Cytosine-5 methylation-directed construction of a Au nanoparticle-based nanosensor for simultaneous detection of multiple DNA methyltransferases at the single-molecule level

DNA methylation at cytosine/guanine dinucleotide islands (CpGIs) is the most prominent epigenetic modification in prokaryotic and eukaryotic genomes. DNA methyltransferases (MTases) are responsible for genomic methylation, and their aberrant activities are closely associated with various diseases including cancers. However, the specific and sensitive detection of multiple DNA MTases has remained a great challenge due to the specificity of the methylase substrate and the rareness of methylation-sensitive restriction endonuclease species. Here, we demonstrate for the first time the cytosine-5 methylation-directed construction of a Au nanoparticle (AuNP)-based nanosensor for simultaneous detection of multiple DNA MTases at the single-molecule level. We used the methyl-directed endonuclease GlaI to cleave the site-specific 5-methylcytosine (5-mC). In the presence of CpG and GpC MTases (i.e., M.SssI and M.CviPI), their hairpin substrates are methylated at cytosine-5 to form the catalytic substrates for GlaI, respectively, followed by simultaneous cleavage by GlaI to yield two capture probes. These two capture probes can hybridize with the Cy5/Cy3–signal probes which are assembled on the AuNPs, respectively, to form the double-stranded DNAs (dsDNAs). Each dsDNA with a guanine ribonucleotide can act as the catalytic substrate for ribonuclease (RNase HII), inducing recycling cleavage of signal probes to liberate large numbers of Cy5 and Cy3 molecules from the AuNPs. The released Cy5 and Cy3 molecules can be simply quantified by total internal reflection fluorescence (TIRF)-based single-molecule imaging for simultaneous measurement of M.SssI and M.CviPI MTase activities. This method exhibits good specificity and high sensitivity with a detection limit of 2.01 × 10⁻³ U mL⁻¹ for M.SssI MTase and 3.39 × 10⁻³ U mL⁻¹ for M.CviPI MTase, and it can be further applied for discriminating different kinds of DNA MTases, screening potential inhibitors, and measuring DNA MTase activities in human serum and cell lysate samples, holding great potential in biomedical research, clinical diagnosis, drug discovery and cancer therapeutics.

Cytosine-5 methylation-directed construction of Au nanoparticle-based nanosensors enables specific and sensitive detection of multiple DNA methyltransferases.     

Protamine/heparin optical nanosensors based on solvatochromism

Optical nanosensors for the detection of polyions, including protamine and heparin, have to date relied upon ion-exchange reactions involving an analyte and an optical transducer. Unfortunately, due to the limited selectivity of the available ionophores for polyions, this mechanism has suffered from severe interference in complex sample matrices. To date no optical polyion nanosensors have demonstrated acceptable performance in serum, plasma or blood. Herein we describe a new type of nanosensor based on our discovery of a “hyper-polarizing lipophilic phase” in which dinonylnaphthalenesulfonate (DNNS⁻) polarizes a solvatochromic dye much more than even an aqueous environment. We have found that the apparent polarity of the organic phase is only modulated when DNNS⁻ binds to large polyions such as protamine, unlike singly charged ions that lack the cooperative binding required to cause a significant shift in the distribution of the polarizing DNNS⁻ ions. Our new sensing mechanism allows solvatochromic signal transduction without the transducer undergoing ion exchange. The result is significantly improved sensitivity and selectivity, enabling for the first time the quantification of protamine and heparin in human plasma using optical nanosensors that correlates with the current gold standard analysis method, the anti-Xa factor assay.

Novel optical nanosensors for the selective detection of the polycationic protamine based on solvatochromic signal change allow one to detect heparin in plasma.     

