Aptamer-based K+ sensor: Process of aptamer transforming into G-quadruplex

Journal of Physical Chemistry B

Volumn 120, Issue 27, 2016, Pages 6606-6611

  Zhang, Dongju ^a   Han, Juan ^a   Li, Yunchao ^a   Fan, Louzhen ^a   Li, Xiaohong ^a  

^a BEIJING NORMAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; DICHROISM; ELECTROPHORESIS; ELECTROSPRAY IONIZATION; FLUORESCENCE; LOGIC DEVICES; MASS SPECTROMETRY; PROBES;

APTAMERS; CONCENTRATION-DEPENDENT; ELECTROSPRAY IONIZATION MASS SPECTROSCOPY; FLUORESCENT PROBES; G-QUADRUPLEXES; NATIVE GEL ELECTROPHORESIS; SENSING PROBE; SMALL MOLECULES;

CIRCULAR DICHROISM SPECTROSCOPY;

APTAMER; FLUORESCENT DYE; GUANINE QUADRUPLEX; POTASSIUM;

CHEMISTRY; CIRCULAR DICHROISM; ELECTROSPRAY MASS SPECTROMETRY; PHASE TRANSITION; SPECTROFLUOROMETRY;

APTAMERS, NUCLEOTIDE; CIRCULAR DICHROISM; FLUORESCENT DYES; G-QUADRUPLEXES; PHASE TRANSITION; POTASSIUM; SPECTROMETRY, FLUORESCENCE; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION;

EID: 84978768121     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/acs.jpcb.6b05002     Document Type: Article

References (42)

1. Gellert, M.; Lipsett, M. N.; Davies, D. R. Helix formation by guanylic acid Proc. Natl. Acad. Sci. U. S. A. 1962, 48, 2013-2018 10.1073/pnas.48.12.2013
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 10.1021/ja9051075
3. Maizels, N. Dynamic roles for G4 DNA in the biology of eukaryotic cells Nat. Struct. Mol. Biol. 2006, 13, 1055-1059 10.1038/nsmb1171
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 10.1039/c1cs15067g
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 10.1093/nar/gkr540
6. Kormuth, K. A.; Woolford, J. L.; Armitage, B. A. Homologous PNA Hybridization to noncanonical DNA G-quadruplexes Biochemistry 2016, 55, 1749-1757 10.1021/acs.biochem.6b00026
7. Bedrat, A.; Lacroix, L.; Mergny, J.-L. Re-evaluation of G-quadruplex propensity with G4Hunter Nucleic Acids Res. 2016, 44, 1746-1759 10.1093/nar/gkw006
8. Tuerk, C.; Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase Science 1990, 249, 505-510 10.1126/science.2200121
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 10.1021/ac300690r
10. 2+ based on allosteric transition of G-quadruplex DNAzyme Electrochem. Commun. 2013, 35, 38-41 10.1016/j.elecom.2013.07.038
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 10.1039/C4RA09936B
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 10.1039/c2cs35472a
13. Du, Y.; Li, B.; Wang, E. Fitting" makes "Sensing" simple: Label-free detection strategies based on nucleic acid aptamers Acc. Chem. Res. 2013, 46, 203-213 10.1021/ar300011g
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 10.1021/ja202639m
15. Lee, J.; Kim, H.-J.; Kim, J. Polydiacetylene liposome arrays for selective potassium detection J. Am. Chem. Soc. 2008, 130, 5010-5011 10.1021/ja709996c
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 10.1021/ac1019446
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 10.1039/B815814B
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 10.1021/ac101894b
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 10.1021/nl503299f
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 10.1021/ac303709w
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 10.1021/acsnano.5b05396
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 10.1021/ac502752g
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 10.1021/ac200058r
24. Huang, C.-C.; Chang, H.-T. Aptamer-based fluorescence sensor for rapid detection of potassium ions in urine Chem. Commun. 2008, 1461-1463 10.1039/b718752a
25. + sensor Anal. Chem. 2014, 86, 1622-1631 10.1021/ac403326m
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 10.1021/acs.analchem.5b04064
27. 2+ detection Anal. Chem. 2010, 82, 1515-1520 10.1021/ac902638v
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 10.1016/j.elecom.2015.10.021
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 10.1021/ac300348v
30. + Anal. Chem. 2013, 85, 2431-2435 10.1021/ac303440d
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 10.1021/ac035219l
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 10.1016/j.bios.2015.08.031
33. 2+ in self-assembled G-quadruplex on the gold electrode Chem. Commun. 2014, 50, 2093-2095 10.1039/c3cc47763k
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 10.1039/C5AN00242G
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 10.1021/ja4125274
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 10.1021/bi100946g
37. + Org. Lett. 2000, 2, 3277-3280 10.1021/ol0065120
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 10.1021/jacs.5b13130
39. Marchand, A.; Gabelica, V. Native electrospray mass spectrometry of DNA G-quadruplexes in potassium solution J. Am. Soc. Mass Spectrom. 2014, 25, 1146-1154 10.1007/s13361-014-0890-3
40. 2+ Biochem. Biophys. Res. Commun. 2007, 358, 298-303 10.1016/j.bbrc.2007.04.126
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 10.1021/ja4125274
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 10.1021/ac300690r