A novel fluorescence aptasensor for 8-hydroxy-2′-deoxyguanosine based on the conformational switching of K + -stabilized G-quadruplex

Aptamer-Based Probes for Cancer Diagnostics and Treatment

Aptamers are single-stranded DNA or RNA oligomers that have the ability to generate unique and diverse tertiary structures that bind to cognate molecules with high specificity. In recent years, aptamer researches have witnessed a huge surge, owing to its unique properties, such as high specificity and binding affinity, low immunogenicity and toxicity, and simplicity of synthesis with negligible batch-to-batch variation. Aptamers may bind to targets, such as various cancer biomarkers, making them applicable for a wide range of cancer diagnosis and treatment. In cancer diagnostic applications, aptamers are used as molecular probes instead of antibodies. They have the potential to detect various cancer-associated biomarkers. For cancer therapeutic purposes, aptamers can serve as therapeutic or delivery agents. The chemical stabilization and modification strategies for aptamers may expand their serum half-life and shelf life. However, aptamer-based probes for cancer diagnosis and therapy still face several challenges for successful clinical translation. A deeper understanding of nucleic acid chemistry, tissue distribution, and pharmacokinetics is required in the development of aptamer-based probes. This review summarizes their application in cancer diagnostics and treatments based on different localization of target biomarkers, as well as current challenges and future prospects.

Current Progress in Aptasensor for Ultra-Low Level Monitoring of Parkinson's Disease Biomarkers

In today's world, Parkinson's disease (PD) has been introduced as a long-term degenerative disorder of the central nervous system which mainly affects approximately more than ten million people worldwide. The vast majority of diagnostic methods for PD have operated based on conventional sensing platforms, while the traditional laboratory tests are not efficient for diagnosis of PD in the early stage due to symptoms of this common neurodegenerative syndrome starting slowly. The advent of the aptasensor has revolutionized the early-stage diagnosis of PD by measuring related biomarkers due to the myriad advantages of originating from aptamers which can be able to sensitive and selective capture various types of related biomarkers. The progress of numerous sensing platforms and methodologies in terms of biosensors based on aptamer application for PD diagnosis has revealed promising results. In this review, we present the latest developments in myriad types of aptasensors for the determination of related PD biomarkers. Working strategies, advantages and limitations of these sensing approaches are also mentioned, followed by prospects and challenges.

Aptamer-based colorimetric detection of the DNA damage marker 8-oxo-dG using cysteamine-stabilised gold nanoparticles

8-Oxo-7,8-dihydro-2′-deoxyguanosine (8-oxo-dG) is a crucial biomarker for oxidative DNA damage and carcinogenesis. Current strategies for 8-oxo-dG detection often require sophisticated instruments and qualified personnel. In this study, cysteamine-stabilised gold nanoparticles (cyst-AuNPs) were synthesised and used for colorimetric detection of 8-oxo-dG in urine. Sensing of 8-oxo-dG is based on the anti-aggregation of cyst-AuNPs, mediated by the specific recognition of 8-oxo-dG and its aptamer. In the absence of 8-oxo-dG, the aptamer was adsorbed onto the surface of cyst-AuNPs, resulting in aggregation and the development of a purple colour solution. Upon addition of the target molecule 8-oxo-dG, the aptamer specifically bound to it and could not induce the aggregation of cyst-AuNPs, leading to the dispersion of cyst-AuNPs in the solution. Simple visual examination could be used to monitor the purple-to-red colour change that started at 12 nM, a threshold concentration for visual analysis. The absorbance at 525 nm increased in direct relation to the number of the target molecule 8-oxo-dG. This aptamer/cyst-AuNPs system showed excellent sensing ability for the 8-oxo-dG concentration in the range of 15–100 nM, with a detection limit as low as 10.3 nM and a detection time of 30 min. Interference experiments showed that the developed colorimetric strategy had a good sensitivity. This simple and rapid colorimetric method has successfully been applied to inspect 8-oxo-dG concentration in real urine samples and provided recoveries between 93.6 and 94.1%, with a limit of quantification (LOQ) of 34.3 nM, which was comparable with an enzyme-linked immunosorbent-based detection of 8-oxo-dG. This new, easy-to-use, and rapid method could be used as an alternative and initiative strategy for the development of an on-site analysis of 8-oxo-dG in urine.