A switchable sensor and scavenger: detection and removal of fluorinated chemical species by a luminescent metal–organic framework

Fluorosis has been regarded as a worldwide disease that seriously diminishes the quality of life through skeletal embrittlement and hepatic damage. Effective detection and removal of fluorinated chemical species such as fluoride ions (F⁻) and perfluorooctanoic acid (PFOA) from drinking water are of great importance for the sake of human health. Aiming to develop water-stable, highly selective and sensitive fluorine sensors, we have designed a new luminescent MOF In(tcpp) using a chromophore ligand 2,3,5,6-tetrakis(4-carboxyphenyl)pyrazine (H₄tcpp). In(tcpp) exhibits high sensitivity and selectivity for turn-on detection of F⁻ and turn-off detection of PFOA with a detection limit of 1.3 μg L⁻¹ and 19 μg L⁻¹, respectively. In(tcpp) also shows high recyclability and can be reused multiple times for F⁻ detection. The mechanisms of interaction between In(tcpp) and the analytes are investigated by several experiments and DFT calculations. These studies reveal insightful information concerning the nature of F⁻ and PFOA binding within the MOF structure. In addition, In(tcpp) also acts as an efficient adsorbent for the removal of F⁻ (36.7 mg g⁻¹) and PFOA (980.0 mg g⁻¹). It is the first material that is not only capable of switchable sensing of F⁻ and PFOA but also competent for removing the pollutants via different functional groups.

A robust In-MOF, In(tcpp), demonstrates sensitive detection of the fluorinated chemical species F⁻ and PFOA via distinctly different luminescence signal change, and effective adsorption and removal of both species from aqueous solution.     

An Exonuclease III‐Powered,On‐Particle Stochastic DNA Walker

DNA‐based machines have attracted rapidly growing interest owing to their potential in drug delivery, biocomputing, and diagnostic applications. Herein, we report a type of exonuclease III (Exo III)‐powered stochastic DNA walker that can autonomously move on a spherical nucleic acid (SNA)‐based 3D track. The motion is propelled by unidirectional Exo III digestion of hybridized DNA tracks in a burnt‐bridge mechanism. The operation of this Exo III‐propelled DNA walker was monitored in real time and at the single‐particle resolution using total internal reflection fluorescence microscopy (TIRF). We further interrogated the morphological effect of the 3D track on the nuclease activity, which suggested that the performance of the DNA walker was critically dependent upon the DNA density and the track conformation. Finally, we demonstrated potential bioanalytical applications of this SNA‐based stochastic DNA walker by exploiting movement‐triggered cascade signal amplification.     

An Exonuclease III‐Powered,On‐Particle Stochastic DNA Walker

DNA‐based machines have attracted rapidly growing interest owing to their potential in drug delivery, biocomputing, and diagnostic applications. Herein, we report a type of exonuclease III (Exo III)‐powered stochastic DNA walker that can autonomously move on a spherical nucleic acid (SNA)‐based 3D track. The motion is propelled by unidirectional Exo III digestion of hybridized DNA tracks in a burnt‐bridge mechanism. The operation of this Exo III‐propelled DNA walker was monitored in real time and at the single‐particle resolution using total internal reflection fluorescence microscopy (TIRF). We further interrogated the morphological effect of the 3D track on the nuclease activity, which suggested that the performance of the DNA walker was critically dependent upon the DNA density and the track conformation. Finally, we demonstrated potential bioanalytical applications of this SNA‐based stochastic DNA walker by exploiting movement‐triggered cascade signal amplification.     

Single-molecule fluorescence detection of a tricyclic nucleoside analogue

Fluorescent nucleobase surrogates capable of Watson–Crick hydrogen bonding are essential probes of nucleic acid structure and dynamics, but their limited brightness and short absorption and emission wavelengths have rendered them unsuitable for single-molecule detection. Aiming to improve on these properties, we designed a new tricyclic pyrimidine nucleoside analogue with a push–pull conjugated system and synthesized it in seven sequential steps. The resulting C-linked 8-(diethylamino)benzo[b][1,8]naphthyridin-2(1H)-one nucleoside, which we name ABN, exhibits ε₄₄₂ = 20 000 M⁻¹ cm⁻¹ and Φ_em,540 = 0.39 in water, increasing to Φ_em = 0.50–0.53 when base paired with adenine in duplex DNA oligonucleotides. Single-molecule fluorescence measurements of ABN using both one-photon and two-photon excitation demonstrate its excellent photostability and indicate that the nucleoside is present to > 95% in a bright state with count rates of at least 15 kHz per molecule. This new fluorescent nucleobase analogue, which, in duplex DNA, is the brightest and most red-shifted known, is the first to offer robust and accessible single-molecule fluorescence detection capabilities.

