Spectroscopic quantification of 5-hydroxymethylcytosine in genomic DNA using boric acid-functionalized nano-microsphere fluorescent probes

Portable, Wireless Potentiostat Sensor for Ultra-Sensitive, Real-Time Detection of 5hmC in Genomic DNA Using Tree-Like Graphene

Aberrant alterations in genomic 5-hydroxymethylcytosine (5hmC), an oxidation product of 5-methylcytosine (5mC) by Ten-eleven translocation (TET) enzymes, are frequently associated with cancers. Quick and precise 5hmC quantification is vital since it is a key biomarker for diagnosis, pathophysiology, and therapy. Here, we present a portable, wireless potentiostat sensor for real-time, ultrasensitive 5hmC-DNA sensing based on a tree-like graphene (teG)-modified screen-printed microelectrode. One-pot electrochemical exfoliation of pencil graphite enabled the cost-effective, eco-friendly, and scalable synthesis of teG, which exhibited high electrical conductivity, excellent electrochemical conductivity, low surface roughness, and high 5hmC-DNA adsorption, surpassing those of pencil graphite (pG) and graphene oxide (GO). The teG-modified gold electrodes exhibited exceptional sensitivity (6.15 × 10-6 mM-1 cm-2), selectivity, and reproducibility, with an ultralow detection limit of 12.6 fM for 5hmC-DNA. The sensor's performance was validated by quantifying 5hmC levels in genomic DNA from various biological specimens, including primary mouse tissues with altered TET function, mouse hepatocellular carcinoma, and human prostate cancer cell lines. To enhance practicality, a flexible, screen-printed microelectrode on mulberry paper was developed and integrated with a portable, wireless potentiostat powered by the Arduino Nano 33 IoT. Open-circuit potential (OCP)-based detection enabled label-free, real-time monitoring with wireless data transmission to an Android mobile application, successfully differentiating 5hmC levels between cancerous and noncancerous cells. These findings highlight teG's high surface area, superior charge transport, and scalability, positioning it as a promising platform for next-generation biosensing. The developed sensor provides a rapid, cost-effective, and highly sensitive tool for 5hmC quantification, with significant implications for early cancer diagnostics and treatment.

Construction of a glycosylation-mediated fluorescent biosensor for label-free measurement of site-specific 5-hydroxymethylcytosine in cancer cells with zero background signal

BACKGROUND

5-hydroxymethylcytosine (5hmC) as an epigenetic modification can regulate gene expression, and its abnormal level is related with various tumor invasiveness and poor prognosis. Nevertheless, the current methods for 5hmC assay usually involve expensive instruments/antibodies, radioactive risk, high background, laborious bisulfite treatment procedures, and non-specific/long amplification time.

RESULTS

We develop a glycosylation-mediated fluorescent biosensor based on helicase-dependent amplification (HDA) for label-free detection of site-specific 5hmC in cancer cells with zero background signal. The glycosylated 5hmC-DNA (5ghmC) catalyzed by β-glucosyltransferase (β-GT) can be cleaved by AbaSI restriction endonuclease to generate two dsDNA fragments with sticky ends. The resultant dsDNA fragments are complementary to the biotinylated probes and ligated by DNA ligases, followed by being captured by magnetic beads. After magnetic separation, the eluted ligation products act as the templates to initiate HDA reaction, generating abundant double-stranded DNA (dsDNA) products within 20 min. The dsDNA products are measured in a label-free manner with SYBR Green I as an indicator. This biosensor can measure 5hmC with a detection limit of 2.75 fM and a wide linear range from 1 × 10-14 to 1 × 10-8 M, and it can discriminate as low as 0.001% 5hmC level in complex mixture. Moreover, this biosensor can measure site-specific 5hmC in cancer cells, and distinguish tumor cells from normal cells.

SIGNIFICANCE

This biosensor can achieve a zero-background signal without the need of either 5hmC specific antibody or bisulfite treatment, and it holds potential applications in biological research and disease diagnosis.

