Guanine rich oligonucleotides allow detection of potassium ions
Oligonucleotides containing sequences from human telomere DNA or a thrombin binding aptamer can form tetraplex structures upon binding of potassium ions. Structural changes associated with the formation of the tetraplex fold allow the development of potassium-sensing oligonucleotide (PSO) probes or sensors.
In a PSO, two fluorescent dyes are attached to both terminal ends of the oligonucleotide. Combining fluorophores with a potassium sensing oligonucleotides that allow for fluorescence resonance energy transfer (FRET) or excimer emission based detection methods upon binding of the K+ ion enabling monitoring of K+ ions in biological systems.
A flexible single-stranded DNA oligonucleotide with a guanine-rich sequence folds into a tetraplex structure in the presence of potassium ions. The single-stranded oligonucleotide, 5’-GGTTGGTGTGGTTGG-3’, when immobilized onto a graphene surface acts as a probe allowing detection of potassium ions in a graphene-based biosensor devise (Lui et al. 2018).
The potassium ion is essential in biological systems such as the human body such as the maintenance of transmembrane potential and hormone secretion. Therefore, a selective and specific detection and quantification of potassium ions in biological systems would be quite significant. Methods such as fluorescent, electrochemical, and electrical methods allow the selective detection and recognition of K+ ions but maybe not sensitive enough to work for biological systems. Therefore, Lui et al. recently reported the development of a guanine-rich DNA aptamer as a highly sensitive and selective biosensor for the detection of K+ ions. The formation of guanine-quadruplexes from guanine-rich oligonucleotides that have a strong affinity for capturing K+ ions is the basis for this biosensor.
Figure 1 shows the structural models for the aptamer-potassium complex as well as for the thrombin-aptamer-potassium complex.
Figure 1: Structural model of a thrombin-potassium aptamer complex (PDB ID 4DII, left) and the potassium binding aptamer (right) as reported by Krauss et al. in 2012.
Liu et al. in 2018 used this aptamer for the fabrication of a Hall-effect-based biosensor using single-layer graphene for the detecting of the K+ ion. The biosensor was prepared over wafer-scale areas by a catalytic growth technique of chemical vapor deposition (CVD) employing the Van der Pauw technique which allows monitoring multiple electrical properties of graphene films during the detection process.
Other potassium sensing oligonucleotides are also possible. For example, Nojima et al. in 2002 synthesized a potassium sensing oligonucleotide with high selectivity for K+ ions as a FRET probe. The researchers connected the fluorophores 6-carboxyfluorescein (6-FAM) and 6-carboxy-tetramethylrhodamine (6-TAMRA) to the oligonucleotide at the 5’- and 3’-terminal ends, respectively, using the DNA sequence GGG TTA GGG TTA GGG TTA GGG for the synthesis. Oligonucleotides carrying this sequence, or a similar one can fold into a tetraplex structure or fold that contains a cavity in which a K+ ion can fit in. The presence of the K+ ion stabilizes the tetraplex structure of the PSO and FRET can occur between the two fluorophores. Circular dichroism (CD) revealed that the two fluorophores are not close to each other in the absence of the potassium ion. This PSO is also reported to detect sodium ions but with a much lower sensitivity, ~43,000-times for K+ over Na+ ions, which suggests that the structure of the tetraplex differs between K+ and Na+.
Reference
Russo Krauss I, Merlino A, Randazzo A, Novellino E, Mazzarella L, Sica F. High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity. Nucleic Acids Res. 2012;40(16):8119-28.
Xiangqi Liu, Chen Ye, Xiaoqing Li, Naiyuan Cui, Tianzhun Wu, Shiyu Du, Qiuping Wei, Li Fu, Jiancheng Yin, and Cheng-Te Lin; Highly Sensitive and Selective Potassium Ion Detection Based on Graphene Hall Effect Biosensors. Materials 2018, 11, 399.
Nojima T, Ueyama H, Takagi M, Takenaka S.; Potassium sensing oligonucleotide, PSO, based on DNA tetraplex formation. Nucleic Acids Res Suppl. 2002;(2):125-6.
Takenaka S, Juskowiak B.; Fluorescence detection of potassium ion using the G-quadruplex structure. Anal Sci. 2011;27(12):1167-72.
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