Colorimetric detection of DNA by modulation of thrombin activity on gold nanoparticles

Using gold nanoparticles to detect single-nucleotide polymorphisms: toward liquid biopsy

The possibility of detecting genetic mutations rapidly in physiological media through liquid biopsy has attracted the attention within the materials science community. The physical properties of nanoparticles combined with robust transduction methods ensure an improved sensitivity and specificity of a given assay and its implementation into point-of-care devices for common use. Covering the last twenty years, this review gives an overview of the state-of-the-art of the research on the use of gold nanoparticles in the development of colorimetric biosensors for the detection of single-nucleotide polymorphism as cancer biomarker. We discuss the main mechanisms of the assays that either are assisted by DNA-based molecular machines or by enzymatic reactions, summarize their performance and provide an outlook towards future developments.

A unique FRET approach toward detection of single-base mismatch DNA in BRCA1 gene

Early detection of mutation carriers in predisposing genes such as BRCA1 plays an important role in disease prevention. This work developed a quantum dots-based (QDs-based) fluorescence resonance energy transfer (FRET) technique for the detection of single-base mismatch DNA in BRCA1 gene. The FRET between QDs as the donor and silver nanocluster (AgNCs) as the acceptor was designed by the strong interaction between CdTe QDs with appropriate size and dsDNA through binding to its major groove. The dsDNA was formed by the hybridization of ssDNA labeled to AgNCs with target DNA, which introduced CdTe QDs into the major grooves to place the AgNCs in close proximity to the QDs. The complementary and single-base mismatch DNA led to obviously different FRET signals. The FRET signal linearly correlated to the concentration of single-base mismatch DNA in the range of 1.5 × 10^-10-1.0 × 10^-6 mol L^-1. The proposed method showed a detection limit of 80 pmol L^-1 and the sensitivity comparable to the previously reported assays, indicating promising potential for single nucleotide polymorphisms diagnosis in clinical application.

A PCR-free colorimetric strategy for visualized assay of telomerase activity

A simple yet powerful polymerase chain reaction (PCR)-free strategy for visualized assay of human telomerase activity was reported in this work. Gold nanoparticles (AuNPs) based colorimetric strategy was applied with well-designed enzyme-aided cyclic amplification. Briefly, the detection relies on the elongated primers of telomerase substrate (TS) induced by telomerase, which open the hairpin DNA and hybridize with linker DNA, the trigger of AuNPs aggregation. Nicking endonuclease was added in the sensing system, which cleaved linker DNA after hybridization and released complimentary strand for cyclic hybridization with linker DNA, resulted in high sensitivity for the detection of telomerase. Down to 25 HeLa cells with high expression of telomerase could be recognized. The proposed strategy provides a good platform for the determination of telomerase activity, differentiation of cancer cell lines from normal cell line and screening of telomerase-targeted anticancer drugs.

Detection of p53 Gene Mutation (Single-Base Mismatch) Using a Fluorescent Silver Nanoclusters

P53 mutation was detected through the application of a biosensing approach based on the decrease in the fluorescence of oligonucleotide-templated silver nanoclusters (DNA-AgNCs). To this end specific DNA scaffolds of two various nucleotide fragments were used. One of the scaffolds was enriched with two cytosine sequence fragment (C12). This led to DNA-AgNCs with a fluorescence intensity through chemical reduction, while the other scaffold acted as the probe fragment (5- GTAGATGGCCATGGCGCGGACGCGGGTG-3). This latter scaffold selectively bound to the specific p53 site. Thus, resulting AgNCs demonstrated decreased fluorescence upon binding to single-base mismatching targets, and this behavior was found to be linearly proportional to the concentration of mutated p53 from 5 to 350 nM and the approach was found to be able to detect concentrations as low as 1.3 nM.

Sensitive fluorescent detection of fibrin based on the inner filter effect of gold nanoparticles

A simple, rapid and sensitive fluorescent assay for determination of fibrin has been developed based on the inner filter effect (IFE) of gold nanoparticles (AuNPs).