A colorimetric assay based on cysteamine-stabilized AuNPs and anti-8-oxo-dG aptamers for the detection of 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxo-dG), which is a critical DNA damage marker, was developed.

An origami paper-based peptide nucleic acid device coupled with label-free DNAzyme probe hybridization chain reaction for prostate cancer molecular screening test

Prostate cancer associated 3 (PCA3) assay has been used to improve prostate cancer diagnosis and reduce unnecessary biopsies. In this work, we successfully developed a new PCA3 assay on an origami paper-based peptide nucleic acid device (oPAD). The PCA3 oPAD comprises an acrylic cassette and shutter slides to facilitate the molecular reaction and liquid control occurring on the paper surface. To quantify PCA3, a pyrrolidinyl peptide nucleic acid (acpcPNA) was immobilized onto the aldehyde-modified oPAD surface as a selective capture probe. A G-quadruplex (GQD) DNAzyme reporter probe was designed so that the PCA3 gene target binding triggered the hybridization chain reaction of the reporter probe, resulting in the accumulation of the GQD on the oPAD. The peroxidase activity of the GQD-hemin generated a deep green color of the oxidized ABTS substrate. Image analyses were performed in Adobe Photoshop CS6. The proposed oPAD was successfully applied in PCA3 detection ranges of 1-5 μM (r² = 0.982) with a limit of detection of 0.5 μM. Our proposed oPAD was demonstrated to measure PCA3 samples in both urine matrix and human cancer cell lines. The results reveal the great potential of our origami paper-based platform to be an alternative approach for facile, rapid, and low-cost detection of PCA3 in real samples.

Aptamer-based fluorescent sensors for the detection of cancer biomarkers

Aptamers are short single-stranded RNA or DNA molecules that can recognize a series of targets with high affinity and specificity. Known as "chemical antibodies", aptamers have many unique merits, including ease of chemical synthesis, high chemical stability, low molecular weight, lack of immunogenicity, and ease of modification and manipulation compared to their protein counterparts. Using aptamers as the recognition groups, fluorescent aptasensors provide exciting opportunities for sensitive detection and quantification of analytes. Herein, we give an overview on the recent development of aptamer-based fluorescent sensors for the detection of cancer biomarkers. Based on various nanostructured sensor designs, we extended our discussions on sensitivity, specificity and the potential applications of aptamer-based fluorescent sensors in early diagnosis, treatment and prognosis of cancers.

A Sensitive FRET Biosensor Based on Carbon Dots-Modified Nanoporous Membrane for 8-hydroxy-2'-Deoxyguanosine (8-OHdG) Detection with Au@ZIF-8 Nanoparticles as Signal Quenchers

A sensitive fluorescence resonance energy transfer (FRET) biosensor is proposed to detect 8-hydroxy-2′-deoxyguanosine (8-OHdG), which is a typical DNA oxidation damage product excreted in human urine. The FRET biosensor was based on carbon dots (CDs)-modified nanoporous alumina membrane with CDs as fluorescence donors. Gold nanoparticles were encapsulated in zeolitic imidazolate framework-8 to form Au@ZIF-8 nanoparticles as signal quenchers. CDs and Au@ZIF-8 nanoparticles were biofunctionalized by 8-OHdG antibody. The capture of 8-OHdG on the membrane substrates can bring Au@ZIF-8 nanoparticles closely to CDs. With 350 nm excitation, the fluorescence of CDs was quenched by Au@ZIF-8 nanoparticles and FRET effect occurred. The quenching efficiency was analyzed. The limit of detection (LOD) was 0.31 nM. Interference experiments of the FRET biosensor showed good specificity for 8-OHdG detection. The biosensor could detect urinary 8-OHdG sensitively and selectively with simple sample pretreatment processes. It shows applicability for detecting biomarkers of DNA damage in urine or other biological fluids.

