Mechanisms of DNA Sensing on Graphene Oxide

Graphene oxide directed in-situ deposition of electroactive silver nanoparticles and its electrochemical sensing application for DNA analysis

The development of high-performance biosensing platform is heavily dependent on the recognition property of the sensing layer and the output intensity of the signal probe. Herein, we present a simple and highly sensitive biosensing interface for DNA detection on the basis of graphene oxide nanosheets (GONs) directed in-situ deposition of silver nanoparticles (AgNPs). The fabrication process and electrochemical properties of the biosensing interface were probed by electrochemical techniques and scanning electron microscopy. The results indicate that GONs can specifically adsorb at the single-stranded DNA probe surface, and induces the deposition of highly electroactive AgNPs. Upon hybridization with complementary oligonucleotides to generate the duplex DNA on the electrode surface, the GONs with the deposited AgNPs will be liberated from the sensing interface due to the inferior affinity of GONs and duplex DNA, resulting in the reduction of the electrochemical signal. Such a strategy combines the superior recognition of GONs toward single-stranded DNA and double-stranded DNA, and the strong electrochemical response of in-situ deposited AgNPs. Under optimal conditions, the biosensor can detect target DNA over a wide range from 10 fM to 10 nM with a detection limit of 7.6 fM. Also, the developed biosensor shows outstanding discriminating ability toward oligonucleotides with different mismatching degrees.

Comparison of Graphene Oxide and Reduced Graphene Oxide for DNA Adsorption and Sensing

Fluorescently labeled DNA adsorbed on graphene oxide (GO) is a well-established sensing platform for detecting a diverse range of analytes. GO is a loosely defined material and its oxygen content may vary depending on the condition of preparation. Sometimes, a further reduction step is intentionally performed to decrease the oxygen content, and the resulting material is called reduced GO (rGO). In this study, DNA adsorption and desorption from GO and rGO is systematically compared. Under the same salt concentration, DNA adsorbs slightly faster with a 2.6-fold higher capacity on rGO. At the same time, DNA adsorbed on rGO is more resistant to desorption induced by temperature, pH, urea, and organic solvents. Various lengths and sequences of DNA probes have been tested. When its complementary DNA is added as a model target analyte, the rGO sample has a higher signal-to-background and signal-to-noise ratio, whereas the GO sample has a slightly higher absolute signal increase and faster signaling kinetics. DNAs adsorbed on GO or rGO are still susceptible to nonspecific displacement by other DNA and proteins. Overall, although rGO adsorbs DNA more tightly, it allows efficient DNA sensing with an extremely low background fluorescence signal.

Biosensors based on graphene oxide and its biomedical application

Graphene oxide (GO) is one of the most attributed materials for opening new possibilities in the development of next generation biosensors. Due to the coexistence of hydrophobic domain from pristine graphite structure and hydrophilic oxygen containing functional groups, GO exhibits good water dispersibility, biocompatibility, and high affinity for specific biomolecules as well as properties of graphene itself partly depending on preparation methods. These properties of GO provided a lot of opportunities for the development of novel biological sensing platforms, including biosensors based on fluorescence resonance energy transfer (FRET), laser desorption/ionization mass spectrometry (LDI-MS), surface-enhanced Raman spectroscopy (SERS), and electrochemical detection. In this review, we classify GO-based biological sensors developed so far by their signal generation strategy and provide the comprehensive overview of them. In addition, we offer insights into how the GO attributed in each sensor system and how they improved the sensing performance.

Aptamer-graphene oxide for highly sensitive dual electrochemical detection of Plasmodium lactate dehydrogenase

A 90 mer ssDNA aptamer (P38) enriched against Plasmodium falciparum lactate dehydrogenase (PfLDH) through SELEX process was immobilized over glassy carbon electrode (GCE) using graphene oxide (GO) as an immobilization matrix, and the modified electrode was investigated for detection of PfLDH. The GO was synthesized from powdered pencil graphite and characterized by XRD based on the increased interlayer distance between graphitic layers from 0.345 nm for graphite to 0.829 nm for GO. The immobilization of P38 on GO was confirmed by I_D/I_G intensity ratio in Raman spectra where, the ratio were 0.67, 0.915, and 1.35 for graphite, GO and P38-GO, respectively. The formation of the P38 layer over GO-GCE was evident from an increase in the surface height in AFM analysis of the electrode from ∼3.5 nm for GO-GCE to ∼27 nm for P38-GO-GCE. The developed aptasensor when challenged with the target, a detection of as low as 0.5 fM of PfLDH was demonstrated. The specificity of the aptasensor was confirmed through a voltametric measurement at 0.65 V of the reduced co-factor generated from the PfLDH catalysis. Studies on interference from some common proteins, storage stability, repeatability and analysis of real samples demonstrated the practical application potential of the aptasensor.

