Surface-plasmon-enhanced fluorescence spectroscopy for DNA detection using fluorescently labeled PNA as "DNA indicator"

Surface Plasmon-Assisted Fluorescence Enhancing and Quenching: From Theory to Application

The integration of surface plasmon resonance and fluorescence yields a multiaspect improvement in surface fluorescence sensing and imaging, leading to a paradigm shift of surface plasmon-assisted fluorescence techniques, for example, surface plasmon enhanced field fluorescence spectroscopy, surface plasmon coupled emission (SPCE), and SPCE imaging. This Review aims to characterize the unique optical property with a common physical interpretation and diverse surface architecture-based measurements. The fundamental electromagnetic theory is employed to comprehensively unveil the fluorophore-surface plasmon interaction, and the associated surface-modification design is liberally highlighted to balance the surface plasmon-induced fluorescence-enhancement efforts and the surface plasmon-caused fluorescence-quenching effects. In particular, all types of surface structures, for example, silicon, carbon, protein, DNA, polymer, and multilayer, are systematically interrogated in terms of component, thickness, stiffness, and functionality. As a highly interdisciplinary and expanding field in physics, optics, chemistry, and surface chemistry, this Review could be of great interest to a broad readership, in particular, among physical chemists, analytical chemists, and in surface-based sensing and imaging studies.

Amplifying the excited state chirality through self-assembly and subsequent enhancement via plasmonic silver nanowires

The development of circularly polarized luminescent materials with a large luminescence dissymmetry factor (g_lum) is continuing to be a big challenge. Here, we present a general approach for amplifying circular polarization of circularly polarized luminescence (CPL) through intergrating molecular self-assembly and surface plasmon resonance (SPR). Molecular self-assembly could amplify the CPL performance. Subsequently, the composites built of nanoassemblies and achiral silver nanowires (AgNWs) show intense CPL activity with an amplified g_lum value. By applying an external magnetic field, the CPL activity of the nanoassemblies/AgNWs composites has been significantly enhanced, confirming a plasmon-enhanced circular polarization. Our design strategy based on SPR-enhanced circular polarization of the chiral emissive systems suggests that combining plasmonic nanomaterials with chiral organic materials could aid in the development of novel CPL active nanomaterials.

A surface plasmon field-enhanced fluorescence reversible split aptamer biosensor

Surface plasmon field-enhanced fluorescence is reported for the readout of a heterogeneous assay that utilizes low affinity split aptamer ligands. Weak affinity ligands that reversibly interact with target analytes hold potential for facile implementation in continuous monitoring biosensor systems. This functionality is not possible without the regeneration of more commonly used assays relying on high affinity ligands and end-point measurement. In fluorescence-based sensors, the use of low affinity ligands allows avoiding this step but it imposes a challenge associated with the weak optical response to the specific capture of the target analyte which is also often masked by a strong background. The coupling of fluorophore labels with a confined field of surface plasmons is reported for strong amplification of the fluorescence signal emitted from the sensor surface and its efficient discrimination from the background. This optical scheme is demonstrated for time-resolved analysis of chosen model analytes - adenoside and adenosine triphosphate - with a split aptamer that exhibits an equilibrium affinity binding constant between 0.73 and 1.35 mM. The developed biosensor enables rapid and specific discrimination of target analyte concentration changes from low μM to mM in buffer as well as in 10% serum.

Portable and sensitive quantitative detection of DNA using personal glucose meters and exonuclease III-assisted signal amplification

A portable and sensitive quantitative DNA detection method using personal glucose meters (PGMs) and Exonuclease III-assisted signal amplification was developed. In the presence of target DNA, a target recycling process that can release target and linker DNA was obtained. The released linker DNA was used to link capture DNA on magnetic beads and the DNA invertase. After the washing away of unbound target DNA and subsequent DNA-invertase conjugation, the bound DNA-invertase can be used to catalyze the hydrolysis of sucrose into glucose with millions of turnovers, which transforms the concentration of target DNA into the level of glucose monitored by PGMs. There was a linear relationship between the signal of PGM and the concentration of target DNA in the range of 0.5 pM to 100 pM. A correlation coefficient of 0.989 was obtained, and the relative standard deviation (RSD) was 4.1% for a concentration of 50 pM target DNA (n = 9). In addition, the method exhibits excellent sequence selectivity, being able to differentiate a single mismatch in the target DNA. What is more, there was almost no effect from biological complexes on detection performance, which suggests our method can be successfully applied to DNA detection in real biological samples.