Rapid Naked-Eye Discrimination of Cytochrome P450 Genetic Polymorphism through Non-Crosslinking Aggregation of DNA-Functionalized Gold Nanoparticles

Involvement of single-nucleotide polymorphism (SNP) genotyping in healthcare should allow for more effective use of pharmacogenomics. However, user-friendly assays without the requirement of a special instrument still remain unavailable. This study describes naked-eye SNP discrimination in exon 5 of the human cytochrome P450 2C19 monooxygenase gene, CYP2C19*1 (the wild-type allele) and CYP2C19*2 (the variant allele with G681A point mutation). The present assay is composed of allele-specific single-base primer extension and salt-induced aggregation of DNA-modified gold nanoparticles (DNA-AuNPs). Genetic samples extracted from human hair roots are subjected to this assay. The results are verified by direct sequencing. This study should promise the prospective use of DNA-AuNPs in gene diagnosis.

Bacterial surface display of metal binding peptides as whole-cell biocatalysts for 4-nitroaniline reduction

Using recombinant microorganisms expressing metal binding peptides as whole-cell biocatalysts for 4-nitroaniline reduction.

Colorimetric detection of controlled assembly and disassembly of aptamers on unmodified gold nanoparticles

Aptamers are nucleic acid ligands that are generated artificially by in vitro selection and behave similar to antibodies. The development of aptamer-based sensing systems or strategies has been in vogue for the past few decades, because aptamers are smaller in size, stable, cheaper and undergo easier modifications. Owing to these advantages, several facile aptamer-based colorimetric strategies have been created by controlling the assembly and disassembly of aptamers on unmodified gold nanoparticle probes. As these kinds of assay systems are rapid and can be visualized unaided by instruments, they have recently become an attractive method of choice. The formation of purple-colored aggregates (attraction) from the red dispersed (repulsion) state of GNPs in the presence of mono- or divalent ions is the key principle behind this assay. Due to its simplicity and versatility, this assay can be an alternative to existing diagnostic assays. Here, we have investigated the critical elements involved in colorimetric assays, and have screened different proteins and small ligands to evaluate biofouling on GNPs.

Localized surface plasmon resonance: a unique property of plasmonic nanoparticles for nucleic acid detection

Localized surface plasmon resonance (LSPR) of noble metal nanoparticles (a.k.a. plasmonic nanoparticles) opens up a new horizon for advanced biomolecule sensing. However, an effective and practical sensing system still requires meticulous design to achieve good sensitivity and distinctive selectivity for routine use and high-throughput detection. In particular, the detection of DNA and RNA is crucial in biomedical research and clinical diagnostics. This review describes the fundamental aspects of LSPR and provides an overall account of how it is exploited to assist in nucleic acid sensing. The detection efficiency of each LSPR-based approach is assessed with respect to the assay design, the selection of plasmonic nanoparticles, and the choice of nucleic acid probes which influence the duplex hybridization. Judicious comparison is made among various LSPR-based approaches in terms of the assaying time, the sensitivity or lowest sensing concentration (i.e. limit of detection or LOD), and the single-base mismatch (SBM) selectivity.

Colorimetric detection of metallothioneins using a thymine-rich oligonucleotide-Hg complex and gold nanoparticles

A simple and sensitive method for label-free, colorimetric detection of metallothioneins (MTs) has been developed by using a thymine (T)-rich oligonucleotide (TRO)-Hg-AuNP system. In this colorimetric strategy, the thiol groups of MTs could interact with mercury from the T-Hg(2+)-T complex to release TRO, resulting in a color change of the system. The response signals linearly correlated with the concentration of MTs over the range of 2.56 × 10(-8) to 3.08 × 10(-7) mol L(-1), and the limit of detection was 7.67 × 10(-9) mol L(-1). The relative standard deviation and the recovery were 2.3-4.8% (n = 11) and 94.2-103.9%, respectively. The proposed method avoids the label and derivatization steps in common methods, allows direct analysis of the samples by the naked eye without costly instruments, and is reliable, inexpensive, and sensitive.

Improving colorimetric assays through protein enzyme-assisted gold nanoparticle amplification

