Aptamer-nanoparticle assembly for logic-based detection

UV light promoted dihydrolipoic acid and its alanine derivative directed rapid synthesis of stable gold nanoparticles and their catalytic activity

In general, colloidal gold nanoparticles (AuNPs) have been synthesized in heated or boiling water containing HAuCl4 precursor with sodium citrate as reducing stabilizing reagent. Although temperature plays a driving for synthesis of AuNPs, elevated temperature in thermal reduction method causes aggregation of the AuNPs. The preferential, rapid and strong binding of dihydro-lipoic acid and its derivatives on surface of AuNPs via thiol - Au chemistry promote the production of very stable AuNPs. In this study, we have developed citric acid (CA), dihydrolipoic acid (DHLA) and DHLA-Alanine (DHLA-Ala) directed rapid synthesis of ultra-stable AuNPs, DHLA@AuNPs and DHLA-Ala@AuNPs, under the UV (311 nm) irradiation at room temperature (RT: 25 °C) in around 10 min (min). CA is used as a potential reducing agent to expedite both reduction of Au3+ ion and AuNP formation, DHLA and DHLA-Ala act as stabilizing agents by replacing CA molecules on surface of AuNPs in order to produce quite stable AuNP. It is worthy to mention that reduction of Au3+ ion, formation and surface stabilization of AuNPs are consequently occurred in one step. We also investigated how experimental parameters including reaction time and temperature, pH of reaction solution, affect formation of the AuNPs. The effects of salt concentration and storage temperature were studied to show stability of the AuNPs. The synthesized DHLA@AuNPs and DHLA-Alanine@AuNPs were characterized via UV-Vis spectrophotometer (UV-Vis), scanning transmission electron microscope (STEM), dynamic light scattering (DLS) and Zeta potential (ZT) devices. The reduction of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) was efficiently catalyzed by the AuNPs in the presence of sodium borohydride in aqueous solution.

Sensing Characteristics of SARS-CoV-2 Spike Protein Using Aptamer-Functionalized Si-Based Electrolyte-Gated Field-Effect Transistor (EGT)

The sensing responses of SARS-CoV-2 spike protein using top-down-fabricated Si-based electrolyte-gated transistors (EGTs) have been investigated. An aptamer was employed as a receptor for the SARS-CoV-2 spike protein. The EGT demonstrated excellent intrinsic characteristics and higher sensitivity in the subthreshold regime compared to the linear regime. The limit of detection (LOD) was achieved as low as 0.94 pg/mL and 20 pg/mL for the current and voltage sensitivity, respectively. To analyze the sensing responses of EGT in detecting the aptamer-SARS-CoV-2 spike protein conjugate, a lumped-capacitive model with the presence of an effective dipole potential and an effective capacitance of the functionalized layer component was employed. The aptamer-functionalized EGT showed high sensitivity even in 10 mM phosphate-buffered saline (PBS) solution. These results suggest that Si-based EGTs are a highly promising method for detecting SARS-CoV-2 spike proteins.

Repeatable detection of Ag+ ions using a DNA aptamer-linked hydrogel biochemical sensor integrated with microfluidic heating system

This paper describes repeatable detection of Ag⁺ ions using a DNA aptamer-linked hydrogel biochemical sensor integrated with a microfluidic heating system. Biochemical sensors that respond to chemical compounds and produce detectable signals have a critical role in many aspects of modern society. In particular, the repeatable measurement of environmental information such as toxic substances including Ag⁺ ions could be expected to improve the environment. The DNA aptamer is an attractive candidate because of the stability and the selectivity of binding to chemicals. However, previous DNA aptamer biochemical sensors could not measure repeatedly because those sensors did not have initializing functions. To overcome this challenge, we proposed a DNA aptamer-linked hydrogel biochemical sensor integrated with the microfluidic heating system enabling repeatable detection of Ag⁺ ions. The binding Ag⁺ ions are dissociated by heating and flushing through the integrated microfluidic heating device. The DNA aptamer-linked hydrogel had the capability to detect a wide range of Ag⁺ ion concentrations (10^-5-10 mM) including a toxic range for various aquatic organisms. Finally, we demonstrated the repeatable detection of the Ag⁺ ions. These results indicated that our proposed biochemical sensor is expected to use for long-term monitoring with high stability in ambient temperature and low power consumption.

The development of a colorimetric biosensing assay for the detection of Helicobacter pylori in feces

As Helicobacter pylori (H. pylori) is closely related to the occurrence of gastric diseases such as chronic gastritis, peptic ulcer, and gastric cancer, early detection of H. pylori is an urgent need. In this study, oligonucleotide probes conjugated with gold nanoparticles (AuNPs) were used in combination with H. pylori-specific aptamers for the rapid detection of H. pylori in stool samples, which converted the method of detection from proteins to nucleic acids. Therefore, qualitative detection of H. pylori can be achieved by observing color changes through the aggregation (red to purple) or deaggregation (purple to red) of AuNPs, and further quantitative detection can be achieved through UV spectrometry. The detection limit of the colorimetric biosensing method is 25 CFU/mL (S/N = 3), which is favorably comparable to other reported detection methods. Compared with the existing detection methods for H. pylori, this colorimetric biosensing method has no limitations to the test subjects. All these features render the colorimetric biosensing assay a promising method for the clinical field detection of H. pylori.

Gold-based nanostructured platforms for oxytetracycline detection from milk by a "signal-on" aptasensing approach

Several gold platforms of different morphologies were investigated in the elaboration of a new aptasensor for oxytetracycline. Au-nanostructures were electrochemically synthesized from solutions of different concentrations of HAuCl₄ in different media by chronoamperometry, multipulse amperometry, and chronopotentiometry, respectively at carbon-based screen-printed electrodes (C-SPE). The nano-/micro-scale morphologies of the patterned surfaces and elemental composition were examined by scanning electron microscopy, atomic force microscopy, and X-ray photoelectron spectroscopy, respectively. The electrochemical properties of the obtained gold nanostructured platforms (AuNSs|C-SPE) were investigated to achieve optimal aptamer coverage. The results showed that the aptasensor developed using the platform with thistle-like AuNSs exhibited the highest conductivity in terms of ferrocene signal and the largest effective area. Under optimal conditions, a linear range from 5.0 × 10^-8 M to 1.2 × 10^-6 M, with a limit of detection (LOD) of 8.7 × 10^-9 M OXT were obtained, which is about 20 times lower than the EU regulations for OXT residues in milk. The electrochemical aptasensor was able to discriminate other antibacterial agents, such as amoxicillin, ampicillin, gentamicin, tetracycline, and vancomycin and was successfully applied in milk samples. This "signal-on" aptasensing approach provides a simple and cost-effective disposable sensor that could be easily applied for the on-site determination of antibiotics.