Oxo-Functionalized Graphene as a Cell Membrane Carrier of Nucleic Acid Probes Controlled by Aging

We applied a fluorescein-containing oligonucleotide (ON) to probe surface properties of oxidized graphene (oxo-G) and observed that graphene-like patches are formed upon aging of oxo-G, indicated by enhanced probe binding and by FTIR spectroscopic analysis. By using a recently developed fluorogenic endoperoxide (EP) probe, we confirmed that during the aging process the amount of EPs on the oxo-G surface is reduced. Furthermore, aging was found to strongly affect cell membrane carrier properties of this material. In particular, freshly prepared oxo-G does not act as a carrier, whereas oxo-G aged for 28 days at 4 °C is an excellent carrier. Based on these data we prepared an optimized oxo-G, which has a low-defect density, binds ONs, is not toxic, and acts as cell membrane carrier. We successfully applied this material to design fluorogenic probes of representative intracellular nucleic acids 28S rRNA and β-actin-mRNA. The results will help to standardize oxidized graphene derivatives for biomedical and bioanalytical applications.

Complex Thermodynamic Behavior of Single-Stranded Nucleic Acid Adsorption to Graphene Surfaces

In just over a decade since its discovery, research on graphene has exploded due to a number of potential applications in electronics, materials, and medicine. In its water-soluble form of graphene oxide, the material has shown promise as a biosensor due to its preferential absorption of single-stranded polynucleotides and fluorescence quenching properties. The rational design of these biosensors, however, requires an improved understanding of the binding thermodynamics and ultimately a predictive model of sequence-specific binding. Toward these goals, here we directly measured the binding of nucleosides and oligonucleotides to graphene oxide nanoparticles using isothermal titration calorimetry and used the results to develop molecular models of graphene-nucleic acid interactions. We found individual nucleosides binding KD values lie in the submillimolar range with binding order of rG < rA < rC < dT < rU, while 5mer and 15mer oligonucleotides had markedly higher binding affinities in the range of micromolar and submicromolar KD values, respectively. The molecular models developed here are calibrated to quantitatively reproduce the above-mentioned experimental results. For oligonucleotides, our model predicts complex binding features such as double-stacked bases and a decrease in the fraction of graphene stacked bases with increasing oligonucleotide length until plateauing beyond ∼10-15 nucleotides. These experimental and computational results set the platform for informed design of graphene-based biosensors, further increasing their potential and application.

A cobalt oxyhydroxide nanoflake-based nanoprobe for the sensitive fluorescence detection of T4 polynucleotide kinase activity and inhibition

Phosphorylation of nucleic acids with 5'-OH termini catalyzed by polynucleotide kinase (PNK) is an inevitable process and has been implicated in many important cellular events. Here, we found for the first time that there was a significant difference in the adsorbent ability of cobalt oxyhydroxide (CoOOH) nanoflakes between single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), which resulted in the fluorescent dye-labeled dsDNA still retaining strong fluorescence emission, while the fluorescence signal of ssDNA was significantly quenched by CoOOH nanoflakes. Based on this discovery, we developed a CoOOH nanoflake-based nanoprobe for the fluorescence sensing of T4 PNK activity and its inhibition by combining it with λ exonuclease cleavage reaction. In the presence of T4 PNK, dye-labeled dsDNA was phosphorylated and then cleaved by λ exonuclease to generate ssDNA, which could adsorb on the CoOOH nanoflakes and whose fluorescence was quenched by CoOOH nanoflakes. Due to the high quenching property of CoOOH nanoflakes as an efficient energy acceptor, a sensitive and selective sensing approach with satisfactory performance for T4 PNK sensing in a complex biological matrix has been successfully constructed and applied to the screening of inhibitors. The developed approach may potentially provide a new platform for further research, clinical diagnosis, and drug discovery of nucleotide kinase related diseases.

