acid. PROC. N. A. S. 1962, 48, 2013-2018. (2) Li, T.; Wang, E.; Dong, S. Potassium−lead-switched G-quadruplexes: A new class of DNA logic gates. J. Am. Chem. Soc 2009, 131, 15082-15083. (3) Maizels, N. Dynamic roles for G4 DNA in the biology of eukaryotic cells. Nat Struct Mol Biol 2006, 13, 1055-1059. (4) Collie, G. W.; Parkinson, G. N. The application of DNA and RNA G-quadruplexes to therapeutic medicines. Chem. Soc. Rev. 2011, 40, 5867-5892. (5) Mukundan, V. T.; Do, N. Q.; Phan, A. T. HIV-1 integrase inhibitor T30177 forms a stacked dimeric G-quadruplex structure containing bulges. Nucleic Acids Res. 2011, 39, 8984-91. (6) Kormuth, K. A.; Woolford, J. L.; Armitage, B. A. Homologous PNA Hybridization to noncanonical DNA G-quadruplexes. Biochemistry 2016, 55, 1749-1757. (7) Bedrat, A.; Lacroix, L.; Mergny, J.-L. Re-evaluation of G-quadruplex propensity with G4Hunter. Nucleic Acids Res. 2016, 44, 1746-1759. (8) Tuerk, C.; Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990, 249, 505-510. (9) Zheng, D.; Zou, R.; Lou, X. Label-free fluorescent detection of ions, proteins, and small molecules using structure-switching aptamers, SYBR gold, and exonuclease I. Anal. Chem. 2012, 84, 3554-3560. (10) Han, D.-M.; Ma, Z.-Y.; Zhao, W.-W.; Xu, J.-J.; Chen, H.-Y. Ultrasensitive photoelectrochemical sensing of Pb2+ based on allosteric transition of G-quadruplex DNAzyme. Electrochem. Commun. 2013, 35, 38-41. (11) Shi, L.; Yu, Y.; Chen, Z.; Zhang, L.; He, S.; Shi, Q.; Yang, H. A label-free hemin/G-quadruplex DNAzyme biosensor developed on electrochemically modified electrodes for detection of a HBV DNA segment. RSC Adv. 2015, 5, 11541-11548. (12) Ma, D.-L.; He, H.-Z.; Leung, K.-H.; Zhong, H.-J.; Chan, D. S.-H.; Leung, C.-H. Label-free luminescent oligonucleotide-based probes. Chem. Soc. Rev. 2013, 42, 3427-3440. (13) Du, Y.; Li, B.; Wang, E. “Fitting” makes “Sensing” simple: Label-free detection strategies based on nucleic acid aptamers. Accounts of Chemical Research 2013, 46, 203-213. (14) Freeman, R.; Liu, X.; Willner, I. Chemiluminescent and chemiluminescence resonance energy transfer (CRET) detection of DNA, metal ions, and aptamer–substrate complexes using hemin/G-quadruplexes and CdSe/ZnS quantum dots. J. Am. Chem. Soc 2011, 133, 11597-11604.


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Page 15 of 19

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(15) Lee, J.; Kim, H.-J.; Kim, J. Polydiacetylene liposome arrays for selective potassium detection. J. Am. Chem. Soc 2008, 130, 5010-5011. (16) Li, T.; Wang, E.; Dong, S. Parallel G-quadruplex-specific fluorescent probe for monitoring DNA structural changes and label-free detection of potassium ion. Anal. Chem. 2010, 82, 7576-7580. (17) Li, T.; Wang, E.; Dong, S. G-quadruplex-based DNAzyme as a sensing platform for ultrasensitive colorimetric potassium detection. Chem. Commun. 2009, 580-582. (18) Qin, H.; Ren, J.; Wang, J.; Luedtke, N. W.; Wang, E. G-quadruplex-modulated fluorescence detection of potassium in the presence of a 3500-fold excess of sodium ions. Anal. Chem. 2010, 82, 8356-8360. (19) Hu, L.; Liu, X.; Cecconello, A.; Willner, I. Dual switchable CRET-induced luminescence of CdSe/ZnS quantum dots (QDs) by the hemin/g-quadruplex-bridged aggregation and deaggregation of two-sized QDs. Nano Lett. 2014, 14, 6030-6035. (20) Xie, L.; Qin, Y.; Chen, H.-Y. Direct fluorescent measurement of blood potassium with polymeric optical sensors based on upconverting nanomaterials. Anal. Chem. 2013, 85, 2617-2622. (21) Ruckh, T. T.; Skipwith, C. G.; Chang, W.; Senko, A. W.; Bulovic, V.; Anikeeva, P. O.; Clark, H. A. Ion-switchable quantum dot förster resonance energy transfer rates in ratiometric potassium sensors. ACS Nano 2016, 10, 4020-4030. (22) Yu, J.; Zhang, L.; Xu, X.; Liu, S. Quantitative detection of potassium ions and adenosine triphosphate via a nanochannel-based electrochemical platform coupled with G-quadruplex aptamers. Anal. Chem. 2014, 86, 10741-10748. (23) Zhu, X.; Zhao, J.; Wu, Y.; Shen, Z.; Li, G. Fabrication of a highly sensitive aptasensor for potassium with a nicking endonuclease-assisted signal amplification strategy. Anal. Chem. 2011, 83, 4085-4089. (24) Huang, C.-C.; Chang, H.-T. Aptamer-based fluorescence sensor for rapid detection of potassium ions in urine. Chem. Commun. 2008, 1461-1463. (25) Liu, L.; Shao, Y.; Peng, J.; Huang, C.; Liu, H.; Zhang, L. Molecular rotor-based fluorescent probe for selective recognition of hybrid G-quadruplex and as a K+ sensor. Anal. Chem. 2014, 86, 1622-1631. (26) Wang, M.; Wang, W.; Kang, T.-S.; Leung, C.-H.; Ma, D.-L. Development of an iridium(III) complex as a G-quadruplex probe and its application for the G-quadruplex-based luminescent detection of picomolar insulin. Anal. Chem. 2016, 88, 981-987. (27) Li, T.; Wang, E.; Dong, S. Lead(II)-Induced allosteric G-quadruplex DNAzyme as a



