Colorimetric detection of single base-pair mismatches based on the interactions of PNA and PNA/DNA complexes with unmodified gold nanoparticles

A highly sensitive and robust electrochemical biosensor for microRNA detection based on PNA-DNA hetero-three-way junction formation and target-recycling catalytic hairpin assembly amplification

Robust and sensitive methods for the detection of microRNAs (miRNAs) are crucial in the clinical diagnosis of cancers. In this study, a novel electrochemical biosensor with high sensitivity for miRNA-21 detection is developed, which relies on the formation of a peptide nucleic acid (PNA)-DNA hetero-three-way junction (H3WJ) and target-recycling catalytic hairpin assembly (CHA) amplification. The electroneutral PNA probes are initially immobilized onto a gold electrode to construct the sensor. Upon introduction of miRNA-21, target-recycling CHA is initiated, resulting in abundant double-stranded CHA products. Subsequently, association between the PNA probes and these products leads to the formation of PNA-DNA H3WJs. Consequently, the electrode surface is densely populated with numerous electroactive Ferrocene (Fc) groups, resulting in a significantly amplified current response for highly sensitive detection of miRNA-21 at concentrations as low as 0.15 fM. This approach demonstrates remarkable specificity towards target miRNAs and can be utilized for quantitative monitoring of miRNA-21 expression in human cancer cells. More importantly, the sensor exhibits exceptional stability and shows a significant reduction in background noise during miRNA detection, making this method a highly promising sensing platform for monitoring various miRNA biomarkers to facilitate the diagnosis of diverse cancers.

Electrochemical peptide nucleic acid functionalized α-Fe2O3/Fe3O4 nanosheets for detection of CYP2C19*2 gene

The CYP2C19*2 gene carriers and non-carriers are closely related to the dosage of clopidogrel. To correctly guide the use of clopidogrel and promote individualized therapy, an ultra-sensitive electrochemical biosensor was developed for the detection of CYP2C19*2 gene. The heterogeneous α-Fe₂O₃/Fe₃O₄ nanosheets were prepared via the hydrothermal-calcination process, and the preparation parameters were optimized. The average diameter and thickness of the nanosheets were approximately 150 nm and 53 nm, respectively; and the saturation magnetization was 80.2 emu/g. The α-Fe₂O₃/Fe₃O₄@Au nanosheets were prepared by sodium borohydride reduction method, and self-assembled to the electrode surface with magnetic field. Ultra-sensitive detection of CYP2C19*2 gene was realized through the recognition ability of strong single base mismatching of peptide nucleic acid and signal amplification effect of magnetic α-Fe₂O₃/Fe₃O₄@Au nanosheets. Under optimal detection conditions, the current had a good linear correlation with the negative logarithm of CYP2C19*2 gene concentration in the range 1 pM-1 nM, and the detection limit was 0.64 pM (S/N = 3). Meanwhile, the electrochemical signals of target DNA and incomplete complementary DNA were detected. The constructed biosensor exhibited good selectivity, reproducibility, and stability, providing a promising strategy for the detection of other gene mutations by electrochemical biosensors.

Identification of single nucleotide polymorphisms by a peptide nucleic acid-based sandwich hybridization assay coupled with toehold-mediated strand displacement reactions

In this work, we developed a simple and accurate peptide nucleic acid (PNA)-based sandwich hybridization assay for single nucleotide polymorphisms (SNPs) in the p53 gene. Our approach combines the enzyme-free toehold-mediated strand displacement reaction (SDR) with real-time enzyme-linked immunosorbent assay (ELISA) to detect SNPs with high sensitivity and specificity. A PNA-DNA heteroduplex with an external toehold is designed and fixed on well surface of a 96-well plate. The strand displacement from PNA-DNA heteroduplexes is initiated by the hybridization of target sequence with the toehold domain and ends with the fully displacing of the incumbent DNA. Finally, the as formed PNA-target DNA duplex with overhang at its 5'-end hybridizes with a biotin-labeled reporter PNA to form a sandwich structure on surface for signal amplification. The proposed PNA-based sandwich biosensor displays high sensitivity and greatly enhanced discriminability to target p53 gene segments against single-base mutant sequences compared to its all-DNA counterpart. Furthermore, the probe design is elegantly simple and the sensing procedure is easy to operate. We believe that this strategy may provide a simple and universal strategy for SNPs detection through easily altering the sequences of probes according to the sequences around target SNPs.

