Quantitative SERRS for DNA sequence analysis

SERRS is an extremely sensitive and selective technique which when applied to the detection of labelled DNA sequences allows detection limits to be obtained which rival, and in most cases are better than, fluorescence. In this tutorial review the conditions are explored which enable the successful detection of DNA using SERRS. The enhancing surface which is used is crucial and in this case suspensions of nanoparticles were the focus as they allow quantitative behaviour to be achieved in systems analogous to current fluorescence based approaches. The aggregation conditions required to obtain SERRS of DNA affect the sensitivity and the reproducibility and we describe the use of spermine as an effective aggregating agent to achieve excellent reproducibility and sensitivity. The nature of the label which is used, be it fluorescent or non-fluorescent, positively or negatively charged, also affects the SERRS response and these conditions are again discussed. Finally, we show how to detect a specific target DNA sequence in a meaningful diagnostic assay using SERRS and how the approaches described previously in the review are vital to the success of such approaches.     

Microarray‐Based Detection of Dye‐Labeled DNA by SERRS Using Particles Formed by Enzymatic Silver Deposition

The growing interest in DNA diagnostics is addressed today by microarrays with fluoresence detection. In our approach, we utilize spatially defined arrays of short oligonucleotides on a modified glass surface. Surface enhanced resonance Raman scattering (SERRS) is used to obtain molecularly specific spectra of the Raman‐active dye‐labeled DNA. Nanoparticles produced by enzymatic silver deposition are used as SERS‐active substrate. They grow directly on the modified oligonucleotides and only in the spatially defined areas on the chip. Furthermore, they potentially offer several advantages for SERS detection. The nanoparticles are characterized and their ability for use as SERS‐ and SERRS‐active substrate is estimated. Three different Raman‐active dyes are investigated for their potential for involvement in sequence specific DNA analysis.     

Quantitative detection of dye labelled DNA using surface enhanced resonance Raman scattering (SERRS) from silver nanoparticles

The detection of dye labelled DNA by surface enhanced resonance Raman scattering (SERRS) is reported. The dye labels used are commercially available and have not previously been used as SERRS dyes. Detection limits using two excitation frequencies were determined for each label. This expands the range of labels which can be used for surface enhanced resonance Raman scattering with silver nanoparticles.     

Enzyme-free detection and quantification of double-stranded nucleic acids

We have developed a fully enzyme-free SERRS hybridization assay for specific detection of double-stranded DNA sequences. Although all DNA detection methods ranging from PCR to high-throughput sequencing rely on enzymes, this method is unique for being totally non-enzymatic. The efficiency of enzymatic processes is affected by alterations, modifications, and/or quality of DNA. For instance, a limitation of most DNA polymerases is their inability to process DNA damaged by blocking lesions. As a result, enzymatic amplification and sequencing of degraded DNA often fail. In this study we succeeded in detecting and quantifying, within a mixture, relative amounts of closely related double-stranded DNA sequences from Rupicapra rupicapra (chamois) and Capra hircus (goat). The non-enzymatic SERRS assay presented here is the corner stone of a promising approach to overcome the failure of DNA polymerase when DNA is too degraded or when the concentration of polymerase inhibitors is too high. It is the first time double-stranded DNA has been detected with a truly non-enzymatic SERRS-based method. This non-enzymatic, inexpensive, rapid assay is therefore a breakthrough in nucleic acid detection.     

Evaluation of the number of modified bases required for quantitative SERRS from labelled DNA

The optimisation of the modification of DNA to facilitate quantitative detection by surface enhanced resonance Raman scattering (SERRS) detection is reported.     

Detection of DNA probes using Diels Alder cycloaddition and SERRS

A number of methods for detecting specific DNA sequences have been used to provide data for use in diagnosis of disease states and examination of gene expression. This study shows how the use of labelled oligonucleotides created by Diels Alder cycloaddition can be used as surface enhanced resonance Raman scattering (SERRS) active probes that provide easily identifiable signals at low concentrations in a mixture. The probes were produced by first tagging the oligonucleotides with a furan residue at the 5'-terminus to act as the diene. Three specifically designed benzotriazole azo maleimide dyes were then used as dienophiles to undergo cycloaddition with the furan modified oligonucleotide to generate SERRS active probes. These probes gave excellent SERRS signals from a silver-PVA film. Surface mapping of the silver PVA film indicated that the distribution of the dyes was uniform and that the number of moles of probe detected at any one time was approximately in the attomole region.     