Rolling circle transcription amplification-directed construction of tandem spinach-based fluorescent light-up biosensor for label-free sensing of β-glucosyltransferase activity

β-glucosyltransferase (β-GT) can specifically catalyze the conversion of 5-hydroxymethylcytosine (5-hmC) to 5-glucosylhydroxy methylcytosine (5-ghmC), and it is associated with the control of phage-specific gene expression by affecting transcription process in vivo and in vitro. The current strategies for β-GT assay usually involve expensive equipment, laborious treatment, radioactive hazard, and poor sensitivity. Here, we report a Spinach-based fluorescent light-up biosensor for label-free measurement of β-GT activity by utilizing 5-hmC glucosylation-initiated rolling circle transcription amplification (RCTA). We design a 5-hmC-modified multifunctional circular detection probe (5-hmC-MCDP) that integrates the functions of target-recognition, signal transduction, and transcription amplification in one probe. The introduction of β-GT catalyzes 5-hmC glucosylation of 5-hmC-MCDP probe, protecting the glucosylated 5-mC-MCDP probe from the cleavage by MspI. The remaining 5-hmC-MCDP probe can initiate RCTA reaction with the aid of T7 RNA polymerase, generating tandem Spinach RNA aptamers. The tandem Spinach RNA aptamers can be lightened up by fluorophore 3,5-difluoro-4-hydroxybenzylidene imidazolinone, facilitating label-free measurement of β-GT activity. Notably, the high specificity of MspI-catalyzed cleavage of nonglucosylated probe can efficiently inhibit nonspecific amplification, endowing this assay with a low background. Due to the higher efficiency of RCTA than the canonical promoter-initiated RNA synthesis, the signal-to-noise ratio of RCTA is 4.6-fold higher than that of linear template-based transcription amplification. This method is capable of sensitively detecting β-GT activity with a limit of detection of 2.03 × 10-5 U/mL, and it can be used for the screening of inhibitors and determination of kinetic parameters, with great potential in epigenetic research and drug discovery.

Epigenetic Quantification of 5-Hydroxymethylcytosine Signatures via Regulatable DNAzyme Motor Triggered by Strand Displacement Amplification

DNA methylation predominantly occurs within the CpG dinucleotide, which is the main epigenetic form of gene expression regulation in mammals. Genomic DNA with CpG sites has different sequence lengths and complex secondary structures, resulting in the complexity and diversity of the samples. Therefore, highly efficient quantification of DNA methylation in complex samples remains challenging. Herein, the regulatable DNAzyme motor triggered by strand displacement amplification (SDA) was designed to quantify 5-hydroxymethylcytosine (5hmC) signatures as a model. Briefly, the 5hmC sites as primary target were specifically labeled with DNA primers and converted into a large number of single-stranded DNA (secondary target) via the SDA reaction which could activate the DNAzyme motor. With the increase of secondary target, the DNAzyme motor gradually recovered its activity and could continuously cleave the track strands labeled quenching probes, causing electrochemiluminescence signal recovery and detection limit down to 0.49 fM for 5hmC. This strategy provides a new route to quantify natural base modifications in DNA and would hold promising potential for the early diagnosis of cancer and other diseases related to 5hmC.

Quantification and mapping of DNA modifications

Apart from the four canonical nucleobases, DNA molecules carry a number of natural modifications. Substantial evidence shows that DNA modifications can regulate diverse biological processes. Dynamic and reversible modifications of DNA are critical for cell differentiation and development. Dysregulation of DNA modifications is closely related to many human diseases. The research of DNA modifications is a rapidly expanding area and has been significantly stimulated by the innovations of analytical methods. With the recent advances in methods and techniques, a series of new DNA modifications have been discovered in the genomes of prokaryotes and eukaryotes. Deciphering the biological roles of DNA modifications depends on the sensitive detection, accurate quantification, and genome-wide mapping of modifications in genomic DNA. This review provides an overview of the recent advances in analytical methods and techniques for both the quantification and genome-wide mapping of natural DNA modifications. We discuss the principles, advantages, and limitations of these developed methods. It is anticipated that new methods and techniques will resolve the current challenges in this burgeoning research field and expedite the elucidation of the functions of DNA modifications.