A colorimetric and SERS dual-readout sensor for sensitive detection of tyrosinase activity based on 4-mercaptophenyl boronic acid modified AuNPs

Tyrosinase (TYR) is as a well-known polyphenol oxidase and important biomarker of melanocytic lesions. Thus, developing powerful methods to determine TYR activity is of great value in the early diagnosis of skin disease. Direct surface-enhanced Raman scattering (SERS) detection of biomolecules is usually affected by non-specific interference and complicate structure of the analytes. It is a challenge to develop Raman-active molecules with specific recognition to analytes in complex media. Here, we report a novel colorimetric and surface-enhanced Raman scattering (SERS) dual-readout assay for the determination of TYR using commercially available and economical 4-mercaptophenyl boronic acid (4-MPBA) as a Raman-active and recognition molecule. 4-MPBA provides a unique interactive boronic acid group to the diol group of TYR substrate and exhibits good SERS signal. Also, the introduction of magnetic beads could promptly improve the anti-interference ability of dual-mode sensor. The TYR-incubated tyramine-modified magnetic beads could obviously change the concentration of 4-MPBA-AuNPs in the presence of O₂ and ascorbic acid, where the ultraviolet visible (UV-vis) absorption and SERS intensity were directly related to the concentration of TYR added. The dual-mode sensor had a rapid response to TYR within 1 min under optimized conditions and had high selectivity for TYR with a limit of detection at 0.001 U/mL. In addition, the dual-mode strategy showed promising prospects in the determination of TYR activity in serum samples and could be used to screen TYR inhibitors.

Investigation of ellagic acid rich-berry extracts directed silver nanoparticles synthesis and their antimicrobial properties with potential mechanisms towards Enterococcus faecalis and Candida albicans

The essential goals of this present study are to elucidate the formation mechanism of ellagic acid rich-blackberry, BBE, (Rubus fruticosus L.) and raspberry, RBE, (Rubus idaeus L.) extracts directed silver nanoparticles and to investigate thier antimicrobial properties towards model dental pathogens E. faecalis and C. albicans compared to BBE, RBE, NaOCl, CHX and EDTA. Both %5 w/w of BBE and RBE reacted with 5 mM Ag ⁺ ions at room temperature (25 °C) under mild-stirring, the formation of BBE and RBE directed b@Ag NP and r@Ag NP was monitored over time by using an Uv-vis spectrophotometer. Both b@Ag and r@Ag NPs were also complementarily characterized with SEM and FT-IR. In terms of the antimicrobial studies, b@Ag NP, r@Ag NP, %5 BBE and RBE, 5 mM AgNO₃, %5 NaOCl, %1,5 CHX and %15 EDTA were separately incubated with E. faecalis and C. albicans suspensions. The results were evaluated with student t-test using GraphPad Prism 8.0.1 statistical software (P < 0.05). While formation of b@Ag NP was confirmed with characteristic absorbance at ~435 nm in 20 min (min) of incubation, r@Ag NP did not give absorbance till 80 min owing to concentration of ellagic acid acted as a reducing and stabilizng agent for formation of the Ag NPs. Intrestingly, 50 ppm r@Ag NP inactivated ∼89% and ∼99% of E. faecalis and C. albicans cell, respectively, ∼25% and ∼40% cell inactivations for E. faecalis and C. albicans were observed respectively with 50 ppm b@Ag NP. We showed that 50 ppm r@Ag NP has effective antimicrobial property as much as mostly used %5 NaOCl and %1,5 CHX solutions.

Development of Synthetic DNA Circuit and Networks for Molecular Information Processing

Deoxyribonucleic acid (DNA), a genetic material, encodes all living information and living characteristics, e.g., in cell, DNA signaling circuits control the transcription activities of specific genes. In recent years, various DNA circuits have been developed to implement a wide range of signaling and for regulating gene network functions. In particular, a synthetic DNA circuit, with a programmable design and easy construction, has become a crucial method through which to simulate and regulate DNA signaling networks. Importantly, the construction of a hierarchical DNA circuit provides a useful tool for regulating gene networks and for processing molecular information. Moreover, via their robust and modular properties, DNA circuits can amplify weak signals and establish programmable cascade systems, which are particularly suitable for the applications of biosensing and detecting. Furthermore, a biological enzyme can also be used to provide diverse circuit regulation elements. Currently, studies regarding the mechanisms and applications of synthetic DNA circuit are important for the establishment of more advanced artificial gene regulation systems and intelligent molecular sensing tools. We therefore summarize recent relevant research progress, contributing to the development of nanotechnology-based synthetic DNA circuits. By summarizing the current highlights and the development of synthetic DNA circuits, this paper provides additional insights for future DNA circuit development and provides a foundation for the construction of more advanced DNA circuits.

High Stability Au NPs: From Design to Application in Nanomedicine

In recent years, Au-based nanomaterials are widely used in nanomedicine and biosensors due to their excellent physical and chemical properties. However, these applications require Au NPs to have excellent stability in different environments, such as extreme pH, high temperature, high concentration ions, and various biomatrix. To meet the requirement of multiple applications, many synthetic substances and natural products are used to prepare highly stable Au NPs. Because of this, we aim at offering an update comprehensive summary of preparation high stability Au NPs. In addition, we discuss its application in nanomedicine. The contents of this review are based on a balanced combination of our studies and selected research studies done by worldwide academic groups. First, we address some critical methods for preparing highly stable Au NPs using polymers, including heterocyclic substances, polyethylene glycols, amines, and thiol, then pay attention to natural product progress Au NPs. Then, we sum up the stability of various Au NPs in different stored times, ions solution, pH, temperature, and biomatrix. Finally, the application of Au NPs in nanomedicine, such as drug delivery, bioimaging, photothermal therapy (PTT), clinical diagnosis, nanozyme, and radiotherapy (RT), was addressed concentratedly.

