G-quadruplexes for luminescent sensing and logic gates

Programmable DNA Templates for Silver Nanoclusters Synthesis To Develop On-Demand FRET Aptasensor

DNA-templated silver nanoclusters (AgNCs-DNA) can be synthesized via a one-pot method bypassing the tedious process of biomolecular labeling. Appending an aptamer to DNA templates results in dual-functionalized DNA strands that can be utilized for synthesizing aptamer-modified AgNCs, thereby enabling the development of label-free fluorescence aptasensors. However, a major challenge lies in the necessity to redesign the dual-functionalized DNA strand for each specific target, thus increasing the complexity and hindering widespread application of these aptasensors. To overcome this challenge, we designed six DNA strands (DNA1-DNA6) that incorporate the templates for AgNCs synthesis and A4-linker for further aptamer coupling. Among all the synthesized AgNCs-DNA samples, it was found that both AgNCs-DNA1 and AgNCs-DNA2 stood out for their excellent long-term stability. After capturing the T4-linker that connected with aptamer1 specific for aflatoxin B1 (AFB1), however, we found that only AgNCs-DNA1/aptamer1 maintained excellent long-term stability. This finding highlighted the potential of AgNCs-DNA1 as a versatile label-free fluorescence probe for the development of on-demand fluorescence aptasensors. To emphasize its benefits in aptasensing applications, we utilized AgNCs-DNA1/aptamer1 as the fluorescence probe and MoS2 nanosheets as the quencher to develop a FRET aptasensor for AFB1 detection. This aptasensor demonstrated remarkable sensitivity, enabling the detection of AFB1 within a wide concentration range of 0.03-120 ng/mL, with a limit of detection as low as 3.6 pg/mL (S/N = 3). The versatility of the aptasensor has been validated through the recognition of diverse targets, employing aptamer2 specific for ochratoxin A and aptamer3 specific for zearalenone, thereby showcasing its extensive applicability for on-demand detection. The universal applicability of this aptasensor holds great promise for future applications in diverse fields including food safety, environmental monitoring, and clinical diagnosis.

Unique development of a new dual application probe for selective detection of antiparallel G-quadruplex sequences

G-Quadruplex (G4) structures play vital roles in many biological processes; consequently, they have been implicated in various human diseases like cancer, Alzheimer's disease etc. The selective detection of G4 DNA structures is of great interest for understanding their roles and biological functions. Hence, development of multifunctional fluorescent probes is indeed essential. In this investigation, we have synthesized a quinolinium based dual application probe (QnMF) that presents molecular rotor properties. This dual application molecular rotor is able to detect selectively antiparallel G4 sequences (22AG in 100 mM NaCl) through a turn-on response over other G4 topologies. The QnMF also contains a distinct fluorine-19 that undergoes a significant chemical shift in response to microenvironmental changes around the molecule when bound to G4 structures. The probe QnMF exhibits significantly brighter fluorescence emissions in glycerol (ε × ϕ = 2800 cm-1 M-1) and relatively less brighter fluorescence emissions in methanol (ε × ϕ = 40.5 cm-1 M-1). The restricted rotation inherent property of the QnMF molecular rotor is responsible for brighter fluorescence and leads to enhancement in the fluorescence upon binding to the G4 structure. Overall, the probe's dual detection method makes it useful for monitoring the G4 structures that are abundant and plays a vital role in living organisms.

Parallel G-Quadruplex DNA Structures from Nuclear and Mitochondrial Genomes Trigger Emission Enhancement in a Nonfluorescent Nano-aggregated Fluorine-Boron-Based Dye

Molecular self-assembly is a powerful tool for the development of functional nanostructures with adaptive optical properties. However, in aqueous solution, the hydrophobic effects in the monomeric units often afford supramolecular architectures with typical side-by-side π-stacking arrangement with compromised emissive properties. Here, we report on the role of parallel DNA guanine quadruplexes (G4s) as supramolecular disaggregating-capture systems capable of coordinating a zwitterionic fluorine-boron-based dye and promoting activation of its fluorescence signal. The dye's high binding affinity for parallel G4s compared to nonparallel topologies leads to a selective disassembly of the dye's supramolecular state upon contact with parallel G4s. This results in a strong and selective disaggregation-induced emission that signals the presence of parallel G4s observable by the naked eye and inside cells. The molecular recognition strategy reported here will be useful for a multitude of affinity-based applications with potential in sensing and imaging systems.

G-wire-based self-quenched fluorescence probe combining with target-activated isothermal cascade amplification for ultrasensitive microRNA detection

Herein, we reported the G-wire-based self-quenched fluorescence probe and its application in ultrasensitive microRNA (miRNA) detection by combining with target-activated isothermal cascade amplification. The terminal-single-fluorescein (FAM)-labeled G-rich oligonucletides self-assembled into G-wire nanostructures (G-wires) with K⁺ and Mg²⁺. Thereafter, the G-wires brought terminal-labeled FAM into close proximity, as a result, the self-quenched signal probe formed. Besides, when there was the target miRNA, target-activated isothermal cascade amplification converted miRNA into the copious trigger DNA. After hybridization between trigger DNA and the self-quenched probe, the G-wires were splited and forced the apart of proximate FAM, and then the self-quenched probe displayed an "on" mechanism. Therefore, the approach gave a limit of detection (LOM) of 0.82 aM to miRNA-21 and could be implemented within a wide linear range of 2 aM to 2 nM. This approach was able to distinguish the single-mismatched miRNA-21, which was selective and sensitive in detecting human spiked serum samples.

