Quantification of the Na+/K+ ratio based on the different response of a newly identified G-quadruplex to Na+ and K+

Research Progress in Construction and Application of Enzyme-Based DNA Logic Gates

As a research hotspot in the field of information processing, DNA computing exhibits several important underlying characteristics-from parallel computing and low energy consumption to high-performance storage capabilities-thereby enabling its wide application in nanomachines, molecular encryption, biological detection, medical diagnosis, etc. Based on DNA computing, the most rapidly developed field focuses on DNA molecular logic-gates computing. In particular, the recent advances in enzyme-based DNA logic gates has emerged as ideal materials for constructing DNA logic gates. In this review, we explore protein enzymes that can manipulate DNA, especially, nicking enzymes and polymerases with high efficiency and specificity, which are widely used in constructing DNA logic gates, as well as ribozyme that can construct DNA logic gates following various mechanism with distinct biomaterials. Accordingly, the review highlights the characteristics and applications of various types of DNAzyme-based logic gates models, considering their future developments in information, biomedicine, chemistry, and computers.

Cy3 Cyanine Dye with Strong Fluorescence Enhancement for AGRO100 and Its Derivative

Nucleic acids, as important substances for biological inheritance, have attracted extensive attention in the biomedical field. More and more cyanine dyes are emerging as one of the probe tools for nucleic acid detection due to their excellent photophysical properties. Here, we discovered that the insertion of the AGRO100 sequence can specifically disrupt the twisted intramolecular charge transfer (TICT) mechanism of the trimethine cyanine dye (TCy3), resulting in a clear "turn-on" response. Moreover, the fluorescence enhancement of TCy3 combined with the T-rich AGRO100 derivative is more obvious. One explanation for the interaction between dT (deoxythymidine) and positively charged TCy3 may be that its outer layer carries the most negative charge. This study provides a theoretical basis for the use of TCy3 as a DNA probe, which has promising applications in the DNA detection of biological samples. It also provides the basis for the following construction of probes with specific ability for recognition.

A label-free G-quadruplex aptamer fluorescent aptasensor for visual and real-time kanamycin detection in lake and human samples

Antibiotic abuse is considered a serious problem affecting human health, necessitating that great attention be paid to explore robust, simple and sensitive methods for rapid evaluation. In this paper, we developed a fluorescent aptasensor for visual and real-time kanamycin detection by taking advantage of the label-free strategy based on H-aggregate disassembly of a chiral cyanine dye induced by a G-quadruplex aptamer. The good sensitivity and selectivity enabled this aptasensor to have a detection limit as low as 43 nM and have high specificity for kanamycin recognition. Furthermore, this assay was successfully applied for the detection of kanamycin in lake water and urine with excellent recoveries.

A label-free T4 polynucleotide kinase fluorescence sensor based on split dimeric G-quadruplex and ligation-induced dimeric G-quadruplex/thioflavin T conformation

The phosphorylation process of DNA by T4 polynucleotide kinase (T4 PNK) plays a crucial role in DNA recombination, DNA replication, and DNA repair. Traditional monomeric G-quadruplex (G4) systems are always activated by single cation such as K⁺ or Na⁺. The conformation transformation caused by the coexistence of multiple cations may interfere with the signal readout and limit their applications in physiological system. In view of the stability of dimeric G4 in multiple cation solution, we reported a label-free T4 PNK fluorescence sensor based on split dimeric G4 and ligation-induced dimeric G4/thioflavin T (ThT) conformation. The dimeric G4 was divided into two independent pieces of one normal monomeric G4 and the other monomeric G4 fragment phosphorylated by T4 PNK in order to decrease the background signal. With the introduction of template DNA, DNA ligase, and invasive DNA, the dimeric G4 could be generated and liberated to combine with ThT to show obvious fluorescence signal. Using our strategy, the linear range from 0.005 to 0.5 U mL^-1, and the detection limit of 0.0021 U mL^-1 could be achieved without the consideration of interference caused by the coexistence of multiple cations. Additionally, research in real sample determination and inhibition effect investigations indicated its further potential application value in biochemical process research and clinic diagnostics.