The discovery of the DNA-mediated assembly of gold nanoparticles was a great moment in the history of science; this understanding and chemical control enabled the rational design of functional nanomaterials as novel probes in biodetection. In contrast with conventional probes such as organic dyes, gold nanoparticles exhibit high photostability and unique size-dependent optical properties. Because of their high extinction coefficients and strong distance dependent optical properties, these nanoparticles have emerged over the past decade as a promising platform for rapid, highly sensitive colorimetric assays that allow for the visual detection of low concentrations of metal ions, small molecules, and biomacromolecules. These discoveries have deepened our knowledge of biological phenomena and facilitated the development of many new diagnostic and therapeutic tools. Despite these many advances and continued research efforts, current nanoparticle-based colorimetric detection systems still suffer from several drawbacks, such as limited sensitivity and selectivity. This Account describes the recent development of colorimetric assays based on protein enzyme-assisted gold nanoparticle amplification. The benefits of such detection systems include significantly improved detection sensitivity and selectivity. First, we discuss the general design of enzyme-modified nanoparticle systems in colorimetric assays. We show that a quantitative understanding of the unique properties of different enzymes is paramount for effective biological assays. We then examine the assays for nucleic acid detection based on different types of enzymes, including endonucleases, ligases, and polymerases. For each of these assays, we identify the underlying principles that contribute to the enhanced detection capability of nanoparticle systems and illustrate them with selected examples. Furthermore, we demonstrate that the combination of gold nanoparticles and specific enzymes can probe enzyme dynamics and function with high specificity, offering substantial advantages in both sensitivity and specificity over conventional detection methods. The screening of nuclease, methyltransferase, protease, and kinase activities can be colorimetrically performed in a straightforward manner. Finally, we discuss examples of colorimetric assays for metal ions and small molecules that constitute important advances toward visual monitoring of enzyme catalytic functions and gene expression. Although these enzyme-assisted assay methods hold great promise for myriad applications in biomedicine and bioimaging, the application of the described techniques in vivo faces formidable challenges. In addition, researchers do not fully understand the interactions of gold nanoparticles with enzyme molecules. This understanding will require the development of new techniques to probe enzyme substrate dynamics at the particle interface with higher spatial resolution and chemical specificity.

Development of a universal colorimetric indicator for G-quadruplex structures by the fusion of thiazole orange and isaindigotone skeleton

The rapid and convenient method for identification of all kinds of G-quadruplex is highly desirable. In the present study, a novel colorimetric indicator for a vast variety of G-quadruplex was designed and synthesized on the basis of thiazole orange and isaindigotone skeleton. Its distinct color change enables label-free visual detection of G-quadruplexes, which is due to the disassembly of dye H-aggregates to monomers. This specific detection of G-quadruplex arises from its end-stacking interaction with G-quartet. On the basis of this universal indicator, a facile approach for large-scale identification of G-quadruplex was developed.

Noble metal nanoparticles for biosensing applications

In the last decade the use of nanomaterials has been having a great impact in biosensing. In particular, the unique properties of noble metal nanoparticles have allowed for the development of new biosensing platforms with enhanced capabilities in the specific detection of bioanalytes. Noble metal nanoparticles show unique physicochemical properties (such as ease of functionalization via simple chemistry and high surface-to-volume ratios) that allied with their unique spectral and optical properties have prompted the development of a plethora of biosensing platforms. Additionally, they also provide an additional or enhanced layer of application for commonly used techniques, such as fluorescence, infrared and Raman spectroscopy. Herein we review the use of noble metal nanoparticles for biosensing strategies—from synthesis and functionalization to integration in molecular diagnostics platforms, with special focus on those that have made their way into the diagnostics laboratory.

Integrated microdevice of reverse transcription-polymerase chain reaction with colorimetric immunochromatographic detection for rapid gene expression analysis of influenza A H1N1 virus

An integrated microdevice of a reverse transcription-polymerase chain reaction (RT-PCR) reactor and an immunochromatographic strip was constructed for colorimetric detection of gene expression of influenza A virus subtype H1N1. An RT-PCR cocktail, which included Texas Red-labeled primers, dNTP including biotin-labeled dUTP, and RNA templates of influenza A H1N1 virus, was filled in the PCR chamber through the micropump, and the RT-PCR was performed to amplify the target H1 gene (102 bp). The resultant amplicons bearing biotin moieties and Texas Red haptens were subsequently eluted to the immunochromatographic strip, in which they were first conjugated with the gold nanoparticle labeled anti-hapten antibody in the conjugation pad, and then captured on the streptavidin coated test line through the biotin–streptavidin interaction. By observing a violet color in the test line which was derived from the gold nanoparticle, we confirmed the H1N1 target virus. The entire process on the integrated microdevice consisting of a micropump, a 2 μL PCR chamber, and an immunochromatographic strip was carried out on the portable genetic analyzer within 2.5 h, enabling on-site colorimetric pathogen identification with detection sensitivity of 14.1 pg RNA templates.