Development of Low-Cost AuNP-Based Aptasensors with Truncated Aptamer for Highly Sensitive Detection of 8-Oxo-dG in Urine

8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG), an oxidized form of guanosine residues, is a critical biomarker for various cancers. Herein, a sensitive citrate-capped gold nanoparticle-based aptasensor device has been developed for the detection of 8-oxo-dG in urine. We previously designed a 38-nt anti-8-oxo-dG-aptamer by a computer simulation and the experimental validation has been performed in the present work. The analytical performance of the 38-nt aptamer from the in silico design was compared with the parent 66-nt aptamer. This assay is based on the principle of salt-induced aggregation of citrate-capped gold nanoparticles. Based on this sensing mechanism, the difference between the absorbance in the presence and absence of 8-oxo-dG at λ = 525 nm (ΔA525) increased linearly as a function of 8-oxo-dG concentrations in the ranges of 10-100 and 15-100 nM for 38-nt and 66-nt aptasensors, respectively. This method can provide detection limits of 6.4 nM for 8-oxo-dG in the 38-nt aptasensor and 13.2 nM in the 66-nt aptasensor. Similar to the 66-nt aptamer, the shortened aptamer, 38-nt long, can provide high sensitivity and selectivity with rapid detection time. In addition, using the 38-nt aptamer as a recognition component in the developed portable low-cost device showed high sensitivity in the detection range of 15-100 nM with a detection limit of 12.9 nM, which is much lower than the threshold value (280 nM) for normal human urine. This easy-to-use device could effectively and economically be utilized for monitoring 8-oxo-dG in real urine samples and potentially serve as a prototype for a commercial device.

A new chemiluminescence method for the determination of 8-hydroxyguanine based on l-histidine bound nickel nanoparticles

A new chemiluminescence aptasensor for sensitive and efficient detection of 8-hydroxyguanine based on the synergistic interaction of Ni NPs@l-histidine@aptamer@MBs has been developed, and it has been applied in the real urine samples of cancer patients.

Combinedin silicoandin vitrostudy of an aptasensor based on citrate-capped AuNPs for naked-eye detection of a critical biomarker of oxidative stress

An elevated level of 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxo-dG) in biosamples has been found to correlate to oxidative stress, and it has been assigned as a critical biomarker of various diseases. Herein, insights into the mechanisms of an aptasensor, based on citrate-capped gold nanoparticles (AuNPs), for 8-oxo-dG detection were elucidated using molecular dynamics (MD) simulations and validated experimentally. We found that the binding mechanism for binding between the anti-8-oxo-dG aptamer and 8-oxo-dG has the following characteristic stages: (i) adsorption stage, (ii) binding stage, and (iii) complex stabilization stage. Our simulations also reveal the binding sites between the anti-8-oxo-dG aptamer and 8-oxo-dG formed through hydrogen bonding during complex formation. A shortened anti-8-oxo-dG-aptamer was also engineered using in silico design, which was expected to improve the analytical performance of the colorimetric aptasensor. The mechanisms of the colorimetric aptasensor in the presence and absence of 8-oxo-dG were also investigated, and found to be in good agreement with the experiments. Complete understanding of the mechanism of the colorimetric aptasensor would open the door for development of novel naked-eye aptasensors.

A visual strategy for 8-oxo-dG monitoring based upon the dispersion of citrate-capped gold nanoparticles has been developed.

