DNA detection by surface enhanced resonance Raman scattering (SERRS)

This Education article outlines the different ways in which surface enhanced resonance Raman scattering (SERRS) can be used for the detection of DNA. The use of various different SERRS detection strategies that have allowed both sensitive and selective detection to be obtained is covered. Detection of DNA by SERRS involves the use of a dye with the DNA, whether as an intercalator or by direct covalent attachment. This generates strong SERRS signals that indicate the presence of the specific DNA sequence. The SERRS detection of DNA in different molecular biological assays is also discussed.     

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.     

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.     

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.     

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.     

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.     

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.     

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.     

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.     

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.     

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.     

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.     

Determination of Benzocaine in Pharmaceutical Formulations by Indirect SERRS Assay Combined with Azo Coupling

Coupled with an azo coupling reaction, a simple, rapid, sensitive, and effective surface-enhanced resonance Raman scattering (SERRS) detection method for benzocaine was developed. In our study, benzocaine which is used clinically as a local anesthetic was derived with p-aminothiophenol into a corresponding azo product within 5 min, resulting in a strong SERRS response with the simple addition of Ag NPs excited with a 532 nm laser. The linear correlation between SERRS intensity of dominant bands and logarithm of benzocaine concentration was investigated for quantitative determination. The method reached a limit of detection (LOD) down to 0.139 and 0.0788 μg/mL calculated with two peak intensity ratios (I₁₅₆₈/I₂₂₆₀ and I₁₃₃₁/I₂₂₆₀), which is comparable to most studies reported previously, and meanwhile had superiority in simplicity and rapidness. The quantitative measurements for pharmaceutical preparations with benzocaine were conducted without complex extraction and enrichment processes. It was indicated that the SERRS assay combined with azo derivatization reaction has implications for practical applications in more complicated systems involving biological samples, in which appropriate and simplified pretreatments were conducted to remove interfering components.     

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.     

Chemically selective sensing through layer-by-layer incorporation of biorecognition into thin film substrates for surface-enhanced resonance Raman scattering

In this work, the fabrication, characterization, and application of avidin/Ag nanoparticle layer-by-layer (LbL) films as chemically selective substrates for surface-enhanced resonance Raman scattering (SERRS) is demonstrated. The biospecific interaction between avidin and the small molecule biotin, one of the strongest known to exist in nature, is exploited to preferentially capture biotinylated species from solution. This highly favored adsorption is shown to yield SERRS concentration enhancements and improved detection sensitivities of ca. 102 for commercially available and in situ prepared biotinylated species over their nontagged counterparts.     

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.     

Semi-quantitative analysis of indigo by surface enhanced resonance Raman spectroscopy (SERRS) using silver colloids

In this paper we report for the first time semi-quantitative analysis of indigo using surface enhanced Raman spectroscopy (SERS) and surface enhance resonance Raman spectroscopy (SERRS). Indigo, a dye widely used today in the textile industry, has been used, historically, both as a dye and as a pigment; the latter in both paintings and in printed material. The molecule is uncharged and largely insoluble in most solvents. The application of SERS/SERRS to the semi-quantitative analysis of indigo has been examined using aggregated citrate-reduced silver colloids with appropriate modifications to experimental protocols to both obtain and maximise SERRS signal intensities. Good linear correlations are observed for the dependence of the intensities of the SERRS band at 1151 cm(-1) using laser exciting wavelengths of 514.5 nm (R=0.9985) and 632.8 nm (R=0.9963) on the indigo concentration over the range 10(-7)-10(-5) and 10(-8)-10(-5) mol dm(-3), respectively. Band intensities were normalised against an internal standard (silver sol band at 243 cm(-1)). Resonance Raman spectra (RRS) of aqueous solutions of indigo could not be collected because of its low solubility and the presence of strong fluorescence. It was, however, possible to obtain RS and RRS spectra of the solid at each laser excitation wavelength. The limits of detection (L.O.D.) of indigo by SERS and SERRS using 514.5 and 632.8 nm were 9 ppm at both exciting wavelengths. Signal enhancement by SERS and SERRS was highly pH dependent due to the formation of singly protonated and possibly doubly protonated forms of the molecule at acidic pH. The SERS and SERRS data provide evidence to suggest that an excess of monolayer coverage of the dye at the surface of silver colloids is observed at concentrations greater than 7.85x10(-6) mol dm(-3) for each exciting wavelength. The data reported herein also strongly suggest the presence of multiple species of the indigo molecule.     

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.     

The first SERRS multiplexing from labelled oligonucleotides in a microfluidics lab-on-a-chip

The first simultaneous detection of three dye-labelled oligonucleotides in a microfluidics chip by SERRS is reported.     

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.