Single-molecule displacement assay reveals strong binding of polyvalent dendrimer ligands to telomeric G-quadruplex

Binding between a ligand and a receptor is a fundamental step in many natural or synthetic processes. In biosensing, a tight binding with a small dissociation constant (Kd) between the probe and analyte can lead to superior specificity and sensitivity. Owing to their capability of evaluating competitors, displacement assays have been used to estimate Kd at the ensemble average level. At the more sensitive single-molecule level, displacement assays are yet to be established. Here, we developed a single-molecule displacement assay (smDA) in an optical tweezers instrument and used this innovation to evaluate the binding of the L2H2-6OTD ligands to human telomeric DNA G-quadruplexes. After measuring Kd of linear and dendrimer L2H2-6OTD ligands, we found that dendrimer ligands have enhanced binding affinity to the G-quadruplexes due to their polyvalent geometry. This increased binding affinity enhanced inhibition of telomerase elongation on a telomere template in a Telomerase Repeated Amplification Protocol (TRAP). Our experiments demonstrate that the smDA approach can efficiently evaluate binding processes in chemical and biological processes.

Regulating Spatial Localization and Reactivity Biasness of DNAzymes by Metal Ions and Oligonucleotides

Chemical gradient sensing behavior of catalytically active colloids and enzymes is an area of immense interest owing to their importance in understanding fundamental spatiotemporal complexity pattern in living systems and designing of dynamic materials. Herein, we have shown peroxidase activity of DNAzyme (G-quadruplex-hemin complex tagged in a micron-sized glass bead) can be modulated by metal ions and metal ion-binding oligonucleotides. Next we demonstrated both experimentally and theoretically that the localization and product formation ability of the DNAzyme containing particle remains biased to the more catalytically active zone where concentration of metal ion (Hg2+) inhibitor is low. Interestingly, this biased localization can be broken by introduction of Hg2+ binding oligonucleotide in the system. Additionally, macroscopically asymmetric catalytic product distributed zone has also been achieved on this process, showing possibility in regulation in autonomous spatially controlled chemical process. This demonstration of autonomous modulation of the localization pattern and spatially specific enhanced product forming ability of DNAzymes will further enable in designing of responsive nucleic acid-based motile materials and surfaces.

Differential interaction of Fluorescein-β-cyclodextrin conjugate to quadruplex kit22 DNA: Inclusion of Berberine and modulation of binding

Clinical applicability of G-quadruplexes as anticancer drugs is an area of current interest. Identification of supramolecular systems for selective targeting G-quartets is particularly intriguing. In this work, the DNA binder Berberine is encapsulated inside the molecular cavity of the synthesised host structure, Fluoresecein-β-cyclodextrin conjugate. The host: guest complex is characterized and the mode of binding is optimized using two dimensional rotating-frame Overhauser effect spectroscopy. The conjugate is examined for its binding to quadruplex DNAs viz., kit22, myc22, telo24 and the duplex calf-thymus DNA before and after Berberine encapsulation. UV-vis and fluorescence spectroscopic methods were employed to determine the strength of binding of the complex with the DNAs. The binding strength and the stoichiometry of the host: guest complex are 1.9 × 10⁶ mol^-1 dm³ and 1:1, respectively. A quenching of fluorescence of the quadruplex kit22 and duplex ctDNA is observed on binding to the Fluorescein-β-cyclodextrin conjugate. The quadruplexes of myc22 and telo24 display an enhanced fluorescence on binding to the modified cyclodextrin. The Stern-Volmer quenching constants are 1.4 × 10⁶ mol^-1 dm³ and 3.8 × 10⁵ mol^-1 dm³ for binding to kit22 and ctDNA respectively. kit22 shows a different emission profile on interacting with the Berberine encapsulated conjugate, whereas all the other quadruplexes and duplex exhibit similar emission profiles. The results indicate a variation in the binding mode and strength of the ligand-quadruplexes and depend on the conformation of the quadruplexes.Communicated by Ramaswamy H. Sarma.

A fluorescent molecular rotor for the selective detection of the hybrid-conformation 22AG G-Quadruplex

G-quadruplex (G4) DNA plays a vital role in myriad biological process and is linked to several human diseases, including Alzheimer's disease. Probing G4s with fluorescent probes can provide a better understanding their mechanisms of action and of their roles in Nature. In this study we developed a quinolinium-vinylaniline molecular rotor probe, featuring a diethylaminosalicylaldehyde unit that could discriminate the hybrid-22AG G4 sequence selectively amongst other G4 sequences. This probe underwent a significant red-shift upon binding to the target G4 (broad 575 nm → sharp 630 nm) with enhanced fluorescence (up to 14-fold). We suspect that the vinylaniline unit of the molecular rotor, when bound to the hybrid-22 A G4, experienced restricted rotation, thereby undergoing enhanced intramolecular charge transfer. The presence of the diethylaminosalicylaldehyde moiety appeared to play a major role in the enhanced selectivity toward the 22AG G4.

Light-Induced Modulation of Chiral Functions in G-Quadruplex-Photochrome Systems

The design of artificially engineered chiral structures has received much attention, but the implementation of dynamic functions to modulate the chiroptical response of the systems is less explored. Here, we present a light-responsive G-quadruplex (G4)-based assembly in which chirality enrichment is induced, tuned, and fueled by molecular switches. In particular, the mirror-image dependence on photoactivated azo molecules, undergoing trans-to-cis isomerization, shows chiral recognition effects on the inherent flexibility and conformational diversity of DNA G4s having distinct handedness (right- and left-handed). Through a detailed experimental and computational analysis, we bring compelling evidence on the binding mode of the photochromes on G4s, and we rationalize the origin of the chirality effect that is associated with the complexation event.