Atomic Oxygen Tailored Graphene Oxide Nanosheets Emissions for Multicolor Cellular Imaging

Graphene oxide (GO) has been widely used as a fluorescence quencher, but its luminescent properties, especially tailor-made controlling emission colors, have been seldom reported due to its heterogeneous structures. Herein, we demonstrated a novel chemical oxidative strategy to tune GO emissions from brown to cyan without changing excitation wavelength. The precise tuning is simply achieved by varying reaction times of GO nanosheets in piranha solution, but there is no need for complex chromatography separation procedures. With increasing reaction times, oxygen content on the lattice of GO nanosheets increased, accompanied by the diminution of their sizes and sp(2) conjugation system, resulting in an increase of emissive carbon cluster-like states. Thereby, the luminescent colors of GO were tuned from brown to yellow, green, and cyan, and its fluorescent quantum yields were enhanced. The obtained multicolored fluorescent GO nanosheets would open plenty of novel applications in cellular imaging and multiplex encoding analysis.

Graphene oxide surface blocking agents can increase the DNA biosensor sensitivity

Graphene oxide adsorbs single-strand fluorescent probe DNA, and the adsorbed probe can be desorbed by adding the complementary target DNA. Using this method, many biosensor studies have been carried out. We recently proposed a two-step mechanism for this sensing reaction: non-specific probe displacement followed by hybridization in the solution. Only about one out of six added target DNA is hybridized with the adsorbed probe to generate signal, leading to relatively low sensitivity. In this work, we aim to test whether surface blocking agents can minimize non-specific target adsorption and increase hybridization efficiency. Over ten blocking agents (polymers, surfactants, and DNA) were screened based on their effect on probe DNA adsorption and target DNA induced probe desorption. DNA oligonucleotides show significant and controllable enhancement in sensor sensitivity. The effect of DNA length and sequence was systematically investigated. Under optimized conditions, the sensor sensitivity was enhanced by nearly 10-fold. Using the same blocking method, sensitivity enhancement of other targets was also achieved, including adenosine and Hg(2+) with DNA aptamer probes. This reported surface blocking strategy can generally improve graphene oxide and potentially other surface adsorption based biosensors for metal ions, small molecules, and DNA.

Hg2+ detection using a phosphorothioate RNA probe adsorbed on graphene oxide and a comparison with thymine-rich DNA

Using phosphorothioate modified RNA probes adsorbed by graphene oxide, Hg²⁺ is detected sensitively with less interference.

A highly sensitive strategy for base excision repair enzyme activity detection based on graphene oxide mediated fluorescence quenching and hybridization chain reaction

We report a highly sensitive strategy for UDG activity detection by combining HCR amplification and a GO-based fluorescence quenching platform.

Amplified binding-induced homogeneous assay through catalytic cycling of analyte for ultrasensitive protein detection

Amplified binding-induced homogeneous assay through catalytic cycling of analytes for ultrasensitive protein detection.

Detection of adenosine triphosphate in HeLa cell using capillary electrophoresis-laser induced fluorescence detection based on aptamer and graphene oxide

A method for ATP quantification based on dye-labeled aptamer/graphene oxide (aptamer/GO) using capillary electrophoresis-laser induced fluorescence (CE-LIF) detecting technique has been established. In this method, the carboxyfluorescein (FAM)-labelled ATP aptamers were adsorbed onto the surface of GO, leading to the fluorescence quenching of FAM; after the incubation with a limited amount of ATP, stronger affinity between ATP aptamer and ATP resulted in the desorption of aptamers and the fluorescence restoration of FAM. Then, aptamer-ATP complex and excess of aptamer/GO and GO were separated and quantified by CE-LIF detection. It was shown that a linear relation was existing in the CE-LIF peak intensity of aptamer-ATP and ATP concentration in range of 10-700 μM, the regression equation was F=1.50+0.0470C(ATP) (R(2)=0.990), and the limit of detection was 1.28 μM (3S/N, n=5), which was one order magnitude lower than that of detection in solution by fluorescence method. The approach with excellent specificity and reproducibility has been successfully applied to detecting concentration of ATP in HeLa cell.