Carbon quantum dots encapsulated in super small platinum nanocrystals core-shell architecture/nitrogen doped graphene hybrid nanocomposite for electrochemical biosensing of DNA damage biomarker-8-hydroxy-2'-deoxyguanosine

In this work, carbon quantum dots (CQD) encapsulated in super small platinum nanocrystals core-shell architecture/nitrogen doped graphene hybrid nanocomposite (CQD@PDA@PtNCs-NGR) was design synthesized. Without using any capping reagent, stabilizer and surfactant, very small CQD was served as template and anchoring point for the synthesis of Pt NCs with a super small size (2.25 nm) and a uniform distribution. Meanwhile, dopamine (DA) was used as bridging agent, positioning agent and weak reducing agent to make Pt²⁺ grow on the CQD. Combine the high dispersed Pt NCs with high specific surface area and high conductivity of NGR, the CQD@PDA@PtNCs-NGR shows excellent electrocatalytic performance towards the biosensing of DNA damage biomarker- 8-Hydroxy-2'-deoxyguanosine (8-OH-dG). A very low detection limit of 0.45 nM and 0.85 nM (S/N = 3), a wide linear range of 0.013 μM-109.78 μM and a high sensitivity of 7.912 μA μM^-1cm^-2 and 4.190 μA μM^-1cm^-2 were obtained. The fabricated CQD@PDA@PtNCs-NGR realized the detection of 8-OH-dG in human urine practical sample. Furthermore, CQD@PDA@PtNCs-NGR was applied for the determination of 8-OH-dG generated from damaged DNA and damaged guanine (G), respectively. This work effectively combines the electrochemical signal of 8-OH-dG with DNA damage, confirms the mechanism of DNA damage, which might pave a new way to establish the associations between degree of DNA damage and 8-OH-dG.

Resonance light scattering aptasensor for urinary 8-hydroxy-2'-deoxyguanosine based on magnetic nanoparticles: a preliminary study of oxidative stress association with air pollution

An aptamer based method is described for the determination of 8-hydroxy-2'-deoxyguanosine (8-OHdG) using resonance light scattering (RLS). Magnetic nanoparticles (MNPs) were employed as RLS probes. The probe DNA was placed on the surface of MNPs, which produces a rather low RLS signal. If, however, probe DNA hybridizes with the aptamer against 8-OHdG, a sandwich structure will be formed. This results in a significant enhancement of RLS intensity. The aptamer was used as the recognition element to capture 8-OHdG. 8-OHdG has a stronger affinity for the aptamer than probe DNA, and the conformation of the aptamer therefore switches from a double-stranded to a G-quadruplex structure. As a result, MNPs labeled with probe DNA are released, and RLS intensity decreases. The method allows 8-OHdG to be detected with a linear response in the 32 pM - 12.0 nM concentration range and an 11 pM limit of detection (at 3.29S_B/m, according to the recent recommendation of IUPAC). The MNPs can be reused 5 times by applying an external magnetic field for collection. The method was successfully applied to analyze human urine samples for its content of 8-OHdG. It was also found that the levels of 8-OHdG noticeably increased with the increase of the Air Quality Index. Conceivably, the method is a viable tool to investigate the relationship between 8-OHdG levels and the effect of air pollution. Graphical abstract A reusable sensing strategy was constructed to detect urinary 8-OHdG based on "turn-off" resonance light scattering. The LOD was as low as 11 pM. This study showed some preliminary data for the association between oxidative stress and air pollution.