Porphyrin Binding and Irradiation Promote G-Quadruplex DNA Dimeric Structure

Nucleic acid sequences rich in guanines can organize into noncanonical DNA G-quadruplexes (G4s) of variable size. The design of small molecules stabilizing the structure of G4s is a rapidly growing area for the development of novel anticancer therapeutic strategies and bottom-up nanotechnologies. Among a multitude of binders, porphyrins are very attractive due to their light activation that can make them valuable conformational regulators of G4s. Here, a structure-based strategy, integrating complementary probes, is employed to study the interaction between TMPyP4 porphyrin and a 22-base human telomeric sequence (Tel22) before and after irradiation with blue light. Porphyrin binding is discovered to promote Tel22 dimerization, while light irradiation of the Tel22-TMPyP4 complex controls dimer fraction. Such a change in quaternary structure is found to be strictly correlated with modifications at the secondary structure level, thus providing an unprecedented link between the degree of dimerization and the underlying conformational changes in G4s.

Beyond small molecules: targeting G-quadruplex structures with oligonucleotides and their analogues

G-Quadruplexes (G4s) are widely studied secondary DNA/RNA structures, naturally occurring when G-rich sequences are present. The strategic localization of G4s in genome areas of crucial importance, such as proto-oncogenes and telomeres, entails fundamental implications in terms of gene expression regulation and other important biological processes. Although thousands of small molecules capable to induce G4 stabilization have been reported over the past 20 years, approaches based on the hybridization of a synthetic probe, allowing sequence-specific G4-recognition and targeting are still rather limited. In this review, after introducing important general notions about G4s, we aim to list, explain and critically analyse in more detail the principal approaches available to target G4s by using oligonucleotides and synthetic analogues such as Locked Nucleic Acids (LNAs) and Peptide Nucleic Acids (PNAs), reporting on the most relevant examples described in literature to date.

Ruthenium(II) Complex-Based G-quadruplex DNA Selective Luminescent 'Light-up' Probe for RNase H Activity Detection

A bis-heteroleptic ruthenium(II) complex, 1[PF₆ ]₂ of benzothiazole amide substituted 2,2'-bipyridine ligand (bmbbipy) has been synthesized for the selective detection of G-quadruplex (GQ) DNA and luminescence-assay-based RNase H activity monitoring. Compound 1[PF₆ ]₂ exhibited aggregation-caused quenching (ACQ) in water. Aggregate formation was supported by DLS, UV-vis, and ¹ H NMR spectroscopy results, and the morphology of aggregated particles was witnessed by SEM and TEM. 1[PF₆ ]₂ acted as an efficient GQ DNA-selective luminescent light-up probe over single-stranded and double-stranded DNA. The competency of 1[PF₆ ]₂ for selective GQ structure detection was established by PL and CD spectroscopy. For 1[PF₆ ]₂ , the PL light-up is exclusively due to the rigidification of the benzothiazole amide side arm in the presence of GQ-DNA. The interaction between the probe and GQ-DNA was analyzed by molecular docking analysis. The GQ structure detection capability of 1[PF₆ ]₂ was further applied in the luminescent 'off-on' RNase H activity detection. The assay utilized an RNA:DNA hybrid, obtained from 22AG2-RNA and 22AG2-DNA sequences. RNase H solely hydrolyzed the RNA of the RNA:DNA duplex and released G-rich 22AG2-DNA, which was detected via the PL enhancement of 1[PF₆ ]₂ . The selectivity of RNase H activity detection over various other restriction enzymes was also demonstrated.

The Construction of DNA Logic Gates Restricted to Certain Live Cells Based on the Structure Programmability and Aptamer-Cell Affinity of G-Quadruplexes

DNA computation is considered a fascinating alternative to silicon-based computers; it has evoked substantial attention and made rapid advances. Besides realizing versatile functions, implementing spatiotemporal control of logic operations, especially at the cellular level, is also of great significance to the development of DNA computation. However, developing simple and efficient methods to restrict DNA logic gates performing in live cells is still a challenge. In this work, a series of DNA logic gates was designed by taking full advantage of the diversity and programmability of the G-quadruplex (G4) structure. More importantly, by further using the high affinity and specific endocytosis of cells to aptamer G4, an INHIBIT logic gate has been realized whose operational site is precisely restricted to specific live cells. The design strategy might have great potential in the field of molecular computation and smart bio-applications.

c-Myc G-quadruplex is sensitively and specifically recognized by a fluorescent probe

The G-quadruplex structure formed by the c-myc gene sequence has attracted much attention due to its important physiological function in biology and wide application in nanotechnology. So far, probes capable of recognition of c-myc G-quadruplex with both high specificity and sensitivity are still scarce. This work presented a cyanine dye fluorescent probe named Cy-1, which has almost no fluorescence in aqueous solution, but showing more than 1000-fold fluorescence enhancement for recognizing c-myc G-quadruplex. Cy-1 also has good specificity and can selectively recognize c-myc G-quadruplex from other a variety of G-quadruplex and non-G-quadruplex structures. These properties make Cy-1 a promising probe for c-myc G-quadruplex recognition in nanotechnology or biology.