Fluorescent nucleoside analogue ABN is readily detected at the single-molecule level and retains a quantum yield >50% in duplex DNA oligonucleotides.     

Advanced Pt hollow nanospheres/rubrene nanoleaves coupled with M-shaped DNA walker for ultrasensitive electrochemiluminescence bioassay

Herein, an intense electrochemiluminescence (ECL) was achieved based on Pt hollow nanospheres/rubrene nanoleaves (Pt HNSs/Rub NLs) without the addition of any coreactant, which was employed for ultrasensitive detection of carcinoembryonic antigen (CEA) coupled with an M-shaped DNA walker (M-DNA walker) as signal switch. Specifically, in comparison with platinum nanoparticles (Pt NPs), Pt HNSs revealed excellent catalytic performance and pore confinement-enhanced ECL, which could significantly amplify ECL intensity of Rub NLs/dissolved O₂ (DO) binary system. Then, the tracks and M-DNA walker were confined on the Pt HNSs simultaneously to promote the reaction efficiency, whose M-structure boosted the interaction sites between walking strands and tracks and reduced the rigidity of their recognition. Once the CEA approached the sensing interface, the M-DNA walker was activated based on highly specific aptamer recognition to recover ECL intensity with the assistance of exonuclease Ⅲ (Exo Ⅲ). As proof of concept, the “on-off-on” switch aptasensor was constructed for CEA detection with a low detection limit of 0.20 fg/mL. The principle of the constructed ECL aptasensor also enables a universal platform for sensitive detection of other tumor markers.     

Self-assembled Nanosheets of Perylene Monoamide Derivative as Sensitive Fluorescent Biosensor for Exonuclease III Activity

Enzymes containing 3'→5' exonuclease activities play an important role in various key cellular and physiological processes. The development of fluorescence biosensor is an efficient method to detecting enzyme activity. Herein, a fluorescence resonance energy transfer(FRET) "on" and "off" strategy for detecting exonuclease III(Exo III) activity has been developed. We report here that the double-stranded DNA(dsDNA) enables to bind tightly to self-assembled nanosheets of cationic perylene monoimide derivative(PMI-O7) through electrostatic interaction, and the 6-carboxyfluorescein(FAM)-modified dsDNA could be efficiently quenched via FRET between FAM and PMI-O7. Upon the addition of Exo III, the dsDNA will be digested and the FAM fluorophore will be released, resulting in the fluorescence recovery of FAM. This method provides a simple and sensitive biosensor platform with a low detection limit of 0.077 U/mL for Exo III. Importantly, this method exhibits similar and calibration curves for the detection of Exo III in both buffer and fetal bovine serum samples, indicating that this platform has potential to detect Exo III activity in complex samples.     

Non-ergodicity of a globular protein extending beyond its functional timescale

Internal motions of folded proteins have been assumed to be ergodic, i.e., that the dynamics of a single protein molecule averaged over a very long time resembles that of an ensemble. Here, by performing single-molecule fluorescence resonance energy transfer (smFRET) experiments and molecular dynamics (MD) simulations of a multi-domain globular protein, cytoplasmic protein-tyrosine phosphatase (SHP2), we demonstrate that the functional inter-domain motion is observationally non-ergodic over the time spans 10⁻¹² to 10⁻⁷ s and 10⁻¹ to 10² s. The difference between observational non-ergodicity and simple non-convergence is discussed. In comparison, a single-strand DNA of similar size behaves ergodically with an energy landscape resembling a one-dimensional linear chain. The observed non-ergodicity results from the hierarchical connectivity of the high-dimensional energy landscape of the protein molecule. As the characteristic time for the protein to conduct its dephosphorylation function is ∼10 s, our findings suggest that, due to the non-ergodicity, individual, seemingly identical protein molecules can be dynamically and functionally different.