Paper-based DNA detection using lanthanide-doped LiYF4 upconversion nanocrystals as bioprobe

A novel sensitive DNA bioassay using lanthanide-doped LiYF4 upconversion nanocrystals as luminescent marker and oligonucleotide hybridization as the selective reaction is developed in a paper-based platform, providing a detection limit of 3.6 fmol.

Tailoring of high-order multiple emulsions by the liquid-liquid phase separation of ternary mixtures

Multiple emulsions with an "onion" topology are useful vehicles for drug delivery, biochemical assays, and templating materials. They can be assembled by ternary liquid phase separation by microfluidics, but the control over their design is limited because the mechanism for their creation is unknown. Herein we show that phase separation occurs through self-similar cycles of mass transfer, spinodal decomposition or nucleation, and coalescence into multiple layers. Mapping out the phase diagram shows a linear relationship between the diameters of concentric layers, the slope of which depends on the initial ternary composition and the molecular weight of the surfactant. These general rules quantitatively predict the number of droplet layers (multiplicity), which we used to devise self-assembly routes for polymer capsules and liposomes. Moreover, we extended the technique to the assembly of lipid-stabilized droplets with ordered internal structures.

Sensitive point-of-care monitoring of HIV related DNA sequences with a personal glucometer

The hybridizations between the HIV target DNA and the capture probes as well as the signal probes conjugated to the multi-invertase/nanoparticle composites lead to the conversion of sucrose to glucose, which is monitored by the personal glucometer and provides quantitative digital readings for point-of-care diagnosis of HIV DNA fragments.

Surface modification of plasmonic nanostructured materials with thiolated oligonucleotides in 10 seconds using selective microwave heating

This study demonstrates the proof-of-principle of rapid surface modification of plasmonic nanostructured materials with oligonucleotides using low power microwave heating. Due to their interesting optical and electronic properties, silver nanoparticle films (SNFs, 2 nm thick) deposited onto glass slides were used as the model plasmonic nanostructured materials. Rapid surface modification of SNFs with oligonucleotides was carried out using two strategies (1) Strategy 1: for ss-oligonucleotides, surface hybridization and (2) Strategy 2: for ds-oligonucleotides, solution hybridization), where the samples were exposed to 10, 15, 30 and 60 seconds microwave heating. To assess the efficacy of our new rapid surface modification technique, identical experiments carried out without the microwave heating (i.e., conventional method), which requires 24 hours for the completion of the identical steps. It was found that SNFs can be modified with ss- and ds-oligonucleotides in 10 seconds, which typically requires several hours of incubation time for the chemisorption of thiol groups on to the planar metal surface using conventional techniques.

Artificial DNA and surface plasmon resonance

The combined use of surface plasmon resonance (SPR) and modified or mimic oligonucleotides have expanded diagnostic capabilities of SPR-based biosensors and have allowed detailed studies of molecular recognition processes. This review summarizes the most significant advances made in this area over the past 15 years.   Functional and conformationally restricted DNA analogs (e.g., aptamers and PNAs) when used as components of SPR biosensors contribute to enhance the biosensor sensitivity and selectivity. At the same time, the SPR technology brings advantages that allows forbetter exploration of underlying properties of non-natural nucleic acid structures such us DNAzymes, LNA and HNA.