Loop-mediated fluorescent probes for selective discrimination of parallel and antiparallel G-Quadruplexes

Herein we report simple pyridinium (1-3) and quinolinium (4) salts for the selective recognition of G-quadruplexes (G4s). Among them, the probe 1, interestingly, selectively discriminated parallel (c-KIT-1, c-KIT-2, c-MYC) G4s from anti-parallel/hybrid (22AG, HRAS-1, BOM-17, TBA) G4s at pH 7.2, through a switch on response in the far-red window. Significant changes in the absorption (broad 575 nm → sharp 505 nm) and emission of probe 1 at 620 nm, attributed to selective interaction with parallel G4s, resulted in complete disaggregation-induced monomer emission. Symmetrical push/pull molecular confinements across the styryl units in probe 1 enhanced the intramolecular charge transfer (ICT) by restricting the free rotation of CC units in the presence of sterically less hindered and highly accessible G4 surface/bottom tetrads in the parallel G4s, which is relatively lower extent in antiparallel/hybrid G4s. We confirm that the disaggregation of probe 1 was very effective in the presence of parallel G4-forming ODNs, due to the presence of highly available free surface area, resulting in additional π-stacking interactions. The selective sensing capabilities of probe 1 were analyzed using UV-Vis spectroscopy, fluorescence spectroscopy, molecular dynamics (MD)-based simulation studies, and ¹H NMR spectroscopy. This study should afford insights for the future design of selective compounds targeting parallel G4s.

The Molecular Tête-à-Tête between G-Quadruplexes and the i-motif in the Human Genome

G-Quadruplex (GQ) and i-motif structures are the paradigmatic examples of nonclassical tetrastranded nucleic acids having multifarious biological functions and widespread applications in therapeutics and material science. Recently, tetraplexes emerged as promising anticancer targets due to their structural robustness, gene-regulatory roles, and predominant distribution at specific loci of oncogenes. However, it is arguable whether the i-motif evolves in the complementary single-stranded region after GQ formation in its opposite strand and vice versa. In this review, we address the prerequisites and significance of the simultaneous and/or mutually exclusive formation of GQ and i-motif structures at complementary and sequential positions in duplexes in the cellular milieu. We discussed how their dynamic interplay Sets up cellular homeostasis and exacerbates carcinogenesis. The review gives insights into the spatiotemporal formation of GQ and i-motifs that could be harnessed to design different types of reporter systems and diagnostic platforms for potential bioanalytical and therapeutic intervention.

Molecular Rotors as Guest Fluorophores Probing the Local Environment inside Host G4 Supramolecular Hydrogels

Fluorescent molecular rotors with a high binding affinity toward the guanosine quartet (G4) were incorporated as guest fluorophores into host supramolecular hydrogels based on the self-assembly of G4 units, to probe the local environment. Torsional dynamics of the rotors were severely inhibited inside the hydrogels in comparison with aqueous solutions, although the hydrogels were composed of >95% water. Moreover, even though all the gels were rigid bodies with no spontaneous deformation or flow property at room temperature, torsional dynamics in G4 borate gels was found to be consistently several orders of magnitude slower than those in the other G4 gels, irrespective of the identity of the molecular rotor probe. This clear difference in the molecular mobilities of the guest fluorophore could be attributed to systematic differences in the internal structure between the two categories of host G4 hydrogels. In specific terms, the borate groups in G4 borate hydrogels serve as bridging units between separate G4 quadruplex strands, generating additional cross-links that reinforce the network structure of the gel. The results demonstrate that molecular rotors act as efficient fluorescent probes for the quantitative assessment of the molecular-level environment and dynamics inside the hydrogels, an aspect that is missed out by most other analytical methods that are routinely employed for studying them.

FRET-MC: A fluorescence melting competition assay for studying G4 structures in vitro

G-quadruplexes (G4) play crucial roles in biology, analytical chemistry and nanotechnology. The stability of G4 structures is impacted by the number of G-quartets, the length and positions of loops, flanking motifs, as well as additional structural elements such as bulges, capping base pairs, or triads. Algorithms such as G4Hunter or Quadparser may predict if a given sequence is G4-prone by calculating a quadruplex propensity score; however, experimental validation is still required. We previously demonstrated that this validation is not always straightforward, and that a combination of techniques is often required to unambiguously establish whether a sequence forms a G-quadruplex or not. In this article, we adapted the well-known FRET-melting assay to characterize G4 in batch, where the sequence to be tested is added, as an unlabeled competitor, to a system composed of a dual-labeled probe (F21T) and a specific quadruplex ligand. PhenDC3 was preferred over TMPyP4 because of its better selectivity for G-quadruplexes. In this so-called FRET-MC (melting competition) assay, G4-forming competitors lead to a marked decrease of the ligand-induced stabilization effect (∆T_m ), while non-specific competitors (e.g., single- or double-stranded sequences) have little effect. Sixty-five known sequences with different typical secondary structures were used to validate the assay, which was subsequently employed to assess eight novel sequences that were not previously characterized.

Specific recognition of telomeric multimeric G-quadruplexes by a simple-structure quinoline derivative

The development of highly sensitive fluorescence probes for telomeric multimeric G-quadruplexes has attracted extensive attention. However, few probes reported have exhibited selectivity for telomeric multimeric G-quadruplexes. Thus, it is challenging to design fluorescence probes with high specificity and selectivity for telomeric multimeric G-quadruplexes. This study employed a commercially available quinoline derivative BEPQ-1 as an effective switch-on sensor for telomeric multimeric G-quadruplexes. The fluorescence intensity enhanced more than 20 folds upon the addition of telomeric multimeric G-quadruplexes. This probe exhibited good selectivity and sensitivity for telomeric multimeric G-quadruplexes. And the detection limit of BEPQ-1 for the telomeric multimeric G-quadruplex TTA45 was calculated to be 0.11 μM. The distinctive feature of BEPQ-1 is the simple structure and small size. In the light of binding mode, BEPQ-1 could even simultaneously bind to the end two G-quartets of the two adjacent G-quadruplex units in telomeric multimeric G-quadruplex by π-π stacking. To our knowledge, this is the first simple-structure fluorescence probe for telomeric multimeric G-quadruplex. This finding might provide a strategy to design specific probes for telomeric multimeric G-quadruplexes and contribute to understand the structures and functions of G-quadruplexes in the telomere region.

