Fluorescent Sensor for Monitoring Structural Changes of G-Quadruplexes and Detection of Potassium Ion

Abstract

G-rich sequences with the potential for quadruplex formation are common in genomic DNA. Considering that the biological functions of G-quadruplexes may well depend on their structures, the development of a sensitive structural probe for distinguishing different types of quadruplexes has received great attention. Crystal violet (CV) is a triphenylmethane dye, which can stack onto the two external G-quartets of a G-quadruplex. The ability of CV to discriminate G-quadruplexes from duplex and single-stranded DNAs has been reported by us. Herein, the ability of CV to discriminate parallel from antiparallel structures of a G-quadruplex was studied. The binding of CV to an antiparallel G-quadruplex can make its fluorescence intensity increase to a high level because of the protection of bound CV from the solvent by quadruplex end loops. The presence of side loops in parallel G-quadruplexes cannot provide bound CV such protection, causing the fluorescence intensity of CV/G-quadruplex mixture to be obviously weaker when the G-quadruplex adopts a parallel structure than that when the G-quadruplex adopts an antiparallel structure. Therefore, CV can be developed as a sensitive fluorescent biosensor for the discrimination of antiparallel G-quadruplexes from parallel G-quadruplexes and for monitoring the structural interconversion of G-quadruplexes. In addition, considering that some G-rich DNA sequences can adopt different G-quadruplex structures under Na(+) or K(+) ion conditions, a novel, cheap and simple K(+) ion detection method was developed. This method displays a high K(+) ion selectivity against Na(+) ion, the change of 200 mM in Na(+) ion concentration only causes a similar fluorescent signal change to 0.3 mM K(+) ion.

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“…4a), which has been popularly used in spectroscopic detection systems for metal ions36. A 12-nucleotide human telomere sequence (5′-TAGGGTTAGGGT-3′; a Telomere Element, TeloE) was attached to the 3′-ends of the staple strands placed at the four sites on each of the levers, spaced every three helical turns on the same side of the fulcrum (sites a , b , c , and d ).…”

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“…The addition of K + ions was found to induce the formation of the G-quadruplex motif, thereby resulting in a switch-on fluorescence response (Figure 11A). Interestingly, the use of other G-quadruplex-forming sequences in conjunction with CV generated switch-on detection modes for the K + ion (60). Wang, Dong and co-workers (25) have developed a variation of this strategy using ion-responsive oligonucleotide PS2.M (5′-GTG 3 TAG 3 CG 3 T 2 G 2 -3′) and the PPIX as a parallel G-quadruplex fluorescent probe.…”

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“…Kong et al have designed a highly sodium-tolerant potassium sensor using a G-quadruplexforming oligonucleotide sequence and the fluorescent dye crystal violet ( Figure 14A) (134); this system is also able to discriminate between parallel and antiparallel G-quadruplexes by characteristic fluorescence intensities ( Figure 14B) (133). The formation of G-quadruplex polymorphisms is known to be cation type-dependent, and this property has already been harnessed to develop a range of cation sensors.…”