Nanomaterial-Based Fluorescence Resonance Energy Transfer (FRET) and Metal-Enhanced Fluorescence (MEF) to Detect Nucleic Acid in Cancer Diagnosis

Nucleic acids, including DNA and RNA, have received prodigious attention as potential biomarkers for precise and early diagnosis of cancers. However, due to their small quantity and instability in body fluids, precise and sensitive detection is highly important. Taking advantage of the ease-to-functionality and plasmonic effect of nanomaterials, fluorescence resonance energy transfer (FRET) and metal-enhanced fluorescence (MEF)-based biosensors have been developed for accurate and sensitive quantitation of cancer-related nucleic acids. This review summarizes the recent strategies and advances in recently developed nanomaterial-based FRET and MEF for biosensors for the detection of nucleic acids in cancer diagnosis. Challenges and opportunities in this field are also discussed. We anticipate that the FRET and MEF-based biosensors discussed in this review will provide valuable information for the sensitive detection of nucleic acids and early diagnosis of cancers.

Label-Free and Template-Free Chemiluminescent Biosensor for Sensitive Detection of 5-Hydroxymethylcytosine in Genomic DNA

5-Hydroxymethylcytosine (5hmC) is a modified base present at low levels in various mammalian cells, and it plays essential roles in gene expression, DNA demethylation, and genomic reprogramming. Herein, we develop a label-free and template-free chemiluminescent biosensor for sensitive detection of 5hmC in genomic DNAs based on 5hmC-specific glucosylation, periodate (IO₄⁺) oxidation, biotinylation, and terminal deoxynucleotidyl transferase (TdT)-assisted isothermal amplification strategy, which we term hmC-GLIB-IAS. This hmC-GLIB-IAS exhibits distinct advantages of bisulfite-free, improved sensitivity, and genome-wide analysis of 5hmC at constant reaction temperature without the involvement of either specially labeled nucleic acid probes or specific templates for signal amplification. This method can sensitively detect 5hmC with a detection limit of 2.07 × 10^-13 M, and it can detect 5hmC in the whole genome DNA with a detection limit of 3.92 × 10^-5 ng/μL. Moreover, this method can distinguish 5hmC from 5-methylcytosine (5mC) and cytosine (C) and even discriminate 0.1% 5hmC in the mixture of 5hmC-DNA and 5mC-DNA. Importantly, this hmC-GLIB-IAS strategy enables genome-wide analysis without the involvement of either isotope-labeled substrates or specific antibodies, providing a powerful platform to detect 5hmC in real genomic DNA with high reproducibility and accuracy.

A water-soluble boronic acid sensor for caffeic acid based on double sites recognition

Due to reversibly and covalently binding with Lewis bases and polyols, boronic acid compounds as fluorescent sensors have been widely reported to recognize carbohydrates, ions, hydrogen peroxide, and so on. However, boronic acid sensors for highly selective recognition of caffeic acid rather than catechol or catechol derivatives have not been reported yet. Herein a novel water-soluble sensor 5c with double recognition sites based on a boronic acid was reported. When 2.3 × 10-4 M of caffeic acid was added, the fluorescence intensity of sensor 5c decreased by 99.6% via inner filter effect (IFE) because its excitation spectrum well overlaps with the absorption spectrum of caffeic acid under neutral condition, while the fluorescence increased or did not change obviously after binding with other analytes including carbohydrates and other catechol derivatives. In addition, the response time to caffeic acid is fast at room temperature, and a high binding constant (9245.7 ± 348.3 M-1) and low LOD (1.81 × 10-6 M) was calculated. Moreover, determination of caffeic acid content in caffeic acid tablets was studied, and the recovery rate is sufficient. Therefore, sensor 5c can be used as a potential tool for detecting biologically significant caffeic acid in real samples.