Internal motions of folded proteins have been assumed to be ergodic, i.e., that the dynamics of a single protein molecule averaged over a very long time resembles that of an ensemble.     

A high-spin diradical dianion and its bridged chemically switchable single-molecule magnet

Triplet diradicals have attracted tremendous attention due to their promising application in organic spintronics, organic magnets and spin filters. However, very few examples of triplet diradicals with singlet–triplet energy gaps (ΔE_ST) over 0.59 kcal mol⁻¹ (298 K) have been reported to date. In this work, we first proved that the dianion of 2,7-di-tert-butyl-pyrene-4,5,9,10-tetraone (2,7-tBu₂-PTO) was a triplet ground state diradical in the magnesium complex 1 with a singlet–triplet energy gap ΔE_ST = 0.94 kcal mol⁻¹ (473 K). This is a rare example of stable diradicals with singlet–triplet energy gaps exceeding the thermal energy at room temperature (298 K). Moreover, the iron analog 2 containing the 2,7-tBu₂-PTO diradical dianion was isolated, which was the first single-molecule magnet bridged by a diradical dianion. When 2 was doubly reduced to the dianion salt 2K2, single-molecule magnetism was switched off, highlighting the importance of diradicals in single-molecule magnetism.

We report a triplet diradical dianion in magnesium complex with ΔE_ST = 0.94 kcal mol⁻¹ (473 K). Its iron analog is the first single-molecule magnet bridged by a diradical dianion, and the SMM property is switched off through two-electron reduction.     

Mechanical unfolding of ensemble biomolecular structures by shear force

Mechanical unfolding of biomolecular structures has been exclusively performed at the single-molecule level by single-molecule force spectroscopy (SMFS) techniques. Here we transformed sophisticated mechanical investigations on individual molecules into a simple platform suitable for molecular ensembles. By using shear flow inside a homogenizer tip, DNA secondary structures such as i-motifs are unfolded by shear force up to 50 pN at a 77 796 s⁻¹ shear rate. We found that the larger the molecules, the higher the exerted shear forces. This shear force approach revealed affinity between ligands and i-motif structures. It also demonstrated a mechano-click reaction in which a Cu(i) catalyzed azide–alkyne cycloaddition was modulated by shear force. We anticipate that this ensemble force spectroscopy method can investigate intra- and inter-molecular interactions with the throughput, accuracy, and robustness unparalleled to those of SMFS methods.

Shear force in a homogenizer mechanically unfolds an ensemble set of biomolecular structures.     

Sensitive electrochemical assaying of DNA methyltransferase activity based on mimic-hybridization chain reaction amplified strategy

A mimic-hybridization chain reaction (mimic-HCR) amplified strategy was proposed for sensitive electrochemically detection of DNA methylation and methyltransferase (MTase) activity In the presence of methylated DNA, DNA-gold nanoparticles (DNA-AuNPs) were captured on the electrode by sandwich-type assembly. It then triggered mimic-HCR of two hairpin probes to produce many long double-helix chains for numerous hexaammineruthenium (III) chloride ([Ru(NH₃)₆]³⁺, RuHex) inserting. As a result, the signal for electrochemically detection of DNA MTase activity could be amplified. If DNA was non-methylated, however, the sandwich-type assembly would not form because the short double-stranded DNAs (dsDNA) on the Au electrode could be cleaved and digested by restriction endonuclease HpaII (HapII) and exonuclease III (Exo III), resulting in the signal decrement. Based on this, an electrochemical approach for detection of M.SssI MTase activity with high sensitivity was developed. The linear range for M.SssI MTase activity was from 0.05 U mL⁻¹ to 10 U mL⁻¹, with a detection limit down to 0.03 U mL⁻¹. Moreover, this detecting strategy held great promise as an easy-to-use and highly sensitive method for other MTase activity and inhibition detection by exchanging the corresponding DNA sequence.     