A Graphene-Based Biosensing Platform Based on Regulated Release of an Aptameric DNA Biosensor

A novel biosensing platform was developed by integrating an aptamer-based DNA biosensor with graphene oxide (GO) for rapid and facile detection of adenosine triphosphate (ATP, as a model target). The DNA biosensor, which is locked by GO, is designed to contain two sensing modules that include recognition site for ATP and self-replication track that yields the nicking domain for Nt.BbvCI. By taking advantage of the different binding affinity of single-stranded DNA, double-stranded DNA and aptamer-target complex toward GO, the DNA biosensor could be efficiently released from GO in the presence of target with the help of a complementary DNA strand (CPDNA) that partially hybridizes to the DNA biosensor. Then, the polymerization/nicking enzyme synergetic isothermal amplification could be triggered, leading to the synthesis of massive DNA amplicons, thus achieving an enhanced sensitivity with a wide linear dynamic response range of four orders of magnitude and good selectivity. This biosensing strategy expands the applications of GO-DNA nanobiointerfaces in biological sensing, showing great potential in fundamental research and biomedical diagnosis.

Preparation of a Three-Dimensional Reduced Graphene Oxide Film by Using the Langmuir-Blodgett Method

The Langmuir-Blodgett method has always been traditionally utilized in the deposition of two-dimensional structures. In this work, however, we employed the method to deposit three-dimensional reduced graphene oxide layers using an unconventional protocol for the first time. This was achieved by carrying out the dipping process after the collapse pressure or breaking point, which results in the formation of a highly porous three-dimensional surface topography. By varying the number of deposition layers, the porosity could be optimized from nanometer to micrometer dimensions. Employed as bioelectrodes, these three-dimensional reduced graphene oxide layers may allow improved adhesion and biocompatibility compared to the conventional two-dimensional surfaces. A larger number of pores also improves the mass transport of materials and therefore increases the charge-sustaining capacity and sensitivity. This could ultimately improve the performance of biofuel cells and other electrode-based systems.

Discriminating a Single Nucleotide Difference for Enhanced miRNA Detection Using Tunable Graphene and Oligonucleotide Nanodevices

In this study we have reported our efforts to address some of the challenges in the detection of miRNAs using water-soluble graphene oxide and DNA nanoassemblies. Purposefully inserting mismatches at specific positions in our DNA (probe) strands shows increasing specificity against our target miRNA, miR-10b, over miR-10a which varies by only a single nucleotide. This increased specificity came at a loss of signal intensity within the system, but we demonstrated that this could be addressed with the use of DNase I, an endonuclease capable of cleaving the DNA strands of the RNA/DNA heteroduplex and recycling the RNA target to hybridize to another probe strand. As we previously demonstrated, this enzymatic signal also comes with an inherent activity of the enzyme on the surface-adsorbed probe strands. To remove this activity of DNase I and the steady nonspecific increase in the fluorescence signal without compromising the recovered signal, we attached a thermoresponsive PEGMA polymer (poly(ethylene glycol) methyl ether methacrylate) to nGO. This smart polymer is able to shield the probes adsorbed on the nGO surface from the DNase I activity and is capable of tuning the detection capacity of the nGO nanoassembly with a thermoswitch at 39 °C. By utilizing probes with multiple mismatches, DNase I cleavage of the DNA probe strands, and the attachment of PEGMA polymers to graphene oxide to block undesired DNase I activity, we were able to detect miR-10b from liquid biopsy mimics and breast cancer cell lines. Overall we have reported our efforts to improve the specificity, increase the sensitivity, and eliminate the undesired enzymatic activity of DNase I on surface-adsorbed probes for miR-10b detection using water-soluble graphene nanodevices. Even though we have demonstrated only the discrimination of miR-10b from miR-10a, our approach can be extended to other short RNA molecules which differ by a single nucleotide.

Monitoring the multitask mechanism of DNase I activity using graphene nanoassemblies

Here we have demonstrated that graphene serves as a remarkable platform for monitoring the multitask activity of an enzyme with fluorescence spectroscopy. Our studies showed that four different simultaneous enzymatic tasks of DNase I can be observed and measured in a high throughput fashion using graphene oxide and oligonucleotide nanoassemblies. We have used phosphorothioate modified oligonucleotides to pinpoint the individual and highly specific functions of DNase I with single stranded DNA, RNA, and DNA/DNA and DNA/RNA duplexes. DNase I resulted in fluorescence recovery in the nanoassemblies and enhanced the intensity tremendously in the presence of sequence specific DNA or RNA molecules with different degrees of amplification. Our study enabled us to discover the sources of this remarkable signal enhancement, which has been used for biomedical applications of graphene for sensitive detection of specific oncogenes. The significant difference in the signal amplification observed for the detection of DNA and RNA molecules is a result of the positive and/or reductive signal generating events with the enzyme. In the presence of DNA there are four possible ways that the fluorescence reading is influenced, with two of them resulting in a gain in signal while the other two result in a loss. Since the observed signal is a summation of all the events together, the absence of the two fluorescence reduction events with RNA gives a greater degree of fluorescence signal enhancement when compared to target DNA molecules. Overall, our study demonstrates that graphene has powerful features for determining the enzymatic functions of a protein and reveals some of the unknowns observed in the graphene and oligonucleotide assemblies with DNase I.