A highly selective and sensitive boronic acid-based sensor for detecting Pd2+ ion under mild conditions

Herein, a boronic acid-based sensor was reported selectively to recognize Pd²⁺ ion. The fluorescence intensity increased 36-fold after sensor binding with 2.47 × 10^-5 M of Pd²⁺ ion. It was carried out in the 99% aqueous solution for binding tests, indicating sensor having good water solubility. In addition, it is discernible that Pd²⁺ ion turned on the blue fluorescence of sensor under a UV-lamp (365 nm), while other ions (Ag⁺, Al³⁺, Ba²⁺, Ca²⁺, Cr²⁺, Cd²⁺, Co²⁺, Cs²⁺, Cu²⁺, Fe²⁺, Fe³⁺, K⁺, Li⁺, Mg²⁺, Mn²⁺, Na⁺, Ni²⁺ and Zn²⁺) did not show the similar change. Furthermore, sensor has a low limit of detection (38 nM) and high selectivity, which exhibits the potential for the development of Pd²⁺ recognition in practical environments.

Homogeneous detection of 5-hydroxymethylcytosine based on electrochemiluminescence quenching of g-C3N4/MoS2 nanosheets by ferrocenedicarboxylic acid polymer

A sensitively homogeneous electrochemiluminescence (ECL) method was developed for 5-hydroxymethylcytosine (5hmC) detection using TiO₂/MoS₂/g-C₃N₄/GCE as substrate electrode, where g-C₃N₄ was employed as the ECL active material, the MoS₂ nanosheets were used as co-catalyst, and TiO₂ was adopted as phosphate group capture reagent. To achieve the specific recognition and capture of 5hmC, the covalent reaction between -CH₂OH and -SH was employed under the catalysis of HhaI methyltransferase, in which, -SH functionalized ferrocenedicarboxylic acid polymer (PFc-SH) was prepared as 5hmC capture reagent and ECL signal quencher. Then, based on the interaction between TiO₂ and phosphate group of 5hmC, the target was recognized and captured on electrode, resulting in a decreased ECL response due to the quenching effect of PFc-SH. Under optimal conditions, the biosensor presented the linear range from 0.01 to 500 nM with the detection limit of 3.21 pM (S/N = 3). The steric effect on electrode surface is a bottle-neck issue restricting devised biosensors advancement. In this work, the reaction between 5hmC and PFc was carried out in the solution, which can avoid steric effect on electrode surface to keep the high activity of enzyme. In addition, the biosensor was successfully applied to detect 5hmC in genomic DNA of chicken embryo fibroblast cells and different tissues of rice seedlings.

Electrochemiluminescence biosensor for DNA hydroxymethylation detection based on enzyme-catalytic covalent bonding reaction of -CH2OH and thiol functionalized Fe3O4 magnetic beads

5-Hydroxymethylcytosine (5 hmC) is a novel epigenetic modification that plays an important role in mammalian nuclear reprogramming, regulation of gene activity, and initiation of DNA demethylation. In this paper, an electrochemiluminescence sensor was constructed for 5 hmC detection based on thiol functional Fe₃O₄ magnetic beads and covalent chemical reaction of -CH₂OH in 5 hmC. First, Fe₃O₄ magnetic beads were prepared and modified with thiol. Then, 5 hmC was captured on the surface of the magnetic beads by the reaction between -CH₂OH of 5 hmC and -SH of the thiol-functionalized Fe₃O₄ under the catalysis of DNA methyltransferase (M. HhaI). After that, through a series of reactions, phos-tag-biotin, avidin, and bis(hexafluorophosphate) (Ru (bpy)₂ (phen-5-NH₂) (PF₆)₂) (Ru) were further successively immobilized on the surface of the magnetic beads. More importantly, these reactions were carried out in a solution to ensure the activity of the biomolecules, and further to ensure that the reaction proceeded sufficiently. Finally, an ECL signal was generated by the introduction of Ru. The concentration of 5 hmC presented a good linear relationship with the ECL signal intensity in the range of 0.01-500 nM, and the detection limit was 2.86 pM. Moreover, we also used this method to study the 5 hmC content change in rice seedlings treated with antibiotics and heavy metal composite pollutants, and in chicken embryo fibroblast cell infected with and without avian leukosis virus subgroup J.