Investigation of enzyme activity by SERRS using poly-functionalised benzotriazole derivatives as enzyme substrates

New methods of measuring biologically relevant concentrations of enzymes are necessary to allow greater understanding of biological systems. We have previously shown that aryl azo benzotriazolyl alkyl esters can act as enzyme substrates, with the progress of the reaction being monitored using SERRS (see Nat. Biotechnol., 2004, 22, 1133, ref. ). This is a wholly novel analytical application of SERRS, and the low detection levels of the technique allow for an ultra-sensitive enzyme assay. Masked enzyme substrates are used that are invisible to SERRS until enzymatic hydrolysis. Turnover of the substrate by the enzyme leads to the release of the surface-seeking dye necessary for SERRS, and intense signals are produced. Here we report an improved synthesis of 2H-benzotriazolyl alkyl esters via nucleophilic substitution of a chloromethyl ester by benzotriazolyl azo dyes, giving up to a ten-fold increase on previously reported yields. Introduction of electron-withdrawing groups to the benzotriazole ring allows control over the SERRS properties of the compounds. This is of great significance in expanding the synthetic flexibility and subsequently the fundamental use of these compounds as ultra-sensitive and selective reporters of enzyme activity.     

Reproducible SERRS from structured gold surfaces

Metallic substrates with ordered spherical cavities have been shown to be very effective for surface-enhanced Raman scattering (SERS) and can be fabricated reproducibly using electrodeposition. The sensitivity of detection is increased by several orders of magnitude by using surface-enhanced resonance Raman scattering (SERRS). In this report we demonstrate SERRS for the first time on electrodeposited gold films templated with colloidal spheres and demonstrate the reproducibility of the response. We also obtain a direct comparison between SERRS and SERS by choosing two dyes, Cy5 and Cy3, which are similar in structure but differ in their excitation maxima, such that one is resonant and the other non-resonant with our laser excitation. As expected, the resonant enhancement is found to be of the order of 10(3) over and above that for SERS. The net SERRS enhancements are shown to be of the order of 10(9). We also find that the resonant enhancement profile of the different peaks for the chromophore follows the plasmonic resonance absorption spectrum obtained for the structured surface.     

Cetylpyridinium Chloride Activated Trinitrotoluene Explosive Lights Up Robust and Ultrahigh Surface‐Enhanced Resonance Raman Scattering in a Silver Sol

Surface‐enhanced resonance Raman scattering (SERRS) is not realized for most molecules of interest. Here, we developed a new SERRS platform for the fast and sensitive detection of 2,4,6‐trinitrotoluene (TNT), a molecule with low Raman cross section. A cationic surfactant, cetylpyridinium chloride (CPC) was modified on the surface of silver sols (CP‐capped Ag). CPC not only acts as the surface‐seeking species to trap sulfite‐sulfonated TNT, but also undergoes complexation with it, resulting in the presence of two charge‐transfer bands at 467 and 530 nm, respectively. This chromophore absorbs the visible light that matches with the incident laser and plasmon resonance of Ag sols by the use of a 532.06 nm laser, and offered large resonance Raman enhancement. This SERRS platform evidenced a fast and accurate detection of TNT with a detection limit of 5×10^?11 M under a low laser power (200 μW) and a short integration time (3 s). The CP‐capped Ag also provides remarkable sensitivity and reliable repeatability. This study provides a facile and reliable method for TNT detection and a viable idea for the SERS detection of various non‐resonant molecules.     

Immunoassay for P38 MAPK using surface enhanced resonance Raman spectroscopy (SERRS)

A micro-bead sandwich assay for P38 mitogen-activated protein kinase using surface enhanced resonance Raman spectroscopy (SERRS) detection is reported. Monoclonal capture antibodies were immobilised on a solid phase of magnetic micro-beads with secondary detection using a rhodamine-labelled antibody. Quantitative SERRS detection of the secondary antibody was possible with a limit of detection of 9.5 x 10(-12) mol dm(-3). The sandwich assay was quantitative and sensitive to 6 ng ml(-1). The mechanism of the SERRS detection in the immunoassay was investigated. The addition of SERRS aggregating agents causes the dissociation of the immuno-complex from the magnetic beads. Scanning electron microscopy images indicate that the colloidal suspension rather than adsorbed silver nanoparticles on the beads provide the SERRS signals, that the aggregate size is partially controlled and that there is some inhomogeneity in the distribution of organic matter on the nanoscale.     

