A cation-driven allosteric G-quadruplex DNAzyme (PW17) was utilized to devise a conceptually new class of DNA logic gate based on cation-tuned ligand binding and release. K(+) favors the binding of hemin to parallel-stranded PW17, thereby promoting the DNAzyme activity, whereas Pb(2+) induces PW17 to undergo a parallel-to-antiparallel conformation transition and thus drives hemin to release from the G-quadruplex, deactivating the DNAzyme. Such a K(+)-Pb(2+) switched G-quadruplex, in fact, functions as a two-input INHIBIT logic gate. With the introduction of another input EDTA, this G-quadruplex can be further utilized to construct a reversibly operated IMPLICATION gate.

Mercury ion (Hg(2+)) is able to specifically bind to the thymine-thymine (T-T) base pair in a DNA duplex, thus providing a rationale for DNA-based selective detection of Hg(2+) with various means. In this work, we for the first time utilize the Hg(2+)-mediated T-T base pair to modulate the proper folding of G-quadruplex DNAs and inhibit the DNAzyme activity, thereby pioneering a facile approach to sense Hg(2+) with colorimetry. Two bimolecular DNA G-quadruplexes containing many T residues are adopted here, which function well in low- and high-salt conditions, respectively. These G-quadruplex DNAs are able to bind hemin to form the peroxidase-like DNAzymes in the folded state. Upon addition of Hg(2+), the proper folding of G-quadruplex DNAs is inhibited due to the formation of T-Hg(2+)-T complex. This is reflected by the notable change of the Soret band of hemin when investigated by using UV-vis absorption spectroscopy. As a result of Hg(2+) inhibition, a sharp decrease in the catalytic activity toward the H(2)O(2)-mediated oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)diammonium salt (ABTS) is observed, accompanied by a change in solution color. Through this approach, aqueous Hg(2+) can be detected at 50 nM (10 ppb) with colorimetry in a facile way, with high selectivity against other metal ions. These results indicate our introduced label-free method for colorimetric Hg(2+) detection is simple, quantitative, sensitive, and highly selective.

A Pb(2+)-driven DNA molecular device which is constructed based on a DNA duplex-quadruplex exchange is utilized for the highly selective and sensitive detection of Pb(2+). The power of this DNA device originates from the excellent efficiency of Pb(2+) for stabilizing G-quadruplexes, which makes the DNA duplex unwind thereby driving the device. This device can be reset to the original state by addition of a strong Pb(2+) chelator DOTA, endowing the device with good reusability. In the whole process, the signal readout is modulated via a fluorescent probe binding to and being released from the G-quadruplex. Such a DNA device can serve as a novel turn-on fluorescent sensor for Pb(2+) detection with high selectivity and sensitivity.

The lead ion (Pb(2+)) has been proven to induce a conformational change of K(+)-stabilized G-quadruplex DNAzyme and inhibit the peroxidase-like activity [Li, T.; Wang, E.; Dong, S. J. Am. Chem. Soc. 2009, 131, 15082-15083]. This provides a rationale for utilizing Pb(2+)-induced allosteric G-quadruplex DNAzyme to probe aqueous Pb(2+). Here, we choose a common G-quadruplex DNAzyme named PS2.M to develop a novel Pb(2+) sensor with two detection means: colorimetry and chemiluminescence (CL). In the presence of K(+), PS2.M (with hemin as a cofactor) exhibits a superior DNAzyme activity and effectively catalyzes the H(2)O(2)-mediated oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) or luminol, which results in a color change or generates CL emission. Upon the addition of Pb(2+), K(+)-stabilized PS2.M is induced to convert to the Pb(2+)-stabilized structure with higher stability but lower DNAzyme activity, which is reflected by an obvious increase in DNA melting temperature but a sharp decrease in readout signal. This allows us to utilize PS2.M for quantitative analysis of aqueous Pb(2+) using the ABTS-H(2)O(2) colorimetric system and luminol-H(2)O(2) CL system. In each case, the readout signal is linearly dependent on the logarithm of Pb(2+) concentration within a certain range. Nevertheless, two sensing systems provide different sensitivity for Pb(2+) analysis. With colorimetry, Pb(2+) can be detected at a level of 32 nM (approximately 7 ppb), whereas the detection limit of Pb(2+) is 1 nM (0.2 ppb) when utilizing the CL method. In addition to high sensitivity, the above sensing systems exhibit good selectivity for Pb(2+) over other metal ions. These results demonstrate the facility and effectivity of our introduced DNAzyme-based sensor for quantitative Pb(2+) analysis.