DNA Aptamer-Conjugated Magnetic Graphene Oxide for Pathogenic Bacteria Aggregation: Selective and Enhanced Photothermal Therapy for Effective and Rapid Killing

Methicillin-resistant Staphylococcus aureus (MRSA), often called "superbug", is a nosocomial and multidrug resistance bacterium that shows resistance to β-lactam antibiotics. There has been high demand to develop an alternative treatment model to antibiotics for efficiently fighting MRSA. Herein, we developed DNA aptamer-conjugated magnetic graphene oxide (Apt@MGO) as a multifunctional and biocompatible nanoplatform for selective and rapid eradication of MRSA and evaluated heat generation and cell death performance of Apt@MGO for the first time under dispersed and aggregated states. The aptamer sequence was specifically selected for MRSA and acted as a molecular targeting probe for selective MRSA recognition and antibiotic-free therapy. Magnetic graphene oxide (MGO) serves as a nanoplatform for aptamer conjugation and as a photothermal agent by converting near-infrared (NIR) light to heat. Iron oxide nanoparticles (Fe3O4 NPs) are formed on GO to prepare MGO, which shows magnetic properties for collecting MRSA cells in a certain area in the reaction tube by an external magnet. The collected MGO induces remarkably high local heating and eventual MRSA cell death under NIR laser irradiation. We demonstrate that Apt@MGO resulted in ∼78% MRSA and over >97% MRSA cell inactivation in dispersed and aggregated states, respectively, under 200 seconds (sn) exposure of NIR irradiation (808 nm, 1.1 W cm-2). An in vitro study highlights that Apt@MGO is considered a targeted, biocompatible, and light-activated photothermal agent for efficient and rapid killing of MRSA in the aggregated state under NIR light.

DNA Computing: NOT Logic Gates See the Light

DNA-based Boolean logic gates (for example, AND, OR, and NOT) can be assembled into complex computational circuits that generate an output signal in response to specific patterns of oligonucleotide inputs. However, the fundamental nature of NOT gates, which convert the absence of an input into an output, makes their implementation within DNA-based circuits difficult. Premature execution of a NOT gate before completion of its upstream computation introduces an irreversible error into the circuit. By utilizing photocaging groups, we developed a novel DNA gate design that prevents gate function until irradiation at a certain time point. Optical activation provides temporal control over circuit performance by preventing premature computation and is orthogonal to all other components of DNA computation devices. Using this approach, we designed NAND and NOR logic gates that respond to synthetic microRNA sequences. We further demonstrate the utility of the NOT gate within multilayer circuits in response to a specific pattern of four microRNAs.

Aptamer-based sensing of breast cancer biomarkers: a comprehensive review of analytical figures of merit

INTRODUCTION

Accurate determination of the aberrantly expressed biomarkers such as human epidermal growth factor receptor 2 (HER2), carcinoembryonic antigen (CEA), platelet-derived growth factor (PDGF), mucin 1 (MUC1), and vascular endothelial growth factor VEGF₁₆₅ have played an essential role in the clinical management of the breast cancer. Assessment of these cancer-specific biomarkers has conventionally relied on time-taking methods like the enzyme-linked immunosorbent assay and immunohistochemistry. However, recent development in the aptamer-based diagnostics has allowed developing tools that may substitute the conventional means of biomarker assessment in breast cancer. Adopting the aptamer-based diagnostic tools (aptasensors) to clinical practices will depend on their analytical performance on clinical samples.

AREAS COVERED

In this review, we provide an overview of the analytical merits of HER2, CEA, PDGF, MUC1, and VEGF₁₆₅ aptasensors. Scopus and Pubmed databases were searched for studies reporting aptasensor development for the listed breast cancer biomarkers in the past one decade. Linearity, detection limit, and response time are emphasized.

EXPERT OPINION

In our opinion, aptasensors have proven to be on a par with the antibody-based methods for detection of various breast cancer biomarkers. Though robust validation of the aptasensors on significant sample size is required, their ability to detect pathophysiological range of biomarkers suggest the possibility of future clinical adoption.

Low-Noise Solid-State Nanopore Enhancing Direct Label-Free Analysis for Small Dimensional Assemblies Induced by Specific Molecular Binding

Solid-state nanopores show special potential as a new single-molecular characterization for nucleic acid assemblies and molecular machines. However, direct recognition of small dimensional species is still quite difficult due the lower resolution compared with biological pores. We recently reported a very efficient noise-reduction and resolution-enhancement mechanism via introducing high-dielectric additives (e.g., formamide) into conical glass nanopore (CGN) test buffer. Based on this advance, here, for the first time, we apply a bare CGN to directly recognize small dimensional assemblies induced by small molecules. Cocaine and its split aptamer (Capt assembly) are chosen as the model set. By introducing 20% formamide into CGN test buffer, high cocaine-specific distinguishing of the 113 nt Capt assembly has been realized without any covalent label or additional signaling strategies. The signal-to-background discrimination is much enhanced compared with control characterizations such as gel electrophoresis and fluorescence resonance energy transfer (FRET). As a further innovation, we verify that low-noise CGN can also enhance the resolution of small conformational/size changes happening on the side chain of large dimensional substrates. Long duplex concatamers generated from the hybridization chain reaction (HCR) are selected as the model substrates. In the presence of cocaine, low-noise CGN has sensitively captured the current changes when the 26 nt aptamer segment is assembled on the side chain of HCR duplexes. This paper proves that the introduction of the low-noise mechanism has significantly improved the resolution of the solid-state nanopore at smaller and finer scales and thus may direct extensive and deeper research in the field of CGN-based analysis at both single-molecular and statistical levels, such as molecular recognition, assembly characterization, structure identification, information storage, and target index.