A topological transition from bimolecular quadruplex to G-triplex/tri-G-quadruplex exhibited by truncated double repeats of human telomere

Human telomeric G-rich sequences can fold back into various conformations depending upon the salt (Na⁺ or K⁺) at physiological pH. On the basis of results obtained by native PAGE electrophoresis, circular dichroism, and UV-melting experiments, we report here that truncated sequences of human telomere (d-GGGTTAGGG; GM9, d-AGGGTTAGGG; GM10, d-TAGGGTTAGGG; GM11) adopt a varied range of quadruplex conformations as a function of the cation present. By correlating CD and gel electrophoresis experiments; it was concluded that the GM9 oligonucleotide can self-associate to form a tetramer quadruplex (antiparallel; AP) in Na⁺ solution and a mixture of G-triplex (AP) or tri-G-quadruplex (parallel; P) along with a tetramer G-quadruplex structure (AP) in K⁺. The GM10 oligonucleotide formed a bimolecular G-quadruplex in both Na⁺ and K⁺ solutions, while GM11 associated to form a bimolecular G-quadruplex (AP) structure in Na⁺ solution and a mixture of bimolecular G-quadruplex (AP) and bimolecular G-quadruplex (P) along with parallel G-triplex or antiparallel tri-G-quadruplex in K⁺. All the UV-melting profiles, thermal difference spectra, and CD melting curves suggested the formation of a variety of G-quadruplex conformations by the DNA sequences studied in Na⁺ and K⁺ ions. Hypothetical models for different conformations adopted by these DNA molecules have also been proposed, which may further enhance our knowledge about the divergent topologies of guanine quadruplexes.

Luminescent Device for the Detection of Oxidative Stress Biomarkers in Artificial Urine

A luminescent paper-based device for the visual detection of oxidative stress biomarkers is reported. The device consists of a polyvinylidene fluoride membrane impregnated with poly(3-alkoxy-4-methylthiophene) (PT) for colorimetric detection. 8-hydroxy-2'-deoxyguanosine (8-OHdG), a biomarker associated with oxidative stress, is used as a model system for validating the proposed methodology. The detection strategy is based on monitoring the changes in optical properties of PT associated with its conformational changes upon interaction with an aptamer in the presence and in the absence of 8-OHdG. Fluorometric and colorimetric monitoring revealed linear responses for 8-OHdG concentrations between 50 pM and 500 nM (∼14 pg/mL to 140 ng/mL), with limits of detection of ∼300 pM and  ∼350 pM, respectively for ( n = 3). Colorimetric responses in artificial urine ascertained rapid, sensitive, and selective detection of 8-OHdG at clinically relevant (pM to nM) concentration levels. Furthermore, the proposed methodology enables point-of-care diagnostics for oxidative stress without requiring sophisticated instrumentation.

A novel aptamer-based online magnetic solid phase extraction method for the selective determination of 8-hydroxy-2'-deoxyguanosine in human urine

In this work, an innovative magnetic aptamer adsorbent (Fe₃O₄-aptamer MNPs) was synthesized for the selective extraction of 8-hydroxy-2'-deoxyguanosine (8-OHdG). Amino-functionalized-Fe₃O₄ was crosslinked with 8-OHdG aptamer by glutaraldehyde and fixed into a steel stainless tube as the sorbent of magnetic solid phase extraction (MSPE). After selective extraction by the aptamer adsorbent, the adsorbed 8-OHdG was desorbed dynamically and online analyzed by high performance liquid chromatography-mass spectrometry (HPLC-MS). The synthesized sorbent presented outstanding features, including specific selectivity, high enrichment capacity, stability and biocompatibility. Moreover, this proposed MSPE-HPLC-MS can achieve adsorption and desorption operation integration, greatly simplify the analysis process and reduce human errors. When compared with offline MSPE, a sensitivity enhancement of 800 times was obtained for the online method. Some experimental parameters such as the amount of the sorbent, sample flow rate and sample volume, were optimized systematically. Under the optimal conditions, low limit of detection (0.01 ng mL^-1, S/N = 3), limit of quantity (0.03 ng mL^-1, S/N = 10) and wide linear range with a satisfactory correlation coefficient (R² ≥ 0.9992) were obtained. And the recoveries of 8-OHdG in the urine samples varied from 82% to 116%. All these results revealed that the method is simple, rapid, selective, sensitive and automated, and it could be expected to become a potential approach for the selective determination of trace 8-OHdG in complex urinary samples.