An increase in DNA G-quadruplex formation in acute myelocytic leukemia is detected by a supramolecular probe

Acute myeloid leukemia (AML) is a common acute leukemia in both adults and children, with poor early detection and diagnosis. Therefore, identifying new indicators for AML detection is significant for effective treatment. Here, we developed a supramolecular probe that exhibits high specificity and sensitivity to G-quadruplex structures in physiological buffer solution, chromosomes, and cells. Using this probe, we tested the DNA extracted from different types of cells and found that the DNA extracted from human acute myeloid leukemia cells HL-60 and KG-1 enhanced the probe fluorescence more significantly than the DNA extracted from other cells. This phenomenon may be related to a large number of G-quadruplexes in acute myeloid leukemia cells, implicating that G-quadruplex levels may be a potential indicator for the detection of acute myeloid leukemia.

Thioflavin T fluorescence and NMR spectroscopy suggesting a non-G-quadruplex structure for a sodium binding aptamer embedded in DNAzymes

Recently, a Na+-binding aptamer was reported to be embedded in a few RNA-cleaving DNAzymes, including NaA43, Ce13d, and NaH1. The Na+ aptamer consists of multiple GG stretches, which is a prerequisite for the formation of G-quadruplex (G4) structures. These DNAzymes require Na+ for activity but show no activity in the presence of K+ or other metal ions. Given that DNA can selectively bind K+ by forming a G4 structure, this work aims to answer whether this Na+ aptamer also uses a G4 to bind Na+. Through comparative ThT fluorescence spectrometry studies, while a control G4 DNA exhibited notable fluorescence enhancement up to 5 mM K+ with a Kd of 0.28 ± 0.06 mM, the Ce13d DNAzyme fluorescence was negligibly perturbed with similar concentrations of K+. Opposed to this, Ce13d displayed specific remarkable fluorescence decrease with low millimolar concentrations of Na+. NMR experiments at two different pH values suggest that Ce13d adopts a significantly different conformation or equilibrium of conformations in the presence of Na+ versus K+ and has a more stable structure in the presence of Na+. Additionally, absence of characteristic G4 peaks in one-dimensional 1H NMR suggest that G4 is not responsible for the Na+ binding. This hypothesis is confirmed by the absence of characteristic peaks in the CD spectra of this sequence. Therefore, we concluded that the aptamer must be selective for Na+ and that it binds Na+ using a structural element that does not contain G4.

Highly Selective Detection of K+ Based on a Dimerized G-Quadruplex DNAzyme

Potassium ion (K⁺) plays a crucial role in biological systems, such as maintaining cellular processes and causing diseases. However, specifically, the detection of K⁺ is extremely challenging because of the coexistence of the chemically similar ion of Na⁺ under physiological conditions. In this work, a K⁺ specific biosensor is constructed on the basis of a dimerized G-quadruplex (GQ) DNA, which is promoted by K⁺, and the enzymatic activity of the resulting DNAzyme depends on the concentration of the K⁺. The K⁺ in a 1-200 mM concentration range can be selectively detected by visual color, UV-Vis absorbance or fluorescence even if the concentration of the accompanying Na⁺ is up to 140 mM at an ambient condition up to 45 °C. In addition, this system can also be used to selectively detect NH₄⁺ in a 5-200 mM concentration range. This dimerized DNAzyme offers a new type of biosensor with a potential application in the biological system.

NMR structural study on the self-trimerization of d(GTTAGG) into a dynamic trimolecular G-quadruplex assembly preferentially in Na+ solution with a moderate K+ tolerance

Vast G-quadruplexes (GQs) are primarily folded by one, two, or four G-rich oligomers, rarely with an exception. Here, we present the first NMR solution structure of a trimolecular GQ (tri-GQ) that is solely assembled by the self-trimerization of d(GTTAGG), preferentially in Na⁺ solution tolerant to an equal amount of K⁺ cation. Eight guanines from three asymmetrically folded strands of d(GTTAGG) are organized into a two-tetrad core, which features a broken G-column and two width-irregular grooves. Fast strand exchanges on a timescale of second at 17°C spontaneously occur between folded tri-GQ and unfolded single-strand of d(GTTAGG) that both species coexist in dynamic equilibrium. Thus, this tri-GQ is not just simply a static assembly but rather a dynamic assembly. Moreover, another minor tetra-GQ that has putatively tetrameric (2+2) antiparallel topology becomes noticeable only at an extremely high strand concentration above 18 mM. The major tri-GQ and minor tetra-GQ are considered to be mutually related, and their reversible interconversion pathways are proposed accordingly. The sequence d(GTTAGG) could be regarded as either a reading frame shifted single repeat of human telomeric DNA or a 1.5 repeat of Bombyx mori telomeric DNA. Overall, our findings provide new insight into GQs and expect more functional applications.