A sensitive fluorescence turn-on assay of bleomycin and nuclease using WS2 nanosheet as an effective sensing platform

As an important antitumor drug, bleomycin (BLM) is widely used in the treatment of a variety of cancers. In addition, nucleases play a crucial role in DNA replication, recombination and repair which are associated with cancer development. Thus, the development of BLM and nuclease detection methods is of great significance in cancer therapy and related biological mechanism research. Here, a WS2 nanosheet-based turn-on fluorescent sensing platform for simple, fast and sensitive detection of BLM and nuclease was reported. WS2 nanosheet exhibits different affinity toward ssDNA with different length and excellent fluorescence quenching ability. A fluorescein (FAM)-labeled long ssDNA could be adsorbed on the surface of WS2 nanosheet and the fluorescence was therefore quenched. In the presence of BLM·Fe(II) or S1 nuclease (a ssDNA-specific nuclease which was used as a model enzyme), an irreversible scission of long ssDNA was underwent through the BLM-induced oxidation cleavage or S1 nuclease-induced enzymatic hydrolysis. Short FAM-linked oligonucleotide fragments which could not be adsorbed on the nanosheet surface were then produced, resulting in a weak fluorescence quenching after mixing WS2 nanosheets. Thus, the fluorescence signal was restored. The proposed sensor displays a wide linear range and a high sensitivity with a detection limit of 0.3 nM for BLM and 0.01 U mL(-1) for S1 nuclease. It also exhibits a good performance in complex biological samples. This method not only provides a strategy for BLM or S1 nuclease assay but also offers a potential application in biomedical and clinical study.

Evaporation induced wrinkling of graphene oxide at the nanoparticle interface

With the thickness of only a single atomic layer, graphene displays many interesting surface properties. A general observation is that wrinkles are formed on graphene oxide (GO) when it is dried in the presence of adsorbed inorganic nanoparticles. In this case, evaporation induced wrinkling is not an elastic deformation but is permanent. Understanding the nanoscale force of wrinkle formation is important for device fabrication and sensing. Herein, we employ surface functionalized gold nanoparticles (AuNPs) as a model system. All tested AuNPs induced wrinkling, including those capped by DNA, polymers and proteins. The size of AuNPs is less important compared to the properties of solvent. Wrinkle formation is attributed to drying related capillary force acting on the GO surface, and a quantitative equation is derived. After drying, the adsorption affinity between GO and AuNPs is increased due to the increased contact area.

High performance system for protein assays: synergistic effect of terminal protection strategy and graphene oxide platform

A straightforward biosensor for protein assay has been developed based on terminal protection of small molecule-linked DNA by target protein and the difference in affinity of graphene oxide for ssDNA containing different numbers of bases in length.

Single-base mismatch discrimination by T7 exonuclease with target cyclic amplification detection

T7 exonuclease is reported for the first time to have high specificity in discriminating single-base mismatch.

The graphene/nucleic acid nanobiointerface

In this critical review, we present the recent advances in the design and fabrication of graphene/nucleic acid nanobiointerfaces, as well as the fundamental understanding of their interfacial properties and various nanobiotechnological applications.

DNA adsorption by indium tin oxide nanoparticles

The high conductivity and optical transparency of indium tin oxide (ITO) has made it a popular material in the electronic industry. Recently, its application in biosensors is also explored. To understand its biointerface chemistry, we herein investigate its interaction with fluorescently labeled single-stranded oligonucleotides using ITO nanoparticles (NPs). The fluorescence of DNA is efficiently quenched after adsorption, and the interaction between DNA and ITO NPs is strongly dependent on the surface charge of ITO. At low pH, the ITO surface is positively charged to afford a high DNA adsorption capacity. Adsorption is also influenced by the sequence and length of DNA. For its components, In2O3 adsorbs DNA more strongly while SnO2 repels DNA at neutral pH. The DNA adsorption property of ITO is an averaging result from both components. DNA adsorption is confirmed to be mainly by the phosphate backbone via displacement experiments using free phosphate or DNA bases. Last, DNA-induced DNA desorption by forming duplex DNA is demonstrated on ITO, while the same reaction is more difficult to achieve on other metal oxides including CeO2, TiO2, and Fe3O4 because these particles adsorb DNA more tightly.