Logic Gates Based on DNA Aptamers

DNA bio-computing is an emerging trend in modern science that is based on interactions among biomolecules. Special types of DNAs are aptamers that are capable of selectively forming complexes with target compounds. This review is devoted to a discussion of logic gates based on aptamers for the purposes of medicine and analytical chemistry. The review considers different approaches to the creation of logic gates and identifies the general algorithms of their creation, as well as describes the methods of obtaining an output signal which can be divided into optical and electrochemical. Aptameric logic gates based on DNA origami and DNA nanorobots are also shown. The information presented in this article can be useful when creating new logic gates using existing aptamers and aptamers that will be selected in the future.

"Plug and Play" logic gate construction based on chemically triggered fluorescence switching of gold nanoparticles conjugated with Cy3-tagged aptamer

Gold nanoparticles (AuNPs) conjugated with Cy3-tagged aptamer which can specifically recognize chloramphenicol (CAP) (referred to as AuNPs-AptCAP) are described. CAP can trigger the configuration change of CAP binding aptamer, and thus switching the fluorescence of AuNPs-AptCAP through changing the efficiency of the fluorescence resonance energy transfer (FRET) system with Cy3 as donors and AuNPs as recipients. AuNPs-AptCAP exhibits a linear range of CAP concentrations from 26.0 to 277 μg L^-1 with a limit of detection of 8.1 μg L^-1 when Cy3 was excited at 530 nm and emission was measured at 570 nm. More importantly, AuNPs-AptCAP can be utilized as signal transducers for the build-up of a series of logic gates including YES, PASS 0, INH, NOT, PASS 1, and NAND. Utilizing the principle of a metal ion-mediated fluorescence switch together with a strong metal ion chelator, the fluorescence of AuNPs-AptCAP could be modulated by adding metal ions and EDTA sequentially. Therefore, a "Plug and Play" logic system based on AuNPs-AptCAP has been realized by simply adding other components to create new logic functions. This work highlights the advantages of simple synthesis and facile fluorescence switching properties, which will provide useful knowledge for the establishment of molecular logic systems. Graphical abstract.

Enhanced sensitivity of VEGF detection using catalase-mediated chemiluminescence immunoassay based on CdTe QD/H2O2 system

Background

Since vascular endothelial growth factor (VEGF) is a significant regulator of cancer angiogenesis, it is essential to develop a technology for its sensitive detection. Herein, we sensitized a chemiluminescence (CL) immunoassay through the combination of H₂O₂-sensitive TGA-CdTe quantum dot (QD) as signal transduction, dextran as a cross-linker to prepare enzyme-labeled antigen and the ultrahigh bioactivity of catalase (CAT) as reporter enzyme.

Results

Under the optimized experimental conditions, the chemiluminescence enzyme-linked immunosorbent assay (CL-ELISA) method can detect VEGF in the excellent linear range of 2–35,000 pg mL⁻¹, with a detection limit (S/N = 3) of 0.5 pg mL⁻¹ which was approximately ten times lower than the commercial colorimetric immunoassay. This proposed method has been successfully applied to the clinical determination of VEGF in the human serum samples, and the results illustrated an excellent correlation with the conventional ELISA method (R² = 0.997). The suitable recovery rate of the method in the serum ranged from 97 to 107%, with a relative standard deviation of 1.2% to 13.4%.

Conclusions

The novel immunoassay proposes a highly sensitive, specific, and stable method for very low levels detection of VEGF that can be used in the primary diagnosis of tumors. With the well-designed sensing platform, this approach has a broad potential to be applied for quantitative analysis of numerous disease-related protein biomarkers for which antibodies are available.

Aptamer-Functionalized Three-Dimensional Carbon Nanowebs for Ultrasensitive and Free-Standing PDGF Biosensor

Research on flexible biosensors is mostly focused on their use in obtaining information on physical signals (such as temperature, heart rate, pH, and intraocular pressure). Consequently, there are hardly any studies on using flexible electronics for detecting biomolecules and biomarkers that cause diseases. In this study, we propose a flexible, three-dimensional carbon nanoweb (3DCNW)-based aptamer sensor to detect the platelet-induced growth factor (PDGF), which is an oncogenic biomarker. As a template for the 3D structure, poly(acrylonitrile) (PAN) nanowebs were synthesized using a facile electrospinning process. The PAN nanowebs were then subjected to chemical vapor deposition with copper powder. This was followed by Cu etching to generate carbon protrusions on the web surface. As an active site, PDGF-B binding aptamer was introduced on the 3DCNW surface to form biosensor electrodes. The 3DCNW-based aptasensor exhibited excellent sensitivity (down to 1.78 fM), with high selectivity, reversibility, and stability to PDGF-BB.

Noble Metals Based Bimetallic and Trimetallic Nanoparticles: Controlled Synthesis, Antimicrobial and Anticancer Applications

Noble bimetallic and trimetallic nanoparticles (NBT-NPs) have superior biomedical applications as compared to their monometallic counterparts. The performance of these nanomaterials depends on their composition, shape and size. Hence, the controlled-synthesis of these nanomaterials is a hot area of research. Till date, no review article in the literature accounts regarding the controlled-synthesis and biomedical applications related to morphology, optimum composition, biocompatibility and versatile chemistry of NBT-NPs. Taking this into contemplation, an effort was made to provide a clear insight into the morphology-controlled synthesis and size/shape-dependent anticancer and bactericidal applications of NBT-NPs. Chemical reduction method for the controlled-synthesis of NBT-NPs is reviewed critically. Furthermore, the potential role of various reaction parameters such as time, reducing agents, stabilizing/capping agents, nature/concentration of precursors, temperature and pH in the shape/size-controlled synthesis of these nanomaterials are discussed. In the second part of this article, anticancer and bactericidal applications of the NBT-NPs are reviewed and the influences of optimum composition, size, surface structure, versatile chemistry and synergism are studied. Finally, the current challenges in the controlled-synthesis and biomedical applications of these nanomaterials, and prospects to resolve related issues are discussed. HighlightsChemical reduction method for the synthesis of NBT-NPs is reviewed.The influences of parameters on the control synthesis of NBT-NPs are discussed.Antibacterial and anticancer applications and cytotoxicity of NBT-NPs are reviewed.Possible solutions for the key challenges are discussed.Outlooks about the synthesis and biomedical applications of NBT-NPs are discussed.