DNA logic circuits based on FokI enzyme regulation

A series of DNA logic devices was constructed based on the allosteric strategy of the enzyme-assisted cleavage regulation system, which are simple in scale, modular, and work efficiently.

A DNA Switch for Detecting Single Nucleotide Polymorphism within a Long DNA Sequence Under Denaturing Conditions

DNA detection is usually conducted under nondenaturing conditions to favor the formation of Watson-Crick base-paring interactions. However, although such a setting is excellent for distinguishing a single-nucleotide polymorphism (SNP) within short DNA sequences (15-25 nucleotides), it does not offer a good solution to SNP detection within much longer sequences. Here we report on a new detection method capable of detecting SNP in a DNA sequence containing 35-90 nucleotides. This is achieved through incorporating into the recognition DNA sequence a previously discovered DNA molecule that forms a stable G-quadruplex in the presence of 7 molar urea, a known condition for denaturing DNA structures. The systems are configured to produce both colorimetric and fluorescent signals upon target binding.

Impact of the Position of the Chemically Modified 5-Furyl-2'-Deoxyuridine Nucleoside on the Thrombin DNA Aptamer-Protein Complex: Structural Insights into Aptamer Response from MD Simulations

Aptamers are functional nucleic acids that bind to a range of targets (small molecules, proteins or cells) with a high affinity and specificity. Chemically-modified aptamers are of interest because the incorporation of novel nucleobase components can enhance aptamer binding to target proteins, while fluorescent base analogues permit the design of functional aptasensors that signal target binding. However, since optimally modified nucleoside designs have yet to be identified, information about how to fine tune aptamer stability and target binding affinity is required. The present work uses molecular dynamics (MD) simulations to investigate modifications to the prototypical thrombin-binding aptamer (TBA), which is a 15-mer DNA sequence that folds into a G-quadruplex structure connected by two TT loops and one TGT loop. Specifically, we modeled a previously synthesized thymine (T) analog, namely 5-furyl-2′-deoxyuridine (5FurU), into each of the six aptamer locations occupied by a thymine base in the TT or TGT loops of unbound and thrombin bound TBA. This modification and aptamer combination were chosen as a proof-of-principle because previous experimental studies have shown that TBA displays emissive sensitivity to target binding based on the local environment polarity at different 5FurU modification sites. Our simulations reveal that the chemically-modified base imparts noticeable structural changes to the aptamer without affecting the global conformation. Depending on the modification site, 5FurU performance is altered due to changes in the local environment, including the modification site structural dynamics, degree of solvent exposure, stacking with neighboring bases, and interactions with thrombin. Most importantly, these changes directly correlate with the experimentally-observed differences in the stability, binding affinity and emissive response of the modified aptamers. Therefore, the computational protocols implemented in the present work can be used in subsequent studies in a predictive way to aid the fine tuning of aptamer target recognition for use as biosensors (aptasensors) and/or therapeutics.

Identification of optimal fluorescent probes for G-quadruplex nucleic acids through systematic exploration of mono- and distyryl dye libraries

A library of 52 distyryl and 9 mono-styryl cationic dyes was synthesized and investigated with respect to their optical properties, propensity to aggregation in aqueous medium, and capacity to serve as fluorescence “light-up” probes for G-quadruplex (G4) DNA and RNA structures. Among the 61 compounds, 57 dyes showed preferential enhancement of fluorescence intensity in the presence of one or another G4-DNA or RNA structure, while no dye displayed preferential response to double-stranded DNA or single-stranded RNA analytes employed at equivalent nucleotide concentration. Thus, preferential fluorimetric response towards G4 structures appears to be a common feature of mono- and distyryl dyes, including long-known mono-styryl dyes used as mitochondrial probes or protein stains. However, the magnitude of the G4-induced “light-up” effect varies drastically, as a function of both the molecular structure of the dyes and the nature or topology of G4 analytes. Although our results do not allow to formulate comprehensive structure–properties relationships, we identified several structural motifs, such as indole- or pyrrole-substituted distyryl dyes, as well as simple mono-stryryl dyes such as DASPMI [2-(4-(dimethylamino)styryl)-1-methylpyridinium iodide] or its 4-isomer, as optimal fluorescent light-up probes characterized by high fluorimetric response (I/I₀ of up to 550-fold), excellent selectivity with respect to double-stranded DNA or single-stranded RNA controls, high quantum yield in the presence of G4 analytes (up to 0.32), large Stokes shift (up to 150 nm) and, in certain cases, structural selectivity with respect to one or another G4 folding topology. These dyes can be considered as promising G4-responsive sensors for in vitro or imaging applications. As a possible application, we implemented a simple two-dye fluorimetric assay allowing rapid topological classification of G4-DNA structures.

Metadevices with Potential Practical Applications

Metamaterials are "new materials" with different superior physical properties, which have generated great interest and become popular in scientific research. Various designs and functional devices using metamaterials have formed a new academic world. The application concept of metamaterial is based on designing diverse physical structures that can break through the limitations of traditional optical materials and composites to achieve extraordinary material functions. Therefore, metadevices have been widely studied by the academic community recently. Using the properties of metamaterials, many functional metadevices have been well investigated and further optimized. In this article, different metamaterial structures with varying functions are reviewed, and their working mechanisms and applications are summarized, which are near-field energy transfer devices, metamaterial mirrors, metamaterial biosensors, and quantum-cascade detectors. The development of metamaterials indicates that new materials will become an important breakthrough point and building blocks for new research domains, and therefore they will trigger more practical and wide applications in the future.