A general strategy to create RNA aptamer sensors using "regulated" graphene oxide adsorption

Aptamers have been used as molecular recognition elements for sensor development in combination with graphene oxide (GO), a nanomaterial with properties including fluorescence quenching, and selective adsorption of single-stranded nucleic acids. However, previous sensor designs based on aptamer-GO adsorption have not demonstrated wide applicability, and few studies have explored the potential of RNA aptamers. Herein, we present a new sensing strategy based on "regulated" GO adsorption that can accommodate various RNA aptamers. First, adsorption of a fluorophore-labeled RNA aptamer to GO results in fluorescence quenching due to close proximity of the fluorophore to GO. The addition of a complementary, "blocking" DNA strand (BDNA) that hybridizes to the 3'-end of the aptamer, weakens aptamer-GO interaction, and enables increased fluorescent signal generation upon the addition of target, as the sensing system becomes completely separated from GO. Our findings can be applied toward different aptamers, and adapted to enhance generality of existing sensing applications.

Intracellular detection of ATP using an aptamer beacon covalently linked to graphene oxide resisting nonspecific probe displacement

Fluorescent aptamer probes physisorbed on graphene oxide (GO) have recently emerged as a useful sensing platform. A signal is generated by analyte-induced probe desorption. To address nonspecific probe displacement and the false positive signal, we herein report a covalently linked aptamer probe for adenosine triphosphate (ATP) detection. A fluorophore and amino dual modified aptamer was linked to the carboxyl group on GO with a coupling efficiency of ∼50%. The linearity, specificity, stability, and regeneration of the covalent sensor were systematically studied and compared to the physisorbed probe. Both sensors have similar sensitivity, but the covalent one is more resistant to nonspecific probe displacement by proteins. The covalent sensor has a dynamic range from 0.125 to 2 mM ATP in buffer at room temperature and is resistance to DNase I. Intracellular ATP imaging was demonstrated using the covalent sensor, which generated a higher fluorescence signal than the physisorbed sensor. After the cells were stimulated with 5 mM Ca(2+) for ATP production, the intracellular signal enhanced by 31.8%. This work highlights the advantages of covalent aptamer sensors using GO as both a quencher and a delivery vehicle for intracellular metabolite detection.

Mechanism of DNA adsorption and desorption on graphene oxide

Graphene oxide (GO) adsorbing a fluorophore-labeled single-stranded (ss) DNA serves as a sensor system because subsequent desorption of the adsorbed probe DNA from GO in the presence of complementary target DNA enhances the fluorescence. In this study, we investigated the interaction of single- and double-stranded (ds) DNAs with GO by using a fluorescently labeled DNA probe. Although GO is known to preferentially interact with ssDNA, we found that dsDNA can also be adsorbed on GO, albeit with lower affinity. Furthermore, the status of ssDNA or dsDNA previously adsorbed on the GO surface was investigated by adding complementary or noncomplementary DNA (cDNA or non-cDNA) to the adsorption complex. We observed that hybridization occurred between the cDNA and the probe DNA on the GO surface. On the basis of the kinetics driven by the incoming additional DNA, we propose a mechanism for the desorption of the preadsorbed probe DNA from the GO surface: the desorption of the GO-adsorbed DNA was facilitated following its hybridization with cDNA on the GO surface; when the GO surface was almost saturated with the adsorbed DNA, nonspecific desorption dominated the process through a simple displacement of the GO-adsorbed DNA molecules by the incoming DNA molecules because of the law of mass action. Our results can be applied to design appropriate DNA probes and to choose proper GO concentrations for experimental setups to improve specific signaling in many biosensor systems based on the GO platform.