Using commercially available personal glucose meters for portable quantification of DNA

DNA detection is commonly used in molecular biology, pathogen analysis, genetic disorder diagnosis, and forensic tests. While traditional methods for DNA detection such as polymerase chain reaction (PCR) and DNA microarrays have been well developed, they require sophisticated equipment and operations, and thus it is still challenging to develop a portable and quantitative DNA detection method for the public use at home or in the field. Although many other techniques and devices have been reported to make the DNA detection simple and portable, very few of them are currently accessible to the public for quantitative DNA detection because of either the requirement of laboratory-based instrument or lack of quantitative detection. Herein we report application of personal glucose meters (PGMs), which are widely available, low cost, and simple to use, for quantitative detection of DNA, including a hepatitis B virus DNA fragment. The quantification is based on target-dependent binding of cDNA-invertase conjugate with the analyte DNA, thereby transforming the concentration of DNA in the sample into glucose through invertase-catalyzed hydrolysis of sucrose. Instead of amplifying DNA strands through PCR, which is vulnerable to contaminations commonly encountered for home and field usage, we demonstrate here signal amplifications based on enzymatic turnovers, making it possible to detect 40 pM DNA using PGM that can detect glucose only at the mM level. The method also shows excellent selectivity toward single nucleotide mismatches.

Synthesis, DNA binding, and cleavage studies of novel PNA binding cyclen complexes

A novel coumarin-appended PNA binding cyclen derivative ligand, C1, and its copper(II) complex, C2, have been synthesized and characterized. The interaction of these compounds with DNA was systematically investigated by absorption, fluorescence, and viscometric titration, and DNA-melting and gel-electrophoresis experiments. DNA Melting and viscometric titration experiments indicate that the binding mode of C1 is a groove binding, and C2 is a multiple binding mode that involves groove binding and electrostatic binding. From the absorption-titration data, we can state that the primary interaction between CT DNA and the two compounds may be H-bonds between nucleobases. Fluorescence studies indicate that the binding ability of C1 to d(A)(9) is as twice or thrice as that of other oligodeoxynucleotides. Agarose gel-electrophoresis experiments demonstrate that C2 is an excellent chemical nuclease, which can cleave plasmid DNA completely within 24 h.

Rapid label-free identification of mixed bacterial infections by surface plasmon resonance

Background

Early detection of mixed aerobic-anaerobic infection has been a challenge in clinical practice due to the phenotypic changes in complex environments. Surface plasmon resonance (SPR) biosensor is widely used to detect DNA-DNA interaction and offers a sensitive and label-free approach in DNA research.

Methods

In this study, we developed a single-stranded DNA (ssDNA) amplification technique and modified the traditional SPR detection system for rapid and simultaneous detection of mixed infections of four pathogenic microorganisms (Pseudomonas aeruginosa, Staphylococcus aureus, Clostridium tetani and Clostridium perfringens).

Results

We constructed the circulation detection well to increase the sensitivity and the tandem probe arrays to reduce the non-specific hybridization. The use of 16S rDNA universal primers ensured the amplification of four target nucleic acid sequences simultaneously, and further electrophoresis and sequencing confirmed the high efficiency of this amplification method. No significant signals were detected during the single-base mismatch or non-specific probe hybridization (P < 0.05). The calibration curves of amplification products of four bacteria had good linearity from 0.1 nM to 100 nM, with all R² values of >0.99. The lowest detection limits were 0.03 nM for P. aeruginosa, 0.02 nM for S. aureus, 0.01 nM for C. tetani and 0.02 nM for C. perfringens. The SPR biosensor had the same detection rate as the traditional culture method (P < 0.05). In addition, the quantification of PCR products can be completed within 15 min, and excellent regeneration greatly reduces the cost for detection.

Conclusions

Our method can rapidly and accurately identify the mixed aerobic-anaerobic infection, providing a reliable alternative to bacterial culture for rapid bacteria detection.