Recent strategies for electrochemical sensing detection of miRNAs in lung cancer

MicroRNAs (miRNAs) associated with lung cancer are diversifying. MiR-21, Let-7, and miR-141 are common diagnostic targets. Some new lung cancer miRNAs, such as miR-25, miR-145, and miR-126, have received increasing attention. Although various techniques are available for the analysis of lung cancer miRNAs, electrochemistry has been recognized for its high sensitivity, low cost, and rapid response. However, how to realize the signal amplification is one of the most important contents in the design of electrochemical biosensors. Herein, we mainly introduce the amplification strategy based on enzyme-free amplification and signal conversion, including non-linear HCR, catalytic hairpin assembly (CHA), electrochemiluminescence (ECL), and Faraday cage. Furthermore, new progress has emerged in the fields of nanomaterials, low oxidation potential, and simultaneous detection of multiple targets. Finally, we summarize some new challenges that electrochemical techniques may encounter in the future, such as improving single-base discrimination ability, shortening electrochemical detection time, and providing real body fluid samples assay.

Responsivity of Fractal Nanoparticle Assemblies to Multiple Stimuli: Structural Insights on the Modulation of the Optical Properties

Multi-responsive nanomaterials based on the self-limited assembly of plasmonic nanoparticles are of great interest due to their widespread employment in sensing applications. We present a thorough investigation of a hybrid nanomaterial based on the protein-mediated aggregation of gold nanoparticles at varying protein concentration, pH and temperature. By combining Small Angle X-ray Scattering with extinction spectroscopy, we are able to frame the morphological features of the formed fractal aggregates in a theoretical model based on patchy interactions. Based on this, we established the main factors that determine the assembly process and their strong correlation with the optical properties of the assemblies. Moreover, the calibration curves that we obtained for each parameter investigated based on the extinction spectra point out to the notable flexibility of this nanomaterial, enabling the selection of different working ranges with high sensitivity. Our study opens for the rational tuning of the morphology and the optical properties of plasmonic assemblies to design colorimetric sensors with improved performances.

Nucleic Acids and Their Analogues for Biomedical Applications

Nucleic acids are emerging as powerful and functional biomaterials due to their molecular recognition ability, programmability, and ease of synthesis and chemical modification. Various types of nucleic acids have been used as gene regulation tools or therapeutic agents for the treatment of human diseases with genetic disorders. Nucleic acids can also be used to develop sensing platforms for detecting ions, small molecules, proteins, and cells. Their performance can be improved through integration with other organic or inorganic nanomaterials. To further enhance their biological properties, various chemically modified nucleic acid analogues can be generated by modifying their phosphodiester backbone, sugar moiety, nucleobase, or combined sites. Alternatively, using nucleic acids as building blocks for self-assembly of highly ordered nanostructures would enhance their biological stability and cellular uptake efficiency. In this review, we will focus on the development and biomedical applications of structural and functional natural nucleic acids, as well as the chemically modified nucleic acid analogues over the past ten years. The recent progress in the development of functional nanomaterials based on self-assembled DNA-based platforms for gene regulation, biosensing, drug delivery, and therapy will also be presented. We will then summarize with a discussion on the advanced development of nucleic acid research, highlight some of the challenges faced and propose suggestions for further improvement.

Enhancing Peptide Nucleic Acid-Nanomaterial Interaction and Performance Improvement of Peptide Nucleic Acid-Based Nucleic Acid Detection by Using Electrostatic Effects

Single-stranded peptide nucleic acid (PNA) probes interact strongly with several nanomaterials, and the interaction was diminished in the presence of complementary nucleic acid targets which forms the basis of many nucleic acid sensing platforms. As opposed to the negatively charged DNA probes, the charges on the PNA probes may be fine-tuned by incorporating amino acids with charged side chains. The contribution of electrostatic effects to the interaction between PNA probes and nanomaterials has been largely overlooked. This work reveals that electrostatic effects substantially enhanced the quenching of dye-labeled conformationally constrained pyrrolidinyl PNA probes by several nanomaterials including graphene oxide (GO), reduced graphene oxide, gold nanoparticles (AuNPs), and silver nanoparticles. The fluorescence quenching and the color change from red to purple in the case of AuNPs because of aggregation were inhibited in the presence of complementary nucleic acid targets. Thus, fluorescence and colorimetric assays for DNA and RNA that can distinguish even single-base-mismatched nucleic acids with improved sensitivity over conventional DNA probes were established. Both the GO- and AuNP-based sensing platforms have been successfully applied for the detection of real DNA and RNA samples in vitro and in living cells. This study emphasizes the active roles of electrostatic effects in the PNA-nanomaterial interactions, which paves the way toward improving the performance of PNA-nanomaterial based assays of nucleic acids.