Boronic acid sensors with double recognition sites: a review

Boronic acids reversibly and covalently bind to Lewis bases and polyols, which facilitated the development of a large number of chemical sensors to recognize carbohydrates, catecholamines, ions, hydrogen peroxide, and so on. However, as the binding mechanism of boronic acids and analytes is not very clear, it is still a challenge to discover sensors with high affinity and selectivity. In this review, boronic acid sensors with two recognition sites, including diboronic acid sensors, and monoboronic acid sensors having another group or binding moiety, are summarized. Owing to double recognition sites working synergistically, the binding affinity and selectivity of sensors can be improved significantly. This review may help researchers to sort out the binding rules and develop ideal boronic acid-based sensors.

Photoelectrochemical assay for DNA hydroxymethylation determination based on the inhibited photoactivity of black TiO2 nanosphere by ZnO

A photoelectrochemical method was proposed for DNA hydroxymethylation determination using black TiO₂ (B-TiO₂) nanosphere as photoactive material and ZnO as photoactivity inhibitor. After hydroxymethylated DNA (5hmC-DNA) was captured on the probe modified B-TiO₂/ITO electrode surface through hybridization, a glycosyl can be then transferred from uridine diphosphoglucose to 5hmC-DNA and formed a covalent structure with -CH₂OH in the presence of T4 β-glucosyltransferase (β-GT). Afterwards, based on a series of covalent reaction, amino functionalized ZnO nanoparticles are further immobilized to the surface of the electrode. Due to the capacity to expend the irradiation light and the photogenerated electron of electron donor, the modified ZnO nanoparticles can result in a decreased photocurrent. The developed method shows wide linear ranges from 0.05-200 nM for hydroxymethylated DNA and 1-220 unit·mL^-1 for T4-β-glucosyltransferase. The corresponding determination limits were 0.013 nM and 0.24 unit·mL^-1, respectively. The enzyme activity inhibited by 4-phenylimidazole was evaluated. This photoelectrochemical method shows high specificity for 5hmC-DNA (compared to 5fC, 5mC, m6A, control) and β-GT (compared to β-AGT, UGT2B7), and shows excellent stability for testing 5hmC (RSD = 2.75%). Graphical abstractSchematic representation of photoelectrochemical method for DNA hydroxymethylation and β-glucosyltransferase detection based on the glycosylation reaction of -CH₂OH in 5-hydroxymethylcytosine and the inhibition activity of ZnO to the photoactivity of black TiO₂ nanospheres.

Unprecedented green-emissive boranyl-hydrazone supramolecular assemblies and their in vitro diagnostic applications

This paper describes a novel symmetric N,N'-diethylsalicylaldehyde boranyl hydrazone (1) and its in situ-generated assemblies displaying opto-analytical capabilities for the diagnosis of nucleic acids under physiological conditions. The sensing capabilities of these unprecedented supramolecular assemblies were characterized using UV-Vis spectroscopy, fluorescence spectroscopy, 1D and 2D NMR spectroscopy, dynamic light scattering, and zeta potential measurements. Model compounds lacking boranyl units (2, 3) were prepared to correlate and evaluate the sensing mechanism. The rationally designed probe 1 displays unusual aggregation-induced emissive (AIE) properties, with an average particle size of 1096 nm exhibiting green emission upon excitation at 377 nm in pH-7.2 TRIZMA buffer. A selective switch on response toward organic PO₄^3- accompanied through specific nano-aggregations patterns and sizes, thereby causing a significant red-shift through AIE. Exploiting such switch on in green channel behavior has allowed the monitoring of DNase I activities and polymerase chain reactions.

Efficient chemoenzymatic synthesis of UDP-α-6-N3-glucose

A novel chemo-enzymatic synthetic method for UDP-α-6-N₃-glucose was developed by combining the versatility of chemical synthesis and natural enzyme stereo-selectivity of Bifidobacterium longum (BLUSP). This flexible and efficient platform expanded the substrate scope for UDP-sugars on an improved scale, particularly for UDP-sugar substrates containing bioorthogonal functional groups.

An efficient 3-acylquinoline synthesis from acetophenones and anthranilviaC(sp3)–H bond activation mediated by Selectfluor

An efficient method for the synthesis of 3-functionalized quinolines from commercially available acetophenones and anthranil has been described. Selectfluor propels the C(sp³)–H bond activation of the acetophenones and aza-Michael addition of anthranil resulting in annulated 3-acylquinolines in moderate to high yields. DMSO acts not only as a solvent but also as a one carbon donor in the reaction.