One step preparation of stable gold nanoparticle using red cabbage extracts under UV light and its catalytic activity

Herein, we have reported the synthesis, characterization and catalytic activity of highly stable gold nanoparticles (Au NPs) using red cabbage extract (RCE) under UV irradiation. The anthocyanin groups predominantly existing in RCE play an essential role for biosynthesis of stable Au NPs. The reasons for using anthocyanins: 1) they act as chelating agents for preferentially reacting with gold ions (Au³⁺) to form Au³⁺- anthocyanin complexes, 2) as light-active reductants for reduction of Au³⁺ to zero valent Au⁰ under UV irradiation and 3) as stabilizing agent for preventing Au NPs from aggregation in high salt concentration owing to their unique salt tolerance property. We also demonstrate that how reaction time, concentration of RCE, pH value of reaction solutions and using one more reducing agent affected formation of the Au NPs. The stability of RCE Au NPs was comparatively studied with commercial (citrate stabilized) Au NPs against 100 mM salt (NaCl) solution. The RCE-Au NP showed reduction ability for conversion of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP). UV-vis spectrometry, transmission electron microscopy (TEM), dynamic light scattering (DLS) and zeta potential (ZT) methods were utilized to characterize the Au NPs. We demonstrated that how whole RCE (anthocyanins molecules are major component) can be used as photo-active reducing and stabilizing agents to form Au NPs in a short time under UV irradiation and strong reducing agent without additional agents.

Low field nuclear magnetic sensing technology based on hydrogel-coated superparamagnetic particles

Based on superparamagnetic nanoparticles, a responsive polyacrylamide hydrogel self-assembled by nucleic acid hairpin hybridization chain reaction was designed, and a universal low field nuclear magnetic resonance sensing platform was successfully constructed. As the target was gradually added, the hydrogel coating on the surface of the magnetic nanoparticle was opened layer by layer through binding with the aptamer, which specifically bonded thereto, causing different degrees of exposure of the magnetic nanoparticle, resulting in changes of low field nuclear magnetic resonance signals. This method was originally applied to the rapid detection of adenosine triphosphate (ATP), and the versatility of the method was verified using polychlorinated biphenyl 77 (PCB77). This method had the advantage of being fast, convenient, and low cost, and it can be easily operated with high repeatability. This universal method can detect a variety of targets by replacing aptamers and may be useful in controlling food quality and for rapidly detecting cancer cells in vitro.

Recent advances on aptamer-based biosensors to detection of platelet-derived growth factor

Platelet-derived growth factor (PDGF-BB), a significant serum cytokine, is an important protein biomarker in diagnosis and recognition of cancer, which straightly rolled in proceeding of various cell transformations, including tumor growth and its development. Fibrosis, atherosclerosis are certain appalling diseases, which PDGF-BB is near to them. Generally, the expression amount of PDGF-BB increases in human life-threatening tumors serving as an indicator for tumor angiogenesis. Thus, identification and quantification of PDGF-BB in biomedical fields are particularly important. Affinity chromatography, immunohistochemical methods and enzyme-linked immunosorbent assay (ELISA), conventional methods for PDGF-BB detection, requiring high-cost and complicated instrumentation, take too much time and offer deficient sensitivity and selectivity, which restrict their usage in real applications. Hence, it is essential to design and build enhanced systems and platforms for the recognition and quantification of protein biomarkers. In the past few years, biosensors especially aptasensors have been received noticeable attention for the detection of PDGF-BB owing to their high sensitivity, selectivity, accuracy, fast response, and low cost. Since the role and importance of developing aptasensors in cancer diagnosis is undeniable. In this review, optical and electrochemical aptasensors, which have been applied by many researchers for PDGF-BB cancer biomarker detection, have been mentioned and merits and demerits of them have been explained and compared. Efforts related to design and development of aptamer-based biosensors using nanoparticles for sensitive and selective detection of PDGF-BB have been reviewed considering: Aptamer importance as recognition elements, principal, application and the recent improvements and developments of aptamer based optical and electrochemical methods. In addition, commercial biosensors and future perspectives for rapid and on-site detection of PDGF-BB have been summarized.

Multiple advanced logic gates made of DNA-Ag nanocluster and the application for intelligent detection of pathogenic bacterial genes

The integration of multiple DNA logic gates on a universal platform to implement advance logic functions is a critical challenge for DNA computing. Herein, a straightforward and powerful strategy in which a guanine-rich DNA sequence lighting up a silver nanocluster and fluorophore was developed to construct a library of logic gates on a simple DNA-templated silver nanoclusters (DNA-AgNCs) platform. This library included basic logic gates, YES, AND, OR, INHIBIT, and XOR, which were further integrated into complex logic circuits to implement diverse advanced arithmetic/non-arithmetic functions including half-adder, half-subtractor, multiplexer, and demultiplexer. Under UV irradiation, all the logic functions could be instantly visualized, confirming an excellent repeatability. The logic operations were entirely based on DNA hybridization in an enzyme-free and label-free condition, avoiding waste accumulation and reducing cost consumption. Interestingly, a DNA-AgNCs-based multiplexer was, for the first time, used as an intelligent biosensor to identify pathogenic genes, E. coli and S. aureus genes, with a high sensitivity. The investigation provides a prototype for the wireless integration of multiple devices on even the simplest single-strand DNA platform to perform diverse complex functions in a straightforward and cost-effective way.