Application of peptide nucleic acid in electrochemical nucleic acid biosensors

The early diagnosis of major diseases, such as malignant tumors, has always been an important field of research. Through screening, early detection of such diseases, and timely and effective treatment can significantly improve the survival rate of patients and reduce medical costs. Therefore, the development of a simple detection method with high sensitivity and strong specificity, and that is low cost is of great significance for the diagnosis and prognosis of the disease. Electrochemical DNA biosensing analysis is a technology based on Watson Crick base complementary pairing, which uses the capture probe of a known sequence to specifically recognize the target DNA and detect its concentration. Because of its advantages of low cost, simple operation, portability, and easy miniaturization, it has been widely researched and has become a cutting-edge topic in the field of biochemical analysis and precision medicine. However, the existing methods for electrochemical DNA biosensing analysis have some shortcomings, such as poor stability and specificity of capture probes, insufficient detection sensitivity, and long detection cycles. In this review, we focus on improving the sensitivity and practicability of electrochemical DNA biosensing analysis methods and summarize a series of research work carried out by using electrically neutral peptide nucleic acid as an immobilized capture probe.

Colorimetric response of lysine-caped gold/silver alloy nanocomposites for mercury(II) ion detection

A simple and rapid colorimetric assay for determination of mercury(II) ion (Hg²⁺) in aqueous solutions was developed based on aggregation of gold/silver alloy nanocomposites (Au/Ag NCs). Au/Ag NCs were aggregated after the addition of Hg²⁺ and the positively charged amino acid, lysine. The different aggregation degrees of Au/Ag NCs is indicated by variations in the absorption spectra and accompanied by a color change from orange yellow to yellowish green. Under the optimal conditions, the shift of absorbance ratio (A₆₅₀/A₄₄₇) was proportional to Hg²⁺ concentrations in the range of 0.01-10.0 μM. The limit of detection is 4.8 nM. The proposed colorimetric assay was extremely specific for Hg²⁺ and other environmentally relevant metal ions did not interfere with the determination.

Peptide nucleic acid-assisted colorimetric detection of single-nucleotide polymorphisms based on the intrinsic peroxidase-like activity of hemin-carbon nanotube nanocomposites

Here, taking the advantage of single-stranded (ss) DNA specific nuclease (S1) and peptide nucleic acid (PNA), we demonstrated a novel, rapid, and label-free colorimetric nanosensor for the sensitive and accurate detection of SNPs based on the intrinsic peroxidase-like activity of hemin-functionalized single-walled carbon nanotubes (hemin-SWCNTs). PNA, a man-made mimic of DNA with extraordinary stability toward enzymatic degradation, can effectively protect DNA in the fully matched DNA/PNA duplexes from nuclease digestion. While the DNA in DNA/PNA duplexes containing a mismatch can be cleaved into small fragments. This difference can be visually monitored from the specific color change of TMB/H₂O₂ system by employing the peroxidase activity of hemin-SWCNTs because of its different aggregation states responding to ssPNA or DNA/PNA duplex. Under optimized conditions, the SNPs in the human tumor suppressor gene TP53 have been successfully genotyped in a linear range of 50-1000 nM with a detection limit of 0.11 nM. Moreover, this platform can effectively discriminate a series of single-base mismatches. This assay avoids the assistance of sophisticated instruments and complicated modifications of probes or nanomaterials, and function well for both cell lysate samples and PCR amplicons from standard cell lines, implying its potential practical applications for bioanalysis and biosensors.

Paper-based DNA sensor enabling colorimetric assay integrated with smartphone for human papillomavirus detection

A colorimetric paper-based DNA sensor that relies on the inhibition of PNA-induced AuNPs aggregation was combined with a simple smartphone readout for the point-of-care detection of HPV type 16 DNA.

Recent advances in nanomaterial-assisted detection coupled with capillary and microchip electrophoresis

Nanomaterials have drawn much attention because of their unique properties enabling them to play important roles in various applications in different areas. This review covers literature data in the Web of Science from January 2017 to August 2020, focusing on the applications of nanomaterials (nanoparticles, quantum dots, nanotubes, and graphene) in CE and MCE to achieve enhanced sensitivity of several detection techniques: fluorescence, colorimetry, amperometry, and chemiluminescence /electrochemiluminescence. For the articles surveyed, the types of nanomaterials used, detection mechanisms, analytical performance, and applications are presented and discussed.