Here we demonstrate an anionic porphyrin, protoporphyrin IX (PPIX), as a parallel G-quadruplex-specific fluorescent probe for monitoring DNA structural changes and utilize it to develop a DNA-based K(+) sensor. The interactions of PPIX with different DNA structures in K(+) or Na(+) solution are investigated by using circular dichroism, fluorescence, and UV-vis spectroscopy. The observations reveal that PPIX has an ∼100-fold selectivity for parallel G-quadruplexes against duplexes and antiparallel G-quadruplexes. Meanwhile, the fluorescence intensity of PPIX increases by over 10-fold upon binding to parallel G-quadruplexes. On the basis of the selectivity and fluorescence property of PPIX, we introduce a facile, label-free approach to monitoring DNA structural changes via fluorescence signal readout that is tuned by PPIX binding and release. To illustrate it, we utilize PPIX and a G-rich DNA PS2.M to construct a fluorescent K(+) sensor based on an antiparallel-to-parallel conformation transition of the G-quadruplex. PS2.M adopts an antiparallel quadruplex structure in Na(+) solution, whereas it gradually converts into a parallel G-quadruplex upon addition of increasing K(+). This conformational change is indicated by a sharp increase in the fluorescence intensity of PPIX, owing to the good ability of PPIX to discriminate parallel G-quadruplexes from antiparallel ones. Even in the presence of 100 mM Na(+), such a "turn-on" fluorescent sensor can respond to low concentrations of K(+), with a limit of detection (0.5 mM) for K(+) analysis. In addition, this sensor exhibits a high selectivity for K(+) over other common metal ions, which ensures its practical applications to real samples. These results reveal that PPIX is promising for use as a specific DNA structural probe in sensing applications.

The folding of various intra- and intermolecular i-motif DNAs is systematically studied to expand the toolbox for the control of mechanical operations in DNA nanoarchitectures. We analyzed i-motif DNAs with two C-tracts under acidic conditions by gel electrophoresis, circular dichroism, and thermal denaturation and show that their intra- versus intermolecular folding primarily depends on the length of the C-tracts. Two stretches of six or fewer C-residues favor the intermolecular folding of i-motifs, whereas longer C-tracts promote the formation of intramolecular i-motif structures with unusually high thermal stability. We then introduced intra- and intermolecular i-motifs formed by DNAs containing two C-tracts into single-stranded regions within otherwise double-stranded DNA nanocircles. By adjusting the length of C-tracts we can control the intra- and intermolecular folding of i-motif DNAs and achieve programmable functionalization of dsDNA nanocircles. Single-stranded gaps in the nanocircle that are functionalized with an intramolecular i-motif enable the reversible contraction and extension of the DNA circle, as monitored by fluorescence quenching. Thereby, the nanocircle behaves as a proton-fueled DNA prototype machine. In contrast, nanorings containing intermolecular i-motifs induce the assembly of defined multicomponent DNA architectures in response to proton-triggered predicted structural changes, such as dimerization, "kiss", and cyclization. The resulting DNA nanostructures are verified by gel electrophoresis and visualized by atomic force microscopy, including different folding topologies of an intermolecular i-motif. The i-motif-functionalized DNA nanocircles may serve as a versatile tool for the formation of larger interlocked dsDNA nanostructures, like rotaxanes and catenanes, to achieve diverse mechanical operations.

Sonodynamic therapy (SDT) is noninvasive and possesses high bodypenetration depth, showing great potential for the treatment of deep-seated solid tumors. The efficacy of SDT, however, is limited by widespread hypoxia in solid tumors. Given this, an ultrasound-activated nanosystem is developed by integrating ferrate(VI) and protoporphyrin IX into biodegradable hollow mesoporous organosilica nanoplatforms, followed by assembling a phasechange material of lauric acid. The ferrate(VI) effectively reacts with water as well as overexpressed hydrogen peroxide and glutathione (GSH) in tumor cells, leading to tumor-microenvironment-independent oxygen production and in situ GSH depletion in tumors. More importantly, significant reactive oxygen species (ROS) overproduction is simultaneously achieved by protoporphyrin-augmented SDT and intracellular Fenton chemistry. Furthermore, the mild hyperthermia induced by ultrasound can trigger the phase change of lauric acid, achieving ultrasound-responsive control over the release of oxygen and ROS, and the depletion of GSH. The simultaneous oxygen generation, in situ GSH depletion, and ROS overproduction play a synergetic role in sensitizing SDT toward hypoxic solid tumors, which is verified by the remarkable improvement of hypoxic environments and more significant growth inhibition of SDT against osteosarcoma both in vitro and in vivo, showing promising application in hypoxic solid tumor treatment.

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