Fabrication of Electrochemical-Based Bioelectronic Device and Biosensor Composed of Biomaterial-Nanomaterial Hybrid

The field of bioelectronics has paved the way for the development of biochips, biomedical devices, biosensors and biocomputation devices. Various biosensors and biomedical devices have been developed to commercialize laboratory products and transform them into industry products in the clinical, pharmaceutical, environmental fields. Recently, the electrochemical bioelectronic devices that mimicked the functionality of living organisms in nature were applied to the use of bioelectronics device and biosensors. In particular, the electrochemical-based bioelectronic devices and biosensors composed of biomolecule-nanoparticle hybrids have been proposed to generate new functionality as alternatives to silicon-based electronic computation devices, such as information storage, process, computations and detection. In this chapter, we described the recent progress of bioelectronic devices and biosensors based on biomaterial-nanomaterial hybrid.

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.

Resettable and enzyme-free molecular logic devices for the intelligent amplification detection of multiple miRNAs via catalyzed hairpin assembly

The integration of multi-level DNA logic gates for biological diagnosis is far from being fully realized. In particular, the simplification of logical analysis to implement advanced logic diagnoses is still a critical challenge for DNA computing and bioelectronics. Here, we developed a magnetic bead/DNA system to construct a library of logic gates, enabling the sensing of multiplex target miRNAs. In this assay, the miRNA-catalyzed hairpin assembly (CHA) was successfully applied to construct two/three-input concatenated logic circuits with excellent specificity extended to design a highly sensitive multiplex detection system. Significantly, the CHA-based multiplex detection system can distinguish individual target miRNAs (such as miR-21, miR-155, and miR let-7a) under a logic function control, which presents great applications in the development of rapid and intelligent detection. Another novel feature is that the multiplex detection system can be reset by heating the output system and the magnetic separation of the computing modules. Overall, the proposed logic diagnostics with high amplification efficiency is simple, fast, low-cost, and resettable, and holds great promise in the development of biocomputing, multiparameter sensing, and intelligent disease diagnostics.

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.

Photodetection of DNA mismatches by dissymmetric Ru(ii) acridine based complexes

Favored radiative deactivation processes in dissymmetric Ru(ii) complexes enable photodetection of DNA mismatches.

Insulin-like growth factor type I selectively binds to G-quadruplex structures

BACKGROUND

G-quadruplex has been viewed as a promising therapeutic target in oncology due to its potentially important roles in physiological and pathological processes. Emerging evidence suggests that the biological functions of G-quadruplexes are closely related to the binding of some proteins. Insulin-like growth factor type I (IGF-1), as a significant modulator of cell growth and development, may serve as a quadruplex-binding protein.

METHODS

The binding affinity and selectivity of IGF-1 to different DNA motifs in solution were measured by using fluorescence spectroscopy, Surface Plasmon Resonance (SPR), and force-induced remnant magnetization (FIRM). The effects of IGF-1 on the formation and stability of G-quadruplex structures were evaluated by circular dichroism (CD) and melting fluorescence resonance energy transfer (FRET) spectroscopy. The influence of quadruplex-specific ligands on the binding of G-quadruplexes with IGF-1 was determined by FIRM.

RESULTS

IGF-1 shows a binding specificity for G-quadruplex structures, especially the G-quadruplex structure with a parallel topology. The quadruplex-specific ligands TMPyP4 and PDS (Pyridostatin) can inhibit the interaction between G-quadruplexes and proteins.

CONCLUSIONS

IGF-1 is demonstrated to selectively bind with G-quadruplex structures. The use of quadruplex-interactive ligands could modulate the binding of IGF-1 to G-quadruplexes.

GENERAL SIGNIFICANCE

This study provides us with a new perspective to understand the possible physiological relationship between IGF-1 and G-quadruplexes and also conveys a strategy to regulate the interaction between G-quadruplex DNA and proteins.

Stereotactic body radiotherapy for centrally-located lung tumors with 56 Gy in seven fractions: A retrospective study

Stereotactic body radiotherapy (SBRT) for centrally-located lung tumors remains a challenge because of the increased risk of treatment-related adverse events (AEs), and uncertainty around prescribing the optimal dose. The present study reported the results of central tumor SBRT with 56 Gy in 7 fractions (fr) at the University of Tokyo Hospital. A total of 35 cases that underwent SBRT with or without volumetric-modulated arc therapy consisting of 56 Gy/7 fr for central lung lesions between 2010 and 2016 at the University of Tokyo Hospital were reveiwed. A central lesion was defined as a tumor within 2 cm of the proximal bronchial tree (RTOG 0236 definition) or within 2 cm in all directions of any critical mediastinal structure. Local control (LC), overall survival (OS), and AEs were investigated. The Kaplan-Meier method was used to estimate LC and OS. AEs were scored per the Common Terminology Criteria for Adverse Events Version 4.0. Thirty-five patients with 36 central lung lesions were included. Fifteen lesions were primary non-small cell lung cancer (NSCLC), 13 were recurrences of NSCLC, and 8 had oligo-recurrences from other primaries. Median tumor diameter was 29 mm. Eighteen patients had had prior surgery. At a median follow-up of 13.1 months for all patients and 18.3 months in surviving patients, 22 patients had died, ten due to primary disease (4 NSCLC), while three were treatment-related. The 1- and 2-year OS were 57.3 and 40.4%, respectively, and median OS was 15.7 months. Local recurrence occurred in only two lesions. 1- and 2-year LC rates were both 96%. Nine patients experienced grade ≥3 toxicity, representing 26% of the cohort. Two of these were grade 5, one pneumonitis and one hemoptysis. Considering the background of the subject, tumor control of our central SBRT is promising, especially in primary NSCLC. However, the safety of SBRT to central lung cancer remains controversial.