Universal sensor array for highly selective system identification using two-dimensional nanoparticles

A typical lock-and-key sensing strategy, relying only on the most dominant interactions between the probe and target, could be too limiting. In reality, the information received upon sensing is much richer. Non-specific events due to various intermolecular forces contribute to the overall received information with different degrees, and when analyzed, could provide a much more powerful detection opportunity. Here, we have assembled a highly selective universal sensor array using water-soluble two-dimensional nanoparticles (nGO, MoS2 and WS2) and fluorescent DNA molecules. The array is composed of 12 fluorescently silent non-specific nanoreceptors (2D-nps) and used for the identification of three radically different systems; five proteins, three types of live breast cancer cells and a structure-switching event of a macromolecule. The data matrices for each system were processed using Partial Least Squares (PLS) discriminant analysis. In all of the systems, the sensor array was able to identify each object or event as separate clusters with 95% confidence and without any overlap. Out of 15 unknown entities with unknown protein concentrations tested, 14 of them were predicted successfully with correct concentration. 8 breast cancer cell samples out of 9 unknown entities from three cell types were predicted correctly. During the assembly of each nanoprobe, the intrinsic non-covalent interactions between unmodified 2D nanoparticles and ssDNAs were exploited. The unmodified 2D materials offer remarkable simplicity in the layout and the use of ssDNAs as probes provides limitless possibilities because the natural interaction of a ssDNA and 2D surface can be fine-tuned with the nucleobase composition, oligonucleotide length and type of 2D nanomaterial. Therefore, the approach described here can be advanced and fine-tuned indefinitely for meeting a particular sensing criterion. Though we have only studied three distinct elements, this approach is universal enough to be applied to a wide-range of systems.

DNA aptamer functionalized gold nanostructures for molecular recognition and photothermal inactivation of methicillin-Resistant Staphylococcus aureus

In this work, we report the development of DNA aptamer-functionalized gold nanoparticles (Apt@Au NPs) and gold nanorods (Apt@Au NRs) for inactivation of Methicillin-resistant Staphylococcus aureus (MRSA) with targeted photothermal therapy (PTT). Although both Apt@Au NPs and Apt@Au NRs specifically bind to MRSA cells, Apt@Au NPs and Apt@Au NRs inactivated ∼5% and over 95% of the cells,respectively through PTT. This difference in inactivation was based on the relatively high longitudinal absorption of near-infrared (NIR) radiation and strong photothermal conversion capability for the Apt@Au NRs compared to the Apt@Au NPs. The Au NRs served as a nanoplatform for the loading of thiolated aptamer and also provided multivalent effects for increasing binding strength and affinity to MRSA. Our results indicate that the type of aptamer and the degree of multivalent effect(s) are important factors for MRSA inactivation efficiency in PTT. We show that the Apt@Au NRs are a very effective and promising nanosystem for specific cell recognition and in vitro PTT.

Nucleic acid-functionalized transition metal nanosheets for biosensing applications

In clinical diagnostics, as well as food and environmental safety practices, biosensors are powerful tools for monitoring biological or biochemical processes. Two-dimensional (2D) transition metal nanomaterials, including transition metal chalcogenides (TMCs) and transition metal oxides (TMOs), are receiving growing interest for their use in biosensing applications based on such unique properties as high surface area and fluorescence quenching abilities. Meanwhile, nucleic acid probes based on Watson-Crick base-pairing rules are also being widely applied in biosensing based on their excellent recognition capability. In particular, the emergence of functional nucleic acids in the 1980s, especially aptamers, has substantially extended the recognition capability of nucleic acids to various targets, ranging from small organic molecules and metal ions to proteins and cells. Based on π-π stacking interaction between transition metal nanosheets and nucleic acids, biosensing systems can be easily assembled. Therefore, the combination of 2D transition metal nanomaterials and nucleic acids brings intriguing opportunities in bioanalysis and biomedicine. In this review, we summarize recent advances of nucleic acid-functionalized transition metal nanosheets in biosensing applications. The structure and properties of 2D transition metal nanomaterials are first discussed, emphasizing the interaction between transition metal nanosheets and nucleic acids. Then, the applications of nucleic acid-functionalized transition metal nanosheet-based biosensors are discussed in the context of different signal transducing mechanisms, including optical and electrochemical approaches. Finally, we provide our perspectives on the current challenges and opportunities in this promising field.

Exonuclease-assisted target recycling amplification for label-free chemiluminescence assay and molecular logic operations

A versatile exonuclease-assisted target recycling amplification strategy is demonstrated to achieve label-free chemiluminescence detection of DNA and construction of a series of two-input molecular logic gates.

Multidimensional hybrid conductive nanoplate-based aptasensor for platelet-derived growth factor detection

In the development of disease diagnoses, rapid responses to and accurate selectivity for target analytes are critical aspects. As one diagnostic approach, biosensors with high sensitivity and selectivity are investigated to detect disorder factors (e.g., endocrine disruptors and cancer oncoproteins). In this report, we demonstrate an aptamer-functionalized multidimensional hybrid conducting-polymer (3-carboxylated polypyrrole) plate (A_MHCPP) based field-effect transistor (FET) sensor to detect a platelet-derived growth factor (PDGF-BB). The multidimensional hybrid conducting-polymer plates (MHCPPs) are formed on the graphene surface by using electrodeposition and vapor deposition polymerization (VDP) steps. The amine-functionalized PDGF-B binding aptamers are then immobilized on the carboxylated polypyrrole surface by means of covalent bond formation (-CONH). The prepared FET sensors present high sensing ability toward PDGF-BB - as low as 1.78 fM among interfering biomolecules at room temperature.

Aptamer-based colorimetric detection of proteins using a branched DNA cascade amplification strategy and unmodified gold nanoparticles

A branched DNA amplification strategy was employed to design a colorimetric aptameric biosensor using unmodified gold nanoparticles (AuNPs). First, a programmed DNA dendritic nanostructure was formed using two double-stranded substrate DNAs and two single-stranded auxiliary DNAs as assembly components via a target-assisted cascade amplification reaction, and it was then captured by DNA sensing probe-stabilized AuNPs. The release of sensing probes from AuNPs led to the formation of unstable AuNPs, promoting salt-induced aggregation. By integrating the signal amplification capacity of the branched DNA cascade reaction and unmodified AuNPs as a sensing indicator, this amplified colorimetric sensing strategy allows protein detection with high sensitivity (at the femtomole level) and selectivity. The limit of detection of this approach for VEGF was lower than those of other aptamer-based detection methods. Moreover, this assay provides modification-free and enzyme-free protein detection without sophisticated instrumentation and might be generally applicable to the detection of other protein targets in the future.