An electrochemical biosensor based on a graphene oxide modified pencil graphite electrode for direct detection and discrimination of double-stranded DNA sequences

The ability to directly recognize double-stranded DNA (ds-DNA) is a major challenge in disease diagnosis and gene therapy because DNA is naturally double-stranded. Herein, a novel electrochemical biosensor for the sequence-specific recognition of ds-DNA using a peptide nucleic acid (PNA) probe and graphene oxide (GO) modified pencil graphite electrode is reported and applied for the direct detection of the desired sequence in plasmid samples. For this purpose, GO was assembled onto the pencil graphite electrode surface (GO/PGE) by a simple casting method and applied for PNA probe immobilization (PNA-GO/PGE). Upon addition of ds-DNA, the interaction of the PNA probe with ds-DNA induces probe detachment from the electrode surface which results in a guanine oxidation signal decrease. Under optimized conditions, the guanine oxidation signal decreased linearly with the ds-DNA concentration increasing in the range from 30 pM to 10 nM, with a detection limit of 1.3 pM. Moreover, the proposed biosensor was applied for the sensitive and selective detection of double-stranded target DNA in plasmid samples. This proposed method could be used as a platform for direct detection of various sequences in double-stranded genomic DNA.

Colorimetric determination of DNA using an aptamer and plasmonic nanoplatform

A facile plasmonic nanoplatform was developed for rapid and sensitive determination of nucleic acid. Hg²⁺-regulated molecular beacon (MB, hairpin) containing rich thymine (T) bases at both ends is used as the probe. A hairpin structure can be formed in the MB probe due to the strong binding of Hg²⁺ to T. However, in the presence of target DNA, the hairpin structure is opened owing to target DNA-specific hybridization with the aptamer. Simultaneously, the opened MB interacts with poly(diallyldimethylammonium chloride) (PDDA) and hinders PDDA-induced aggregation of AuNPs, accompanied by a color change from blue to red and a decrease in absorption ratio (A₆₂₀/A₅₂₀). Hence, a good linear relationship was observed between the decreased absorption ratio (A₆₂₀/A₅₂₀) and DNA concentration ranging from 0.02 to 2 nmol/L with a low detection limit of 4.42 pmol/L. Moreover, this nanoplatform has been successfully utilized to discriminate between perfect target and mismatch sequences. More importantly, the bioassay is simple, versatile, rapid, and cost-effective compared with other common methods, which holds great promise for clinical diagnosis and biomedical application. Graphical abstract.

A peptide nucleic acid-regulated fluorescence resonance energy transfer DNA assay based on the use of carbon dots and gold nanoparticles

A convenient fluorometric method was developed for specific determination of DNA based on peptide nuclei acid (PNA)-regulated fluorescence resonance energy transfer (FRET) between carbon dots (CDs) and gold nanoparticles (AuNPs). In this system, CDs that display lake blue fluorescence with excitation/emission maxima at 345/445 nm were used as fluorometric reporter, while AuNPs were used as fluorescence nanoquencher. A neutral PNA probe, which is designed to recognize the target DNA, was used as a coagulant to control the dispersion and aggregation of AuNPs. Without DNA, PNA can induce immediate AuNP aggregation, thus leading to the recovery of the FRET-quenched fluorescence emission of CDs. However, the addition of the complementary target DNA can protect AuNPs from being aggregated due to the formation of DNA/PNA complexes, which subsequently produces a high fluorescence quenching efficiency of CDs by dispersed AuNPs. Under optimized conditions, quantitative evaluation of DNA was achieved in a linear range of 5-100 nM with a detection limit of 0.21 nM. This method exhibited an excellent specificity towards fully matched DNA. In addition, the application of this assay for sensitive determination of DNA in cell lysate demonstrates its potential for bioanalysis and biodetection. Graphical abstract A simple fluorometric biosensor for specific detection of DNA was developed based on peptide nuclei acid (PNA)-regulated fluorescence resonance energy transfer (FRET) between carbon dots (CDs) and gold nanoparticles (AuNPs).

Colorimetric Sensor for Thiocyanate Based on Anti-aggregation of Gold Nanoparticles in the Presence of 2-Aminopyridine

Based on the anti-aggregation mechanism of citrate stabilized gold nanoparticle (AuNPs), a new specific and sensitive colorimetric sensor for thiocyanate (SCN^-) was developed. In this scheme, the AuNPs were aggregated in the presence of the aggregating agent 2-aminopyridine (2-AP) due to electrostatic attraction. The solution color changed from red to blue. When SCN^- was present, SCN^- formed a sulfur-gold bond with the AuNPs to protect the AuNPs from aggregation. Thiocyanate can be detected by the color change of the solution from blue to red. The results showed that the absorbance ratio A₆₇₅/A₅₂₀ was linear with the concentration of SCN^- in the range of 0.4 - 1.2 μmol L^-1 by UV-Vis spectroscopy. The limit of detection (LOD) of this assay was 0.37 μmol L^-1. The system also had excellent selectivity and anti-interference ability. In addition, this method was successfully used for the detection of SCN^- in actual water samples and achieved good results.