Reversible electronic nanoswitch based on DNA G-quadruplex conformation: A platform for single-step, reagentless potassium detection

Functional nucleic acid nanostructures and DNA machines

The information encoded in the base sequence of DNA provides instructions for the structural and functional properties of this biopolymer. Structural information includes the formation of duplexes, supramolecular crossover tiles, G-quadruplexes, i-motifs, base-metal-ion complexes, and more. Functional information encoded in the DNA is reflected by specific binding (aptamers) or catalytic properties (DNAzymes). Recent advances in tailoring supramolecular DNA structures for DNA-based machinery and for amplified biosensing are reviewed. Different DNA machines that perform 'tweezer', 'walker' or 'metronome' functions are discussed, and the control of macroscopic surface properties or the motility of micro-objects by molecular DNA devices is introduced. Furthermore, the design of DNA machines for the ultrasensitive detection of DNA, low-molecular-weight substrates, and macromolecules is discussed. Supramolecular aptamer and DNAzyme structures are used as molecular tools for amplified sensing.

G-quadruplex signaling probe for highly sensitive DNA detection

Ferrocene-conjugated oligonucleotides that can form intermolecular guanine (G)-quadruplexes are prepared and used as signaling probes for detecting target DNA, improving substantially assay characteristics (e.g. a considerably wider linear dynamic range and lower detection limit).

A new fluorescent chemosensor detecting Co2+ and K+ in DMF buffered solution

A new fluorescent chemosensor 2-(2-thiophene)imidazo [4,5,f]-1,10-phenanthroline (L) was prepared and characterized. By adding univalent or divalent metal ions such as Na(+), K(+), Mg(2+), Ba(2+), Mn(2+), Fe(2+), Co(2+), Ni(2+), Cu(2+), Ag(+), Zn(2+), Cd(2+) and Hg(2+) ions into the solution of L in DMF under buffered conditions with the working pH ranging from 7.0 to 8.0, we found that L could be used to detect K(+) ratiometricly and it could also be applied to sense Co(2+) with the phenomenon of fluorescence quenching of L. While the response behavior of L was not discernibly affected by other examined metal ions.

Determination of urinary adenosine using resonance light scattering of gold nanoparticles modified structure-switching aptamer

A novel sensitive method has been developed for the detection of adenosine (AD) in human urine by using enhanced resonance light scattering (RLS). This method is based on the specific recognition and signal amplification of adenosine aptamer (Apt) coupled with gold nanoparticles (GNPs) via G-quartet-induced nanoparticle assembly, which was fabricated by triggering a structure switching of the 3' terminus G-rich sequence and aptamer duplex. RLS signal linearly correlated with the concentration of adenosine over the range of 6-115nM. The limit of detection (LOD) for adenosine is 1.8nM with relative standard deviations (RSD) of 2.90-4.80% (n=6). The present method has been successfully applied to determination of adenosine in real human urine, and the obtained results were in good agreement with those obtained by the HPLC method. Our investigation shows that the combination of the excellent selectivity of aptamer with the high sensitivity of the RLS technique could provide a promising potential for aptamer-based small molecule detection, and be beneficial in extending the application of RLS.

Crystal violet-G-quadruplex complexes as fluorescent sensors for homogeneous detection of potassium ion

A novel K(+) detection method was reported using a label-free G-quadruplex-forming oligonucleotide and a triphenylmethane fluorescent dye crystal violet (CV). This method is based on the fluorescence difference of some CV/G-quadruplex complexes in the presence of K(+) or Na(+), and the fluorescence change with the variation of K(+) concentration. According to the nature of the fluorescence change of CV as a function of ionic conditions, two K(+) detection modes can be developed. One is a fluorescence-decreasing mode, in which T(3)TT(3) (5'-GGGTTTGGGTGGGTTTGGG) is used, and the fluorescence of CV decreases with an increased concentration of K(+). The other is a fluorescence-increasing mode, in which Hum21 (5'-GGGTTAGGGTTAGGGTTAGGG) is used, and the fluorescence of CV increases with an increased concentration of K(+). Compared with some published K(+) detection methods, this method has some important characteristics, such as lower cost of the test, higher concentrations of Na(+) that can be tolerated, adjustable linear detection range and longer excitation and emission wavelengths. Preliminary results demonstrated that the method might be used in biological systems, for example in urine.

On the Signaling of Electrochemical Aptamer-Based Sensors: Collision- and Folding-Based Mechanisms

Recent years have seen the emergence of a new class of electrochemical sensors predicated on target binding-induced folding of electrode-bound redox-modified aptamers and directed against targets ranging from small molecules to proteins. Previous studies of the relationship between gain and probe-density for these electrochemical, aptamer-based (E-AB) sensors suggest that signal transduction is linked to binding-induced changes in the efficiency with which the attached redox tag strikes the electrode. This, in turn, suggests that even well folded aptamers may support E-AB signaling if target binding sufficiently alters their flexibility. Here we investigate this using a thrombin-binding aptamer that undergoes binding-induced folding at low ionic strength but can be forced to adopt a folded conformation at higher ionic strength even in the absence of its protein target. We find that, under conditions in which the thrombin aptamer is fully folded prior to target binding, we still obtain a ca. 30% change in E-AB signal upon saturated target levels. In contrast, however, under conditions in which the aptamer is unfolded in the absence of target and thus undergoes binding-induced folding the observed signal change is twice as great. The ability of folded aptamers to support E-AB signaling, however, is not universal: a fully folded anti-IgE aptamer, for example, produces only an extremely small, ca. 2.5% signal change in the presence of target despite the larger steric bulk of this protein. Thus, while it appears that binding-induced changes in the dynamics in fully folded aptamers can support E-AB signaling, this signaling mechanism may not be general, and in order to ensure the design of high-gain sensors binding must be linked to a large-scale conformational change.

Fluorescent sensor for monitoring structural changes of G-quadruplexes and detection of potassium ion

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.