CREDVW-Linked Polymeric Micelles As a Targeting Gene Transfer Vector for Selective Transfection and Proliferation of Endothelial Cells

Nowadays, gene transfer technology has been widely used to promote endothelialization of artificial vascular grafts. However, the lack of gene vectors with low cytotoxicity and targeting function still remains a pressing challenge. Herein, polyethylenimine (PEI, 1.8 kDa or 10 kDa) was conjugated to an amphiphilic and biodegradable diblock copolymer poly(ethylene glycol)-b-poly(lactide-co-glycolide) (mPEG-b-PLGA) to prepare mPEG-b-PLGA-g-PEI copolymers with the aim to develop gene vectors with low cytotoxicity while high transfection efficiency. The micelles were prepared from mPEG-b-PLGA-g-PEI copolymers by self-assembly method. Furthermore, Cys-Arg-Glu-Asp-Val-Trp (CREDVW) peptide was linked to micelle surface to enable the micelles with special recognition for endothelial cells (ECs). In addition, pEGFP-ZNF580 plasmids were condensed into these CREDVW-linked micelles to enhance the proliferation of ECs. These CREDVW-linked micelle/pEGFP-ZNF580 complexes exhibited low cytotoxicity by MTT assay. The cell transfection results demonstrated that pEGFP-ZNF580 could be transferred into ECs efficiently by these micelles. The results of Western blot analysis showed that the relative ZNF580 protein level in transfected ECs increased to 76.9%. The rapid migration of transfected ECs can be verified by wound healing assay. These results indicated that CREDVW-linked micelles could be a suitable gene transfer vector with low cytotoxicity and high transfection efficiency, which has great potential for rapid endothelialization of artificial blood vessels.

The Coupling between Gold or Silver Nanocubes in Their Homo-Dimers: A New Coupling Mechanism at Short Separation Distances

Using the DDA method, we investigated the near-field coupling between two excited Au or Ag 42 nm nanocubes in a face-to-face dimer configuration at small separation distances where the exponential coupling behavior distinctly changes. This could be due to the failure of the dipole approximation at short distances or a change in the electromagnetic field distribution between the adjacent monomers. A detailed calculation of the plasmonic field distribution strongly suggests that the latter mechanism is responsible for the failure of the expected exponential coupling behavior at small separation distances. The results suggest that the observed optical properties of the pair of Au or Ag nanocubes separated by distances larger than 6 nm, result from the electromagnetic coupling between the oscillating dipoles at the corners of the adjacent facets of the nanocubes. At separations smaller than 6 nm, the distribution of the plasmonic dipoles along both the facets and the corners of the adjacent monomers control the plasmonic spectra and the distance dependent optical properties of the dimer.

Molecular encoder-decoder based on an assembly of graphene oxide with dye-labelled DNA

A general strategy was developed to fabricate 2-to-1, 4-to-2 and 8-to-3 molecular encoders and a 1-to-2 decoder by assembling graphene oxide with various dye-labeled DNAs.

Colorimetric logic response based on aptamer functionalized colloidal crystal hydrogels

A novel colorimetric logic system based on the aptamer-cross-linked colloidal crystal hydrogel (CCH) was developed. With the input stimuli of Hg(2+) and Ag(+), the CCH displayed shrinking response and colour change corresponding to the logical "OR" and "AND" gate. The visualization of the logic output signals is realized.

A survey of advancements in nucleic acid-based logic gates and computing for applications in biotechnology and biomedicine

Nucleic acid-based logic devices were first introduced in 1994. Since then, science has seen the emergence of new logic systems for mimicking mathematical functions, diagnosing disease and even imitating biological systems. The unique features of nucleic acids, such as facile and high-throughput synthesis, Watson-Crick complementary base pairing, and predictable structures, together with the aid of programming design, have led to the widespread applications of nucleic acids (NA) for logic gate and computing in biotechnology and biomedicine. In this feature article, the development of in vitro NA logic systems will be discussed, as well as the expansion of such systems using various input molecules for potential cellular, or even in vivo, applications.

Aptamer-functionalized hybrid carbon nanofiber FET-type electrode for a highly sensitive and selective platelet-derived growth factor biosensor

Precise selectivity and rapid responses to target biomolecules are important in the development of biosensors. In particular, highly sensitive and selective biosensors have been used in clinical treatment to detect factors such as cancer oncoproteins and endocrine disruptors. Herein, highly sensitive liquid electrolyte field-effect transistor (FET) system biosensors were fabricated to detect platelet-derived growth factor (PDGF) using a PDGF-B binding aptamer conjugated with carboxylic polypyrrole-coated metal oxide-decorated carbon nanofibers (CPMCNFs) as the signal transducer. First, CPMCNFs were fabricated using vapor deposition polymerization (VDP) of the carboxylic pryrrole monomer (CPy) on metal oxide-decorated carbon nanofiber (MCNF) surfaces with no treatment for carbon surface functionalization. Furthermore, a 3 nm thick uniformly coated carboxylic polypyrrole (CPPy) layer was formed without aggregation. The CPMCNFs were integrated with the PDGF-B binding aptamer and immobilized on the interdigitated array substrate by covalent anchoring to produce a FET-type biosensor transducer. The PDGF-B binding aptamer conjugated CPMCNF (CPB-Apt) FET sensor was highly sensitive (5 fM) and extremely selective for isoforms of PDGFs. Additionally, the CPB-Apt FET sensor could be reused over a few weeks.

Logic nanoparticle beacon triggered by the binding-induced effect of multiple inputs

Recently, the toehold-mediated DNA strand displacement reaction has been widely used in detecting molecular signals. However, traditional strand displacement, without cooperative signaling among DNA inputs, is insufficient for the design of more complicated nanodevices. In this work, a logic computing system is established using the cooperative "binding-induced" mechanism, based on the AuNP-based beacons, in which five kinds of multiple-input logic gates have been constructed. This system can recognize DNA and protein streptavidin simultaneously. Finally, the manipulations of the logic system are also demonstrated by controlling programmed conjugate DNA/AuNP clusters. This study provides the possibility of detecting multiple input signals and designing complex nanodevices that can be potentially applied to the detection of multiple molecular targets and the construction of large-scale DNA-based computation.