Programmable mismatch-fueled high-efficiency DNA signal amplifier

Herein, by introducing mismatches, a high-efficiency mismatch-fueled catalytic multiple-arm DNA junction assembly (M-CMDJA) with high-reactivity and a high-threshold is developed as a programmable DNA signal amplifier for rapid detection and ultrasensitive intracellular imaging of miRNA. Compared with traditional nucleic acid signal amplification (NASA) with a perfect complement, the M-CMDJA possesses larger kinetic and thermodynamic favorability owing to the more negative reaction standard free energy (ΔG) as driving force, resulting in much higher efficiency and rates. Once traces of the input initiator react with the mismatched substrate DNA, it could be converted into amounts of output multiple-arm DNA junctions via the M-CMDJA as the functional DNA conversion nanodevice. Impressively, the mismatch-fueled catalytic four-arm DNA junction assembly (M-CFDJA) exhibits high conversion efficiency up to 1.05 × 10⁸ in 30 min, which is almost ten times more than those of conventional methods. Therefore, the M-CMDJA could easily address the challenges of traditional methods: slow rates and low efficiency. In application, the M-CFDJA as a DNA signal amplifier was successfully used to develop a biosensing platform for rapid miRNA detection with a LOD of 6.11 aM and the ultrasensitive intracellular imaging of miRNA, providing a basis for the next-generation of versatile DNA signal amplification methods for ultimate applications in DNA nanobiotechnology, biosensing assay, and clinical diagnoses.

We proposed an ingenious mismatch-enhanced catalytic multiple-arm DNA junction assembly (M-CMDJA) which possesses more negative reaction standard free energy (ΔG) as the driving force, resulting in quite high conversion efficiency and much faster reaction speed.     

Isolation of the elusive bisbenzimidazole Bbim3−˙ radical anion and its employment in a metal complex

The discovery of singular organic radical ligands is a formidable challenge due to high reactivity arising from the unpaired electron. Matching radical ligands with metal ions to engender magnetic coupling is crucial for eliciting preeminent physical properties such as conductivity and magnetism that are crucial for future technologies. The metal-radical approach is especially important for the lanthanide ions exhibiting deeply buried 4f-orbitals. The radicals must possess a high spin density on the donor atoms to promote strong coupling. Combining diamagnetic ⁸⁹Y (I = 1/2) with organic radicals allows for invaluable insight into the electronic structure and spin-density distribution. This approach is hitherto underutilized, possibly owing to the challenging synthesis and purification of such molecules. Herein, evidence of an unprecedented bisbenzimidazole radical anion (Bbim³⁻˙) along with its metalation in the form of an yttrium complex, [K(crypt-222)][(Cp*₂Y)₂(μ-Bbim˙)] is provided. Access of Bbim³⁻˙ was feasible through double-coordination to the Lewis acidic metal ion and subsequent one-electron reduction, which is remarkable as Bbim²⁻ was explicitly stated to be redox-inactive in closed-shell complexes. Two molecules containing Bbim²⁻ (1) and Bbim³⁻˙ (2), respectively, were thoroughly investigated by X-ray crystallography, NMR and UV/Vis spectroscopy. Electrochemical studies unfolded a quasi-reversible feature and emphasize the role of the metal centre for the Bbim redox-activity as neither the free ligand nor the Bbim²⁻ complex led to analogous CV results. Excitingly, a strong delocalization of the electron density through the Bbim³⁻˙ ligand was revealed via temperature-dependent EPR spectroscopy and confirmed through DFT calculations and magnetometry, rendering Bbim³⁻˙ an ideal candidate for single-molecule magnet design.

The long sought-after bisbenzimidazole radical was isolated through complexation to two rare earth metallocenes followed by reduction, and analysed through crystallography, VT EPR spectroscopy, electrochemistry, magnetometry, and DFT computations.     