Practical understanding and use of surface enhanced Raman scattering/surface enhanced resonance Raman scattering in chemical and biological analysis

The unique ability to obtain molecular recognition of an analyte at very low concentrations in situ in aqueous environments using surface enhanced Raman scattering (SERS) and surface enhanced resonance Raman scattering (SERRS) detection makes these spectroscopies of considerable interest. Improved understanding of the effect coupled to improvements in practical techniques make the use of SERS/SERRS much simpler than has been the case in the past. This article is designed as a tutorial review targeted at aiding in the development of practical applications.     

SERRS as a more sensitive technique for the detection of labelled oligonucleotides compared to fluorescence

This communication contains data from a comparison between the detection limits obtained using surface enhanced resonance Raman scattering (SERRS) and fluorescence detection of dye labelled oligonucleotides. The results show that the detection limits for SERRS are generally at least three orders of magnitude lower than those obtained for fluorescence.     

SERRS-based enzymatic probes for the detection of protease activity

Measurement of protease activity, for the first time using SERRS as a detection method, is reported herein. Synthetic introduction of phenylalanine to a benzotriazole azo dye allows the SERRS response to be "switched off" and subsequent exposure to protease restores the SERRS response. The substrates exhibit varying reactivity for a range of proteases and allow for in situ, real-time analysis of protease reactivity. A limit of detection for one protease, Subtilisin carlsberg, was investigated and was established to be 50 ng ml-1.     

Quantitative analysis of methyl green using surface-enhanced resonance Raman scattering

Surface-enhanced resonance Raman scattering (SERRS) spectra of aqueous solutions of the triphenylmethane dye methyl green have been obtained for the first time by use of citrate-reduced silver colloids and a laser excitation wavelength of 632.8 nm. Given the highly fluorescent nature of the analyte, which precluded collection of normal Raman spectra of the dye in solution and powdered state, it was highly encouraging that SERRS spectra showed no fluorescence due to quenching by the silver sol. The pH conditions for SERRS were optimised over the pH range 0.5–10 and the biggest enhancement for SERRS of this charged dye was found to be at pH 2.02, thus this condition was used for quantitative analysis. SERRS was found to be highly sensitive and enabled quantitative determination of methyl green over the range 10⁻⁹ to 10⁻⁷ mol dm⁻³. Good fits to correlation coefficients were obtained over this range using the areas under the vibrational bands at 1615 and 737 cm⁻¹. Finally, a limit of detection of 83 ppb was calculated, demonstrating the sensitivity of the technique.     

Au nanowire-on-film SERRS sensor for ultrasensitive Hg2+ detection

We report an ultrasensitive and selective single nanowire-on-film (SNOF) surface-enhanced resonance Raman scattering (SERRS) sensor for Hg(2+) detection based on structure-switching double stranded DNAs (dsDNAs). Binding of Hg(2+) induces conformational changes of the dsDNAs and let a Raman reporter get close to the SNOF structure, thereby turning on SERRS signal. The well-defined SNOF structure provides a detection limit of 100 pM with improved accuracy in Hg(2+) detection. This sensor is stable over a considerable amount of time and reusable after simple treatment. Since this SNOF sensor is composed of a single Au NW on a film, development of a multiplex sensor would be possible by employing NWs modified by multiple kinds of aptamers.     

Inherent complexities of trace detection by surface-enhanced Raman scattering.

Surface-enhanced Raman scattering (SERS) and surface-enhanced resonance Raman scattering (SERRS) are powerful optical scattering techniques used in such frontier areas of research as ultrasensitive chemical analysis, the characterization of nanostructures, and the detection of single molecules. However, measuring and, most importantly, interpreting SERS/SERRS spectra can be incredibly challenging. This is the result of modifications to the measured spectra that are due to of a variety of instabilities and contributions. These interferences and modifications arise from the nature of the enhancement itself, as well as the conditions used to attain SERS spectra. The present report is an attempt to collect in one place the analytical interferences that are most commonly found during the collection of SERS/SERRS spectra.     