Glutathione-facilitated design and fabrication of gold nanoparticle-based logic gates and keypad lock

In this paper, we describe how we developed a simple design and fabrication method for logic gates and a device by using a commercially available tripeptide, namely glutathione (GSH), together with metal ions and disodium ethylenediaminetetraacetate (EDTA) to control the dispersion and aggregation of gold nanoparticles (NPs). With the fast adsorption of GSH on gold NPs and the strong coordination of GSH with metal ions, the addition of GSH and Pb(2+) ions immediately resulted in the aggregation of gold NPs, giving rise to an AND function. Either Pb(2+) or Ba(2+) ions induced the aggregation of gold NPs in the presence of GSH, supporting an OR gate. Based on the fact that EDTA has a strong capacity to bind metal ions, thus preventing the aggregation of gold NPs, an INHIBIT gate was also fabricated. More interestingly, we found that the addition sequence of GSH and Hg(2+) ions influenced the aggregation of gold NPs in a controlled manner, which was used to design a sequential logic gate and a three-input keypad lock for potential use in information security. The GSH strategy addresses concerns of low cost, simple fabrication, versatile design and easy operation, and offers a promising platform for the development of functional logic systems.

Fluorometric/colorimetric logic gates based on BODIPY-functionalized mesoporous silica

We have demonstrated that metal ions acting as modulators in BODIPY-functionalized SiO₂ nanoparticles can generate absorbance changes in accordance with the operation of a half-adder digital circuit.

A fluorescent nanoprobe based on graphene oxide fluorescence resonance energy transfer for the rapid determination of oncoprotein vascular endothelial growth factor (VEGF)

Oncoprotein vascular endothelial growth factor (VEGF) is one of the most critical growth factors that regulates tumor growth and division. The vascular endothelial growth factor (VEGF) is also an important biomarker for different diseases and clinical disorders. Herein, we propose a graphene oxide (GO) fluorescence resonance energy transfer (FRET)-based aptasensor for rapid, sensitive, and selective detection of VEGF in homogeneous solution. The fluorescent dye-labeled anti-VEGF aptamer is adsorbed on the surface of GO via π-π interaction between the flat planar GO sheets and the ring structures in the nucleobases, which results in the fluorescence quenching of the dye due to the highly effective FRET from the dye to GO. Upon recognition and binding with the target VEGF, it specifically forms a VEGF/aptamer complex and then release from the GO surface, leading to the restoration of fluorescence signal of the dye. This GO-based sensing platform exhibits high sensitivity and specificity toward VEGF versus other proteins, with the detection limits corresponding to 2.5×10(-10) M. The sensitivity of this new type of aptamer-based assay is at least one order of magnitude higher than that of conventional homogeneous optical assays. Moreover, the application of this nanosensor for human serum sample analysis is also demonstrated. The GO/aptamer-based assay approach holds great promise as a general platform for detection of a variety of target molecules.

Logical regulation of the enzyme-like activity of gold nanoparticles by using heavy metal ions

In this study we employed self-deposition and competitive or synergistic interactions between metal ions and gold nanoparticles (Au NPs) to develop OR, AND, INHIBIT, and XOR logic gates through regulation of the enzyme-like activity of Au NPs. In the presence of various metal ions (Ag(+), Bi(3+), Pb(2+), Pt(4+), and Hg(2+)), we found that Au NPs (13 nm) exhibited peroxidase-, oxidase-, or catalase-like activity. After Ag(+), Bi(3+), or Pb(2+) ions had been deposited on the Au NPs, the particles displayed strong peroxidase-like activity; on the other hand, they exhibited strong oxidase- and catalase-like activities after reactions with Ag(+)/Hg(2+) and Hg(2+)/Bi(3+) ions, respectively. The catalytic activities of these Au NPs arose mainly from the various oxidation states of the surface metal atoms/ions. Taking advantage of this behavior, we constructed multiplex logic operations-OR, AND, INHIBIT, and XOR logic gates-through regulation of the enzyme-like activity after the introduction of metal ions into the Au NP solution. When we deposited Hg(2+) and/or Bi(3+) ions onto the Au NPs, the catalase-like activities of the Au NPs were strongly enhanced (>100-fold). Therefore, we could construct an OR logic gate by using Hg(2+)/Bi(3+) as inputs and the catalase-like activity of the Au NPs as the output. Likewise, we constructed an AND logic gate by using Pt(4+) and Hg(2+) as inputs and the oxidase-like activity of the Au NPs as the output; the co-deposition of Pt and Hg atoms/ions on the Au NPs was responsible for this oxidase-like activity. Competition between Pb(2+) and Hg(2+) ions for the Au NPs allowed us to develop an INHIBIT logic gate-using Pb(2+) and Hg(2+) as inputs and the peroxidase-like activity of the Au NPs as the output. Finally, regulation of the peroxidase-like activity of the Au NPs through the two inputs Ag(+) and Bi(3+) enabled us to construct an XOR logic gate.

Double-functionalized gold nanoparticles with split aptamer for the detection of adenosine triphosphate

A newly designed functionalization type for gold nanoparticles (AuNP) with split aptamer has been developed for the detection of adenosine triphosphate (ATP). The ATP aptamer was split into two parts with their 5' prime or 3' prime modified with thiol. Both the 5' SH and 3' SH modified strands for each split aptamer fragment were functionalized onto the same AuNP to construct double-functionalized AuNP-DNA conjugates. Thus, the split aptamer can be reassembled into intact folded structure in the presence of ATP molecule with two potential assembly types, which induces the assembly of AuNP-DNA conjugates. In this double-functionalized system, the traditional assembly type might facilitate another assembly type, which was found to give much higher LSPR change in the presence of ATP than the traditional assembly type, and improve the sensitivity for ATP detection. Time courses of the assemble processes with different assembly types, Mg(2+) concentrations, and aptamer fragments densities on AuNP were followed using the absorption ratio at 650 nm and 520 nm. ATP response with this newly designed system was investigated using absorption spectra and dynamic light scattering method.