A novel logic gate based on liquid-crystals responding to the DNA conformational transition

Described herein is a novel liquid crystal (LC)-based DNA logic gate constructed via employing the reorientation of LCs triggered by metal-ion-mediated DNA probe conformational changes.

Novel Angiotensin-Converting Enzyme Inhibitory Peptides Derived from Oncorhynchus mykiss Nebulin: Virtual Screening and In Silico Molecular Docking Study

Excessive concentrations of angiotensin-converting enzyme (ACE) can give rise to high blood pressure, and is harmful to the body. ACE inhibitory peptides from food proteins are considered good sources of function food. However, the preparation of ACE inhibitory peptides by classical method faces many challenges. Three novel ACE inhibitory peptides were identified by in silico methods, and showed potent activity against ACE in vitro. The simulation hydrolysis of nebulin was performed with ExPASy PeptideCutter program. Potential activity, solubility, and absorption, distribution, metabolism, excretion, and toxicity properties of generated peptides were predicted using program online. Molecular docking displayed that EGF, HGR, and VDF were docked into the S₁ and S₂ pockets of ACE. Meanwhile, Phe and Arg at the C-terminal enhance ACE affinity. The IC₅₀ values of EGF, HGR, and VDF were 474.65 ± 0.08, 106.21 ± 0.52, and 439.27 ± 0.09 μM, respectively. Three peptides EGF, HGR, and VDF from Oncorhynchus mykiss nebulin were identified, and the molecular mechanism between ACE and peptides was clarified using in silico methods. The results suggested that Oncorhynchus mykiss nebulin would be an attractive raw material of antihypertensive nutraceutical ingredients.

PRACTICAL APPLICATION

This study has shown the potential of Oncorhynchus mykiss nebulin as good sources for producing ACE inhibitory peptides. According to this finding, in silico approach is the feasible way for prediction and identification of food-derived ACE inhibitory peptides in emerging nutraceutical field.

Enzyme-Regulated DNA-Based Logic Device

Herein, we report a carbazole (Cz) ligand that displays distinct turn-on fluorescence signals upon interaction with human telomeric G-quadruplex ( h-TELO) and nuclease enzymes. Interestingly, Cz selectively binds and stabilizes the mixed hybrid topology of h-TELO G-quadruplex that withstands digestion by exonucleases and nuclease S1. The distinct fluorescence signatures of Cz-stabilized h-TELO with nucleases are used to design conceptually novel DNA devices for selectively detecting the enzymatic activity of DNase I as well as performing logic operations. An INHIBIT logic gate is constructed using h-TELO and DNase I as the inputs while the inputs of h-TELO and nuclease S1 form a YES logic gate. Furthermore, a two-input two-output reusable logic device with "multireset" function is developed by using h-TELO and DNase I as inputs. On the basis of this platform, combinatorial logic systems (INHIBIT-INHIBIT and NOR-OR) have been successfully installed using different combinations of nucleases as inputs. Moreover, this new strategy of using a synthetic dual emissive probe and enzyme/DNA inputs for constructing reusable logic device may find important applications in biological computing and information processing.

Evaluation of the effect of polymorphism on G-quadruplex-ligand interaction by means of spectroscopic and chromatographic techniques

Guanine-rich sequences may fold into highly ordered structures known as G-quadruplexes. Apart from the monomeric G-quadruplex, these sequences may form multimeric structures that are not usually considered when studying interaction with ligands. This work studies the interaction of a ligand, crystal violet, with three guanine-rich DNA sequences with the capacity to form multimeric structures. These sequences correspond to short stretches found near the promoter regions of c-kit and SMARCA4 genes. Instrumental techniques (circular dichroism, molecular fluorescence, size-exclusion chromatography and electrospray ionization mass spectrometry) and multivariate data analysis were used for this purpose. The polymorphism of G-quadruplexes was characterized prior to the interaction studies. The ligand was shown to interact preferentially with the monomeric G-quadruplex; the binding stoichiometry was 1:1 and the binding constant was in the order of 10⁵M^-1 for all three sequences. The results highlight the importance of DNA treatment prior to interaction studies.

Comparative investigation of binding interactions with three steroidal derivatives of d(GGGT)4 G-quadruplex aptamer

Steroidal derivatives have attracted tremendous attentions in biological and biomedical areas, due to their variety biological activities. The investigation of structural influences helps in understanding their biological activities. The interactions of steroidal derivatives with DNA may play important roles in biological activities, however only a few investigations were reported on this issue. Herein, the structural influences of three steroidal derivatives were investigated based on their binding interactions with d(GGGT)₄ G-quadruplex aptamer by spectroscopic approaches, nuclear magnetic resonance (NMR), electrochemical methods, and molecular modeling techniques. Three compounds were found to selectively bind with parallel G-quadruplex aptamer to form three complexes through end-stacking binding modes. Three compounds stabilized the G-quadruplex structure of the aptamer at different levels, which enhanced the biological activity of this aptamer to some extent. The space steric hindrance was responsible for differences in the binding interactions between d(GGGT)₄ G-quadruplex aptamer and three compounds. These results provide new information for the molecular understanding of binding interactions of steroidal derivatives with DNA and the strategy for research of structural influences.

