Validation of circular dichroic spectroscopy of synthetic oligonucleotide PS2.M for K + concentration measurements

Abstract

The single-stranded synthetic oligonucleotide PS2.M is known to provide a basis for developing sensors since it tends to fold into structures called G-quadruplexes (G4) having characteristic topology and orientation with probabilities that depend on the chemical environment. The presence and concentration of cation species are among the key factors that determine the outcome of such a process. PS2.M and other aptamers have been used in several applications in conjunction with various probes, such as hemin, at the cost of increased technical complexity and applicability limitations. We instead validated the application limits of Circular Dichroic spectroscopy (CD) as only measurement method to assay PS2.M as ${\text{K}}^{+}$ sensor in a variety of solutions having different chemical complexity. The tested solutions range from simple $\text{NaCl}$ and $\text{KCl}$ solutions to chemically complex solutions like DMEM-Dulbecco's Modified Eagle Medium-which is widely used in a biological laboratory. PS2.M was also evaluated in solutions of ${\text{KHCO}}_3$ and D-ribose (K:D-rib), an antioxidant potassium compound, to compare its response to the simple $\text{KCl}$ solution case. Our findings show that, within specific concentration applicability ranges, CD spectra can estimate the ${\text{K}}^{+}$ concentration in the examined water solutions even at high $\text{Na}+$ concentrations with respect to ${\text{K}}^{+}$ and in the presence of antioxidant molecules.

Supplementary information: The online version supplementary material available at 10.1140/epjp/s13360-022-02581-2.