Electric field assisted surface plasmon-coupled directional emission: an active strategy on enhancing sensitivity for DNA sensing and efficient discrimination of single base mutation

We have demonstrated the proof-of-principle of electric field assisted surface plasmon-coupled directional emission (E-SPCDE). The combination of SPCDE and electric field control produced a significant synergistic effect to amplify the right signal and suppress the wrong signal intelligently in an active strategy. A novel hairpin structured DNA biosensor based on the quenching and enhancing of fluorescence in SPCDE has been designed. With modulation of the fluorescence coupling efficiency, a high discrimination ratio up to more than 20-fold has been achieved by enhancing the signal of match and suppressing that of mismatch. E-SPCDE has shown a successful application in DNA sensing, eliminating false positives and false negatives in the detection. E-SPCDE should provide an opportunity to create a new generation of miniaturized high-performance sensing platforms especially in chip-based microarrays and to make the manipulation of the nanometer-scale processes more accessible and detectable.

Ultrasensitive detection of non-amplified genomic DNA by nanoparticle-enhanced surface plasmon resonance imaging

Technologies today available for the DNA detection rely on a combination of labeled probes hybridized to target sequences which are amplified by polymerase chain reaction (PCR). Direct detection methods that eliminate the requirement for both PCR and labeling steps could afford faster, cheaper and simpler devices for the analysis of small amounts of unamplified DNA. In this work we describe the results obtained in the ultrasensitive detection of non-amplified genomic DNA. We analyzed certified reference materials containing different amounts of genetically modified DNA by using a detection method which combines the nanoparticle-enhanced surface plasmon resonance imaging (SPRI) biosensing to the peptide nucleic acids (PNAs) improved selectivity and sensitivity in targeting complementary DNA sequences. The method allowed us to obtain a 41 zM sensitivity in targeting genomic DNA even in the presence of a large excess of non-complementary DNA.

Real-time DNA microarrays: reality check

DNA microarrays are plagued with inconsistent quantifications and false-positive results. Using established mechanisms of surface reactions, we argue that these problems are inherent to the current technology. In particular, the problem of multiplex non-equilibrium reactions cannot be resolved within the framework of the existing paradigm. We discuss the advantages and limitations of changing the paradigm to real-time data acquisition similar to real-time PCR methodology. Our analysis suggests that the fundamental problem of multiplex reactions is not resolved by the real-time approach itself. However, by introducing new detection chemistries and analysis approaches, it is possible to extract target-specific quantitative information from real-time microarray data. The possible scope of applications for real-time microarrays is discussed.

Gold-nanorod-based sensing of sequence specific HIV-1 virus DNA by using hyper-Rayleigh scattering spectroscopy

Infectious diseases caused by the human immunodeficiency virus (HIV) remain the leading killers of human beings worldwide, and function to destabilize societies in Africa, Asia, and the Middle East. Driven by the need to detect the presence of HIV viral sequence, here we demonstrate that the second-order nonlinear optical (NLO) properties of gold nanorods can be used for screening HIV-1 viral DNA sequence without any modification, with good sensitivity (100 pico-molar) and selectivity (single base-pair mismatch). The hyper-Rayleigh scattering (HRS) intensity increases 45 times when a label-free 145-mer, ss-gag gene DNA, was hybridized with 100 pM target DNA. The mechanism of HRS intensity change has been discussed with experimental evidence for higher multipolar contribution to the NLO response of gold nanorods.

Molecular architectures for electrocatalytic amplification of oligonucleotide hybridization

In this work, we describe a new platform suitable for electrocatalytic amplification of oligonucleotide hybridization based on the use of supramolecular bioconjugates incorporating ferrocene-labeled streptavidin. Our goals were aimed at designing a biosensing platform which could support highly reproducible and stable electrocatalytic amplification with maximum efficiency. The use of nonlabeled streptavidin as an underlying layer promotes a major improvement on the characteristics of the amplified electrochemical signal. In addition, the electrocatalytic current can be easily amplified by tuning the concentration of electron donor species in solution. Because of the fact that the redox labels are bioconjugated to the DNA strands, increasing the ionic strength does not lead to the loss of redox labels. More importantly, increasing the concentration of donors only involves the magnification of the signal without implying the permeation of donors (thus reducing the efficient electrocatalysis). This approach represents a major improvement on the use of electrocatalytically amplified DNA-sensing platforms, thus overcoming any possible limitation in connection with the reproducibility and reliability of this well-established method.