Bioderived DNA Nanomachines for Potential Uses in Biosensing, Diagnostics, and Therapeutic Applications

Beside its genomic properties, DNA is also recognized as a novel material in the field of nanoengineering. The specific bonding of base pairs can be used to direct the assembly of highly structured materials with specific nanoscale features such as periodic 2D arrays, 3D nanostructures, assembly of nanomaterials, and DNA nanomachines. In recent years, a variety of DNA nanomachines are developed because of their many potential applications in biosensing, diagnostics, and therapeutic applications. In this review, the fuel-powered motors and secondary structure motors, whose working mechanisms are inspired or derived from natural phenomena and nanomachines, are discussed. The combination of DNA motors with other platforms is then discussed. In each section of these motors, their mechanisms and their usage in the biomedical field are described. Finally, it is believed that these DNA-based nanomachines and hybrid motifs will become an integral point-of-care diagnostics and smart, site-specific therapeutic delivery.

An aptasensor for staphylococcus aureus based on nicking enzyme amplification reaction and rolling circle amplification

An ultra-sensitive aptamer-based biosensor for the detection of staphylococcus aureus was established by adopting the nicking enzyme amplification reaction (NEAR) and the rolling circle amplification (RCA) technologies. Aptamer-probe (AP), containing an aptamer and a probe sequence, was developed to act as the recognition unit of the biosensor, which was specifically bound to S. aureus. The probe was released from AP and initiated into the subsequent DNA amplification reactions where S. aureus was present, converting the detection of S. aureus to the investigation of probe oligonucleotide. The RCA amplification products contained a G-quadruplex motif and formed a three dimensional structure in presence of hemin. The G4/hemin complex showed horseradish peroxidase (HRP)-mimic activity and catalyzed the chemiluminescence reaction of luminol mediated by H₂O₂. The results showed that the established biosensor could detect S. aureus specifically with a good linear correlation at 5-10⁴ CFU/mL. The signal values based on NEAR-RCA two-step cycle were boosted acutely, much higher than that relied on one-cycle magnification. The limit of detection (LoD) was determined to be as low as 5 CFU/mL. The established aptasensor exhibited a good discrimination of living against dead S. aureus, and can be applied to detect S. aureus in the food industry.

A light-up probe targeting for Bcl-2 2345 G-quadruplex DNA with carbazole TO

As its significant role, the selective recognition of G-quadruplex with specific structures and functions is important in biological and medicinal chemistry. Carbazole derivatives have been reported as a kind of fluorescent probe with many excellent optical properties. In the present study, the fluorescence of the dye (carbazole TO) increased almost 70 fold in the presence of bcl-2 2345 G4 compared to that alone in aqueous buffer condition with almost no fluorescence and 10-30 fold than those in the presence of other DNAs. The binding study results by activity inhibition of G4/Hemin peroxidase experiment, NMR titration and molecular docking simulation showed the high affinity and selectivity to bcl-2 2345 G4 arises from its end-stacking interaction with G-quartet. It is said that a facile approach with excellent sensitive, good selectivity and quick response for bcl-2 2345 G-quadruplex was developed and may be used for antitumor recognition or antitumor agents.

DNAzyme Feedback Amplification: Relaying Molecular Recognition to Exponential DNA Amplification

Technologies capable of linking DNA amplification to molecular recognition are very desirable for ultrasensitive biosensing applications. We have developed a simple but powerful isothermal DNA amplification method, termed DNAzyme feedback amplification (DFA), that is capable of relaying molecular recognition to exponential DNA amplification. The method incorporates both an RNA-cleaving DNAzyme (RCD) and rolling circle amplification (RCA) carried out by a special DNA polymerase using a circular DNA template. DFA begins with a stimulus-dependent RCA reaction, producing tandemly linked RCDs in long-chain DNA products. These RCDs cleave an RNA-containing DNA sequence to form additional primers that hybridize to the circular DNA molecule, giving rise to DNA assemblies that act as the new inputs for RCA. The RCA reaction and the cleavage event keep on feeding each other autonomously, resulting in exponential growth of repetitive DNA sequences that can be easily detected. This method can be used for the detection of both nucleic acid based targets and non-nucleic acid analytes. In this article, we discuss the conceptual framework of the feedback amplification approach, the essential features of this method as well as remaining challenges and possible solutions.

A label-free and universal platform for the construction of an odd/even detector for decimal numbers based on graphene oxide and DNA-stabilized silver nanoclusters

Molecular logic devices with different functions can perform various tasks in the areas of biological molecule detection, disease diagnosis, multivariate analysis, and bioimaging. Herein, a series of logic circuits based on silver nanoclusters (AgNCs)/graphene oxide (GO) are constructed to execute nonarithmetic functions, including 3-, 4-, and 5-bit odd/even checking. The resulting devices can differentiate between even and odd decimal numbers in the range from 0 to 31. Moreover, the devices can be expanded to operate with wider ranges of numbers when more inputs are added. The signal reporter is structured using AgNCs and GO, preventing laborious modification of biomolecules. The designed DNA-based logic nanodevices share the same DNA platform and a constant threshold value, showing great potential for application in information processing at the molecular level. Additionally, these devices can stably carry out their logic operations in a biological matrix, indicating that the AgNC/GO-based system can operate in a complicated biological environment. Given the biocompatibility and design flexibility of DNA, this study provides novel outcomes towards the development of label-free intelligent nanodevices. This may open a new path for the application of AgNCs/GO in molecular logic circuits and fluorescence imaging.

The Development of G-Quadruplex-Based Assays for the Detection of Small Molecules and Toxic Substances

G-Quadruplexes can be induced to form guanine-rich DNA sequences by certain small molecules or metal ions. In concert with an appropriate signal transducer, such as a fluorescent dye or a phosphorescent metal complex, the ligand-recognition event can be transduced into a luminescent response. This focus review aims to highlight recent examples of aptamer-based and metal-mediated G-quadruplex assays for the detection of small molecules and toxic substances in the last three years. We discuss the mechanisms and features of the different assays and present an outlook and a perspective for the future of this field.