Label-free triple-helix aptamer as sensing platform for "signal-on" fluorescent detection of thrombin

The design of a label-free aptamer for separation of recognition sequence from signal reporter is significant to ensure the high-efficiency affinity between aptamer and target. This work develops a label-free triple-helix aptamer (THA) as sensing platform for "signal-on" fluorescent detection of thrombin. THA was composed of aptamer sequence and help DNA 1 (H1), which contained the complementary sequence of hexachloro-fluorescein (HEX) labeled help DNA 2 (H2). The specific recognition event between aptamer and thrombin triggered the dismission of THA to release H1. The released H1 then reacted with the signal probe of H2/graphene oxide (GO) nanocomposite to form H1-H2 duplex, leading to the fluorescence recovery of H2 due to the detachment of H1-H2 duplex from the surface of GO. With employment of THA as a signal transducer and GO as a "superquencher", this method shows a sensitive response to thrombin with a wide concentration range from 5 to 1200 nM. The limit of detection is 1.8 nM (S/N=3) with excellent selectivity. Considering the universality of THA, the proposed aptasensor would provide a platform for homogeneous fluorescent detection of a wide range of analytes.

A base-modified PNA-graphene oxide platform as a turn-on fluorescence sensor for the detection of human telomeric repeats

Given the biological and therapeutic significance of telomeres and other G-quadruplex forming sequences in human genome, it is highly desirable to develop simple methods to study these structures, which can also be implemented in screening formats for the discovery of G-quadruplex binders. The majority of telomere detection methods developed so far are laborious and use elaborate assay and instrumental setups, and hence, are not amenable to discovery platforms. Here, we describe the development of a simple homogeneous fluorescence turn-on method, which uses a unique combination of an environment-sensitive fluorescent nucleobase analogue, the superior base pairing property of PNA, and DNA-binding and fluorescence quenching properties of graphene oxide, to detect human telomeric DNA repeats of varying lengths. Our results demonstrate that this method, which does not involve a rigorous assay setup, would provide new opportunities to study G-quadruplex structures.

Recent advances in aptasensors based on graphene and graphene-like nanomaterials

Graphene and graphene-like two-dimensional nanomaterials have aroused tremendous research interest in recent years due to their unique electronic, optical, and mechanical properties associated with their planar structure. Aptamers have exhibited many advantages as molecular recognition elements for sensing devices compared to traditional antibodies. The marriage of two-dimensional nanomaterials and aptamers has emerged many ingenious aptasensing strategies for applications in the fields of clinical diagnosis and food safety. This review highlights current advances in the development and application of two-dimensional nanomaterials-based aptasensors with the focus on two main signal-transducing mechanisms, i.e. electrochemical and optical. A special attention is paid to graphene, a one-atom thick layer of graphite with exceptional properties, representing a fastgrowing field of research. In view of the unique properties of two-dimensional nanostructures and their inherent advantages of synthetic aptamers, we expect that high-performance two-dimensional nanomaterials-based aptasensing devices will find extensive applications in environmental monitoring, biomedical diagnostics, and food safety.

In situ simultaneous monitoring of ATP and GTP using a graphene oxide nanosheet-based sensing platform in living cells

Here we present a detailed protocol for in situ multiple fluorescence monitoring of adenosine-5'-triphosphate (ATP) and guanosine-5'-triphosphate (GTP) in MCF-7 breast cancer cells by using graphene oxide nanosheet (GO-nS) and DNA/RNA aptamers. FAM-labeled ATP aptamer and Cy5-modified GTP aptamer are used to construct the multiple aptamer/GO-nS sensing platform through 'π-π stacking' between aptamers and GO-nS. Binding of aptamers to GO-nS guarantees the fluorescence resonance energy transfer between fluorophores and GO-nS, resulting in 'fluorescence off'. When the aptamer/GO-nS are transported inside the cells via endocytosis, the conformation of the aptamers will change on interaction with cellular ATP and GTP. On the basis of the fluorescence 'off/on' switching, simultaneous sensing and imaging of ATP and GTP in vitro and in situ have been realized through fluorescence and confocal microscopy techniques. In this protocol, we describe the synthesis of GO and GO-nS, preparation of aptamer/GO-nS platform, in vitro detection of ATP and GTP, and how to use this platform to realize intracellular ATP and GTP imaging in cultured MCF-7 cells. The preparation of GO-nS is anticipated to take 7-14 d, and assays involving microscopy imaging and MCF-7 cells culturing can be performed in 2-3 d.