Optical and Photoacoustic Properties of Laser-Ablated Silver Nanoparticles in a Carbon Dots Solution

This study used the carbon dots solution for the laser ablation technique to fabricate silver nanoparticles. The ablation time range was from 5 min to 20 min. Analytical methods, including Fourier transform infrared spectroscopy (FTIR), UV-visible spectroscopy, transmission electron microscopy, and Raman spectroscopy were used to categorize the prepared samples. The UV-visible and z-scan techniques provided optical parameters such as linear and nonlinear refractive indices in the range of 1.56759 to 1.81288 and 7.3769 × 10⁻¹⁰ cm² W⁻¹ to 9.5269 × 10⁻¹⁰ cm² W⁻¹ and the nonlinear susceptibility was measured in the range of 5.46 × 10⁻⁸ to 6.97 × 10⁻⁸ esu. The thermal effusivity of prepared samples, which were measured using the photoacoustic technique, were in the range of 0.0941 W s^1/2 cm⁻² K⁻¹ to 0.8491 W s^1/2 cm⁻² K⁻¹. The interaction of the prepared sample with fluoride was investigated using a Raman spectrometer. Consequently, the intensity of the Raman signal decreased with the increasing concentration of fluoride, and the detection limit is about 0.1 ppm.     

Pseudo-mono-axial ligand fields that support high energy barriers in triangular dodecahedral Dy(iii) single-ion magnets

The synthesis of air-stable, high-performance single-molecule magnets (SMMs) is of great significance for their practical applications. Indeed, Ln complexes with high coordination numbers are satisfactorily air stable. However, such geometries easily produce spherical ligand fields that minimize magnetic anisotropy. Herein, we report the preparation of three air-stable eight-coordinate mononuclear Dy(iii) complexes with triangular dodecahedral geometries, namely, [Dy(BPA-TPA)Cl](BPh₄)₂ (1) and [Dy(BPA-TPA)(X)](BPh₄)₂·nCH₂Cl₂ (X = CH₃O⁻ and n = 1 for 2; L = PhO⁻ and n = 2 for 3), using a novel design concept in which the bulky heptadentate [2,6-bis[bis(2-pyridylmethyl)amino]methyl]-pyridine (BPA-TPA) ligand enwraps the Dy(iii) ion through weak coordinate bonds leaving only a small vacancy for a negatively charged (Cl⁻), methoxy (CH₃O⁻) or phenoxy (PhO⁻) moiety to occupy. Magnetic measurements reveal that the single-molecule magnet (SMM) property of complex 1 is actually poor, as there is almost no energy barrier. However, complexes 2 and 3 exhibit fascinating SMM behavior with high energy barriers (U_eff = 686 K for 2; 469 K for 3) and magnetic hysteresis temperatures up to 8 K, which is attributed to the pseudolinear ligand field generated by one strong, highly electrostatic Dy–O bond. Ab initio calculations were used to show the apparent difference in the magnetic dynamics of the three complexes, confirming that the pseudo-mono-axial ligand field has an important effect on high-performance SMMs compared with the local symmetry. This study not only presents the highest energy barrier for a triangular dodecahedral SMM but also highlights the enormous potential of the pseudolinear Dy–L ligand field for constructing promising SMMs.

Air-stable triangular dodecahedral Dy(iii) single-ion magnets with pseudo-mono-axial linear ligand fields exhibit high energy barrier exceeding 600 K, which represent the highest energy barrier for mononuclear SMMs with triangular dodecahedron.     

DNA microspot assay using single-molecule detection and requiring 1.8 nL samples only

An ultra-sensitive DNA microspot assay was developed that required 1.8?nL samples and was based on single-molecule detection. The solution of the target DNA (tDNA) was spotted onto the coverslip modified with capture DNA (DNA1) and blocked with ethanolamine and bovine serum albumin using a pintool type microspoting robot. The microspot had a diameter of ~300???m. The tDNA was captured by the DNA1, and the tDNA was then labeled with a detection DNA that previously was labeled with a quantum dot. Next, a fluorescence microscopic image of the microspot was acquired using a single-molecule microspot reader during total internal reflection fluorescence excitation. As little as 4?×?10^?22 mole (240 molecules) of tDNA can be detected by this method. The response is linear in the range from 6.0?×?10^?22 to 1.2?×?10^?19 mole of tDNA. All operations (including the acquisition of microspot images and single-molecule counting) were performed using the MetaMorph software. The assay was applied to the determination of osteopontin messenger RNA in single decidual stromal cells without the need for PCR amplification.