A supramolecular aggregation-based constitutional dynamic network for information processing

Concepts and strategies offered by constitutional dynamic chemistry (CDC) hold great promise for designing molecular computing systems adaptive to external environments. Despite demonstrable success in storing and processing chemical information using CDC, further employment of such constitutional dynamic networks (CDNs) for processing more complex digital information has not been realized yet. Herein, we introduced a supramolecular CDN based on the aggregation of cyanine MTC (Agg-CDN), which is composed of four reversibly interconvertible constituents, i.e. monomers, dimers, J-aggregates, and H-aggregates. We demonstrated that the equilibrated Agg-CDN is reconfigurable through constituent exchange in response to well-defined chemical inputs. More importantly, the equilibrated states of the Agg-CDN are spectroscopically distinguishable because of the unique optical properties of MTC. We further tuned the Agg-CDN to at least nine unique states for transforming the chemical inputs into digital outputs, and successfully employed it for encoding and encrypting complex digital information, such as multi-pixel images.

We constructed a supramolecular cyanine MTC aggregation-based constitutional dynamic network, which can transform the chemical information into image information reversibly.

Direct detection of potassium and lead (II) ions based on assembly-disassembly of a chiral cyanine dye /TBA complex

A highly selective and sensitive direct detection of potassium (K⁺) and lead (Pb²⁺) ions was developed by using the assembly and disassembly of a chiral cyanine dye/TBA complex. The dye DMSB (3-ethyl-2-[3-(3-ethyl-3H-benzoselenazol-2-ylidene)-2-methylprop-1-enyl] benzoselenazolium bromide) loses the ability of self-assembly, but it can be activated by thrombin-binding aptamer (TBA) G-quadruplex structure. And only the TBA G-quadruplex formed in the presence of K⁺, can strongly induce J-aggregate signals of DMSB. Because the Pb²⁺ ions can bind and stabilize the TBA G-quadruplex with much higher efficiency than K⁺, the J-aggregate signals of DMSB falls sharply when the Pb²⁺ is present. As a result, the assembly and disassembly of DMSB allows the selective detection of 10 μM K⁺ and 20 nM Pb²⁺ respectively, even the competitive sodium ion (Na⁺) was as high as 145 mM. The linear correlation existed between the J-aggregate intensity and the concentration of K⁺ and Pb²⁺ over the range of 0.5-5.0 mM and 200-2000 nM, respectively. Moreover, the concentration of K⁺ (∼3 mM) and Pb²⁺ (below 20 nM) in human blood serum samples were determined by the present method, which agreed well with inductively coupled plasma mass spectrometry (ICP-MS). This work not only opens a door for the further development of G-quadruplex-based aptasensor in complex real system, but also provides a simple and versatile sensing platform for ion detection in clinic.

Spontaneous formation and reversible transformation between achiral J- and chiral H-aggregates of cyanine dye MTC

Chirality at a supramolecular level is currently attracting great attention attributed to rapid developments in supramolecular chemistry. Herein, we report a new type of chiral self-assembly based on the cyanine dye MTC. The chiral H-aggregates of MTC could form spontaneously from achiral J-aggregates, and could return back to achiral J-aggregates in high concentration on increasing the solution temperature.

Spontaneous transformation from achiral J-aggregates to chiral H-aggregates of cyanine dye MTC was investigated.

G-Quadruplexes as An Alternative Recognition Element in Disease-Related Target Sensing

G-quadruplexes are made up of guanine-rich RNA and DNA sequences capable of forming noncanonical nucleic acid secondary structures. The base-specific sterical configuration of G-quadruplexes allows the stacked G-tetrads to bind certain planar molecules like hemin (iron (III)-protoporphyrin IX) to regulate enzymatic-like functions such as peroxidase-mimicking activity, hence the use of the term DNAzyme/RNAzyme. This ability has been widely touted as a suitable substitute to conventional enzymatic reporter systems in diagnostics. This review will provide a brief overview of the G-quadruplex architecture as well as the many forms of reporter systems ranging from absorbance to luminescence readouts in various platforms. Furthermore, some challenges and improvements that have been introduced to improve the application of G-quadruplex in diagnostics will be highlighted. As the field of diagnostics has evolved to apply different detection systems, the need for alternative reporter systems such as G-quadruplexes is also paramount.