An efficient method for the synthesis of 3-functionalized quinolines from acetophenones and anthranil mediated by Selectfluor was achieved.

Label-Free and Immobilization-Free Electrochemical Magnetobiosensor for Sensitive Detection of 5-Hydroxymethylcytosine in Genomic DNA

DNA 5-hydroxymethylcytosine (5-hmC) is an important epigenetic biomarker for tumorigenesis, and the loss of 5-hmC levels is associated with leukemia and melanoma cancers. However, it is a great challenge to discriminate 5-hmC from 5-methylcytosine (5-mC) using the conventional bisulfite conversion methods. Herein, we report a label-free and immobilization-free electrochemical magnetobiosensor for sensitive quantification of 5-hmC in genomic DNA based on a dual signal amplification strategy coupled with terminal deoxynucleotidyl transferase (TDT) enzymatic amplification and Ru(III) redox cycling. This screen-printed carbon electrode (SPCE)-based electrochemical magnetobiosensor shows distinct advantages of having low cost and simple fabrication and being label-free, immobilization-free, PCR-free, and radioactive-free. It exhibits high sensitivity with a detection limit of as low as 9.06 fM and a large dynamic range from 0.01 to 1000 pM. Importantly, this biosensor can discriminate 5-hmC from cytosine and 5-mC, and it can successfully detect 5-hmC in live cells.

Recent development of boronic acid-based fluorescent sensors

As Lewis acids, boronic acids can bind with 1,2- or 1,3-diols in aqueous solution reversibly and covalently to form five or six cyclic esters, thus resulting in significant fluorescence changes. Based on this phenomenon, boronic acid compounds have been well developed as sensors to recognize carbohydrates or other substances. Several reviews in this area have been reported before, however, novel boronic acid-based fluorescent sensors have emerged in large numbers in recent years. This paper reviews new boron-based sensors from the last five years that can detect carbohydrates such as glucose, ribose and sialyl Lewis A/X, and other substances including catecholamines, reactive oxygen species, and ionic compounds. And emerging electrochemically related fluorescent sensors and functionalized boronic acid as new materials including nanoparticles, smart polymer gels, and quantum dots were also involved. By summarizing and discussing these newly developed sensors, we expect new inspiration in the design of boronic acid-based fluorescent sensors.

A sensitive signal-off electrogenerated chemiluminescence biosensing method for the discrimination of DNA hydroxymethylation based on glycosylation modification and signal quenching from ferroceneboronic acid

In this study, a new and sensitive signal-off electrogenerated chemiluminescence (ECL) biosensing method for the quantification of 5-hydroxymethylcytosine in DNA (5-hmC-DNA) was developed. The method achieved simple and sensitive detection of 5-hmC-DNA based on the glycosylation of 5-hmC, combining both the amplification function of gold nanoparticles (AuNPs) and the high quenching efficiency of the tris(2, 2'-ripyridine) dichlororuthenium(II) (Ru(bpy)₃²⁺)-ferrocene (Fc) system. First, the electrode modified with a mixture of Nafion and AuNPs was utilized as the platform for electrostatically adsorbing Ru(bpy)₃²⁺(an ECL-emitting species) and assembling 5-hmC-DNA. The 5-hmC-DNA was glycosylated by T4 β-glucosyltransferase, yielding β-glucosyl-5-hydroxymethyl-cytosine in DNA (5-ghmC-DNA). Finally, quencher-FcBA was further covalently bound to 5-ghmC-DNA through formation of boronate ester covalent bonds between boronic acid and cis-diols of 5-ghmC, resulting in a decrease in ECL intensity. The results indicated that the decreased ECL intensity was directly linear to the concentration of 5-hmC-DNA in the range from 1.0×10^-8 to 5.0×10^-11M with a low detection limit of 1.63×10^-11M. In addition, this ECL method was demonstrated to be useful for the quantification of 5-hmC in clinical serum samples. Moreover, the method allowed good discrimination among cytosine (5-C), 5-methylcytosine (5-mC), and 5-hmC in DNA.