Nano-graphene oxide as a novel platform for monitoring the effect of LNA modification on nucleic acid interactions

Graphene oxide has gained significant attention due to its exceptional physical properties at biological interfaces. It has extraordinary quenching, fast adsorption and desorption properties that are suitable for detection of molecular interactions in nucleic acids. Here we studied the interaction between locked nucleic acid (LNA) modified oligonucleotides and its complementary miR-10b DNA analog. We demonstrate that LNA modification does not alter the hybridization yield, despite a slight difference in the rate, however it does increase the duplex stability dramatically. The noncovalent nucleic acid-graphene oxide complex maintained the stability between 25 and 90 °C in the absence of oligonucleotide-induced desorption. The melting temperatures of duplexes with or without LNA base modification were determined due to remarkable fluorescence quenching and fast oligonucleotide adsorption with graphene oxide. The difference in melting temperatures was used to control the release of surface adsorbed nucleic acids at 70 °C. Finally, a mutation in the oligonucleotide sequence is detected by the complementary oligonucleotides on the graphene oxide surface. Due to its extraordinary physical properties, graphene oxide represents a remarkable platform for studying nucleic acid interactions and serves as a promising material for biomedical applications.

Fluorescent sensors using DNA-functionalized graphene oxide

In the past few years, graphene oxide (GO) has emerged as a unique platform for developing DNA-based biosensors, given the DNA adsorption and fluorescence-quenching properties of GO. Adsorbed DNA probes can be desorbed from the GO surface in the presence of target analytes, producing a fluorescence signal. In addition to this initial design, many other strategies have been reported, including the use of aptamers, molecular beacons, and DNAzymes as probes, label-free detection, utilization of the intrinsic fluorescence of GO, and the application of covalently linked DNA probes. The potential applications of DNA-functionalized GO range from environmental monitoring and cell imaging to biomedical diagnosis. In this review, we first summarize the fundamental surface interactions between DNA and GO and the related fluorescence-quenching mechanism. Following that, the various sensor design strategies are critically compared. Problems that must be overcome before this technology can reach its full potential are described, and a few future directions are also discussed.

Platinated DNA oligonucleotides: new probes forming ultrastable conjugates with graphene oxide

Metal containing polymers have expanded the property of polymers by involving covalently associated metal complexes. DNA is a special block copolymer. While metal ions are known to influence DNA, little is explored on its polymer property when strong metal complexes are associated. In this work, we study cisplatin modified DNA as a new polymer and probe. Out of the complexes formed between cisplatin-A15, HAuCl4-A15, Hg(2+)-T15 and Ag(+)-C15, only the cisplatin adduct is stable under the denaturing gel electrophoresis condition. Each Pt-nucleobase bond gives a positive charge and thus makes DNA a zwitterionic polymer. This allows ultrafast adsorption of DNA by graphene oxide (GO) and the adsorbed complex is highly stable. Non-specific DNA, protein, surfactants and thiolated compounds cannot displace platinated DNA from GO, while non-modified DNA is easily displaced in most cases. The stable GO/DNA conjugate is further tested for surface hybridization. This is the first demonstration of using metallated DNA as a polymeric material for interfacing with nanoscale materials.

A WS2 nanosheet based sensing platform for highly sensitive detection of T4 polynucleotide kinase and its inhibitors

DNA phosphorylation, catalyzed by polynucleotide kinase (PNK), plays significant regulatory roles in many biological events. Here, a novel fluorescent nanosensor based on phosphorylation-specific exonuclease reaction and efficient fluorescence quenching of single-stranded DNA (ssDNA) by a WS2 nanosheet has been developed for monitoring the activity of PNK using T4 polynucleotide kinase (T4 PNK) as a model target. The fluorescent dye-labeled double-stranded DNA (dsDNA) remains highly fluorescent when mixed with WS2 nanosheets because of the weak adsorption of dsDNA on WS2 nanosheets. While dsDNA is phosphorylated by T4 PNK, it can be specifically degraded by λ exonuclease, producing ssDNA strongly adsorbed on WS2 nanosheets with greatly quenched fluorescence. Because of the high quenching efficiency of WS2 nanosheets, the developed platform presents excellent performance with a wide linear range, low detection limit and high signal-to-background ratio. Additionally, inhibition effects from adenosine diphosphate, ammonium sulfate, and sodium chloride have been investigated. The method may provide a universal platform for PNK activity monitoring and inhibitor screening in drug discovery and clinic diagnostics.