Recent Progress in Fluorescence Signal Design for DNA-Based Logic Circuits

DNA-based logic circuits, encoding algorithms in DNA and processing information, are pushing the frontiers of molecular computers forward, owing to DNA's advantages of stability, accessibility, manipulability, and especially inherent biological significance and potential medical application. In recent years, numerous logic functions, from arithmetic to nonarithmetic, have been realized based on DNA. However, DNA can barely provide a detectable signal by itself, so that the DNA-based circuits depend on extrinsic signal actuators. The signal strategy of carrying out a response is becoming one of the design focuses in DNA-based logic circuit construction. Although work on sequence and structure design for DNA-based circuits has been well reviewed, the strategy on signal production lacks comprehensive summary. In this review, we focused on the latest designs of fluorescent output for DNA-based logic circuits. Several basic strategies are summarized and a few designs for developing multi-output systems are provided. Finally, some current difficulties and possible opportunities were also discussed.

Electrochemical aptasensor based on a potassium ion-triggered DNA conformation transition and self-assembly on an electrode

A sensitive and selective electrochemical aptasensor was developed for the detection of potassium ions based on a simple sensing principle and straightforward operation.

Reversible regulation of the supramolecular chirality of a cyanine dye by using the G-quadruplex structure as a template

Multiple cycle regulation of the supramolecular chirality of a cyanine dye has been successfully achieved by using DNA G-quadruplexes as templates, which is easily controllable by repeated addition of Ag(+) and cysteine (Cys). This work provides an easy and controllable strategy for the chiral regulation of supramolecules.

A benzindole substituted carbazole cyanine dye: a novel targeting fluorescent probe for parallel c-myc G-quadruplexes

Many organic ligands were synthesized to recognize G-quadruplexes. However, different kinds of G-quadruplexes (G4s) possess different structures and functions. Therefore, selective recognition of certain types of G4s is important for the study of G4s. In this paper, a novel cyanine dye, 3-(2-(4-vinylpyridine))-6-(2-((1-(4-sulfobutyl))-3,3-dimethyl-2-vinylbenz[e]indole)-9-ethyl-carbazole (9E PBIC), composed of benzindole and carbazole was designed and synthesised. The studies on UV-vis and fluorescence properties of the dye with different DNA forms showed that the dye exhibits almost no fluorescence under aqueous buffer conditions, but it increased over 100 fold in the presence of c-myc G4 and 10-30 fold in the presence of other G4s, while little in the presence of single/double-stranded DNA, indicating that it has excellent selectivity to c-myc 2345 G4. For the binding studies the dye is interacted with the c-myc 2345 G-quadruplex by using the end-stack binding model. It can be said that the dye is an excellent targeting fluorescent probe for c-myc G-quadruplexes.

G-quadruplex induced chirality of methylazacalix[6]pyridine via unprecedented binding stoichiometry: en route to multiplex controlled molecular switch

Nucleic acid based molecular device is a developing research field which attracts great interests in material for building machinelike nanodevices. G-quadruplex, as a new type of DNA secondary structures, can be harnessed to construct molecular device owing to its rich structural polymorphism. Herein, we developed a switching system based on G-quadruplexes and methylazacalix[6]pyridine (MACP6). The induced circular dichroism (CD) signal of MACP6 was used to monitor the switch controlled by temperature or pH value. Furthermore, the CD titration, Job-plot, variable temperature CD and ¹H-NMR experiments not only confirmed the binding mode between MACP6 and G-quadruplex, but also explained the difference switching effect of MACP6 and various G-quadruplexes. The established strategy has the potential to be used as the chiral probe for specific G-quadruplex recognition.

A supramolecular probe for colorimetric detection of Pb2+ based on recognition of G-quadruplex

A colorimetric probe of Pb²⁺ has been designed based on the mechanism that a supramolecular probe selectively recognized the Pb²⁺-induced conformational transition of G-quadruplexes.

Targeting of parallel c-myc G-quadruplex by dimeric cyanine dye supramolecular assembly: dependence on the linker length

The recognizing ability of parallel c-myc G-quadruplex by dimeric cyanine dyes depends on their linker length.

Visual detection of mercury(ii) based on recognition of the G-quadruplex conformational transition by a cyanine dye supramolecule

Visual detection of mercury(ii) based on recognition of the G-quadruplex conformational transition by a cyanine dye supramolecule is reported.

Microwave-assisted synthesis of arene ruthenium(ii) complexes [(η6-RC6H5)Ru(m-MOPIP)Cl]Cl (R = -H and -CH3) as groove binder to c-myc G4 DNA

Two arene Ru(ii) complexes are prepared under microwave irradiation and display application potential as small molecule inhibitors of c-myc G4 DNA.