SERRS immunoassay for quantitative human CRP analysis

SERRS has been used for the first time for the measurement of C-reactive protein (CRP) in an immunoassay. CRP, a biological marker for the diagnosis of infection and inflammation, is quantified in an ELISA using conventional reagents, but the usual colorimetric detection step is replaced by SERRS detection, offering improved sensitivity and potential for multiplexing analysis.     

Identification and characterization of active and inactive species for surface-enhanced resonance Raman scattering

The surface-enhanced resonance Raman scattering (SERRS) activity of a statistically significant number of silver nanoparticles has been studied using a correlated SERRS mapping and transmission electron microscopy (TEM) method. TEM allowed the nature of each entity to be directly identified, and the SERRS activity was obtained from the corresponding SERRS map. Particles in various states of aggregation were analyzed to establish relative activities. It was established that SERRS activity is dependent on the specific batch of colloid tested. By averaging different colloid batches, it was shown that increasing SERRS activity is observed with increasing numbers of particles in the aggregates. By reducing the surface coverage of the particles to the extent that single moieties could be examined optically, the ratio of the relative activities of single particles, dimers, trimers, and larger aggregates was estimated. High-resolution TEM images of a number of active and inactive particles are reported. However, no clear correlation between microstructure and SERRS activity was observed.     

Silver-particle-based surface-enhanced resonance Raman scattering spectroscopy for biomolecular sensing and recognition

We demonstrate in this work that 2-μm-sized Ag (μAg) powders can be used as a core material for constructing biomolecular sensing/recognition units operating via surface-enhanced resonance Raman scattering (SERRS). This is possible because μAg powders are very efficient substrates for both the diffuse reflectance IR and the surface-enhanced Raman scattering–SERRS spectroscopic characterization of molecular adsorbates prepared in a similar manner on silver surfaces. Besides, the agglomeration of μAg particles in a buffer solution can be prevented by the layer-by-layer deposition of cationic and anionic polyelectrolytes such as poly(allylamine hydrochloride) (PAH) and poly(acrylic acid) (PAA). In this particular study, we used rhodamine B isothiocyanate (RhBITC) as a SERRS marker molecule, and μAg powders adsorbed consecutively with RhBITC and PAH–PAA bilayers were finally derivatized with biotinylated poly(l-lysine). On the basis of the nature of the SERRS peaks of RhBITC, those μAg powders were confirmed to selectively recognize streptavidin molecules down to concentrations of 10⁻¹⁰ g mL⁻¹. Since a number of different molecules can be used as SERS–SERRS marker molecules, the present method proves to be an invaluable tool for multiplex biomolecular sensing/recognition via SERS and SERRS.     

Single molecular detection of a perylene dye dispersed in a Langmuir-Blodgett fatty acid monolayer using surface-enhanced resonance Raman scattering

The Langmuir-Blodgett (LB) monolayer technique was used to fabricate single molecule LB monolayer containing bis(phenethylimido)perylene (PhPTCD), a red dye dispersed in arachidic acid (AA) with an average doping of 1 molecule per microm2. The monolayer was transferred onto Ag island films to obtain spatially resolved surface-enhanced resonance Raman scattering (SERRS) spectra. The mixed LB monolayers were fabricated with a concentration, on average, of 1, 6, 19 and 118 PhPTCD molecules per microm2 in AA. The AA provides a two-dimensional host matrix whose background signal does not interfere with the detection of the probe molecule's SERRS signal. The properties of the single molecule detection were investigated using micro-Raman with a 514.5-nm laser line. The Ag island surfaces coated with the LB monolayer were mapped with spatial steps of 3 microm and global chemical imaging of the most intense SERRS band in the spectrum was also recorded. The SERRS and surface-enhanced fluorescence (SEF) of the neat and single molecule LB monolayer were recorded in a temperature range from liquid nitrogen to + 200 degrees C. Neat PhPTCD LB monolayer spectra served as reference for the identification of characteristic signatures of the single molecule behavior. The spatial resolution of Raman-microscopy experiments, the multiplicative effect of resonance Raman and SERRS, and the high sensitivity of the new dispersive Raman instruments, allow SERRS to be part of the family of single molecular spectroscopies.