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

colorimetric and chemiluminescence sensor for highly sensitive and selective Pb2+ detection. Anal. Chem. 2010, 82, 1515-1520. (28) Wang, G.-L.; Gu, T.-T.; Dong, Y.-M.; Wu, X.-M.; Li, Z.-J. Photoelectrochemical aptasensing of lead(II) ion based on the in situ generation of photosensitizer of a self-operating photocathode. Electrochem. Commun. 2015, 61, 117-120. (29) Zhang, Z.; Sharon, E.; Freeman, R.; Liu, X.; Willner, I. Fluorescence detection of DNA, adenosine-5′-triphosphate (ATP), and telomerase activity by zinc(II)-protoporphyrin IX/G-quadruplex labels. Anal. Chem. 2012, 84, 4789-4797. (30) Zhou, Z.; Zhu, J.; Zhang, L.; Du, Y.; Dong, S.; Wang, E. G-quadruplex-based fuorescent assay of S1 nuclease activity and K+. Anal. Chem. 2013, 85, 2431-2435. (31) Pavlov, V.; Xiao, Y.; Gill, R.; Dishon, A.; Kotler, M.; Willner, I. Amplified chemiluminescence surface detection of DNA and telomerase activity using catalytic nucleic acid labels. Anal. Chem. 2004, 76, 2152-2156. (32) Guo, Y.; Wang, Y.; Liu, S.; Yu, J.; Wang, H.; Wang, Y.; Huang, J. Label-free and highly sensitive electrochemical detection of E. coli based on rolling circle amplifications coupled peroxidase-mimicking DNAzyme amplification. Biosens Bioelectron 2016, 75, 315-319. (33) Zhai, W.; Du, C.; Li, X. A series of logic gates based on electrochemical reduction of Pb2+ in self-assembled G-quadruplex on the gold electrode. Chem. Commun. 2014, 50, 2093-2095. (34) Xu, L.; Sun, N.; Zhou, L.; Chen, X.; Wang, J.; Wang, Q.; Wang, K.; Zhang, J.; Pei, R. A label-free fluorescence assay for potassium ions using riboflavin as a G-quadruplex ligand. Analyst 2015, 140, 3352-3355. (35) Adrian, M.; Ang, D. J.; Lech, C. J.; Heddi, B.; Nicolas, A.; Phan, A. T. Structure and conformational dynamics of a stacked dimeric G-quadruplex formed by the human CEB1 minisatellite. J. Am. Chem. Soc 2014, 136, 6297-6305. (36) Hatzakis, E.; Okamoto, K.; Yang, D. Thermodynamic stability and folding kinetics of the major G-quadruplex and its loop isomers formed in the nuclease hypersensitive element in the human c-Myc promoter: Effect of loops and flanking segments on the stability of parallel-stranded intramolecular G-quadruplexes. Biochemistry 2010, 49, 9152-9160. (37) Kotch, F. W.; Fettinger, J. C.; Davis, J. T. A lead-filled G-quadruplex: Insight into the G-quartet's selectivity for Pb2+ over K+. Org. Lett. 2000, 2, 3277-3280. (38) Largy, E.; Marchand, A.; Amrane, S.; Gabelica, V.; Mergny, J.-L. Quadruplex turncoats: cation-dependent folding and stability of quadruplex-DNA double switches. J. Am. Chem. Soc 2016, 138, 2780-2792. (39) Marchand, A.; Gabelica, V. Native electrospray mass spectrometry of DNA


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G-quadruplexes in potassium solution. J. Am. Soc. Spectrom. 2014, 25, 1146-1154. (40) Pedroso, I. M.; Duarte, L. F.; Yanez, G.; Baker, A. M.; Fletcher, T. M. Induction of parallel human telomeric G-quadruplex structures by Sr2+. biochem bioph res co 2007, 358, 298-303. (41) Adrian, M.; Ang, D. J.; Lech, C. J.; Heddi, B.; Nicolas, A.; Phan, A. T. Structure and conformational dynamics of a stacked dimeric G-quadruplex formed by the human CEB1 Minisatellite. J. Am. Chem. Soc 2014, 136, 6297-6305. (42) Zheng, D.; Zou, R.; Lou, X. Label-free fluorescent detection of ions, proteins, and small molecules using structure-switching aptamers, SYBR gold, and exonuclease I. Anal. Chem. 2012, 84, 3554-3560.

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Aptamer-Based K+ Sensor: Process of Aptamer Transforming into G

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