SERS-based detection of biomolecules

3.1 Nucleotides and nucleic acids

Nucleotides are composed of a sugar, a phosphoryl group and a nucleobase, which can be a purine or a pyrimidine. There are two purine bases, adenine (A) and guanine (G) and three pyrimidine bases, cytosine (C), thymine (T) and uracil (U). Ribonucleic acid (RNA) and Deoxyribonucleic acid (DNA) are the polymers of nucleotides, which are designated by the type of the sugar in the backbone. In the case of RNA the sugar is D-ribose and for DNA it is 2-deoxy-D-ribose. The intrinsic genetic information of the DNA is translated via the messenger RNA (mRNA) into a defined peptide or protein sequence. Thus, mRNA molecules function as intermediate information storage. The expression of the DNA-coded information into a given amino acid chain can be regulated at various stages. One important regulation mechanism involves so-called non-coding RNAs that trigger gene silencing in eukaryotic cells.

Since the SERS spectra of DNA and RNA are dominated by adenine related modes [64, 65], the interpretation of adenine SERS spectra and the discussion of the high diversity of adenine compounds within the SERS fingerprints play an important role. Moreover, the attachment sites to the metal surface of adenine are often investigated and discussed in the literature. For clarification, the molecular structure of adenine is depicted in Figure 1. SERS spectra of adenine were recorded applying low concentrations of the nucleotide [66]. Adenine shows a strong Raman mode at 730 cm^-1, which can be assigned to a breathing vibration and is dominating the SERS spectrum. In general, it is found that the SERS spectrum is dominated by in-plane vibrational modes. Thus, according to the surface selection rules, it is concluded, that the orientation of the adenine rings should be perpendicular to the silver surface. Due to the decreased intensity of the vibrational modes involving the nitrogen atoms N1, N3 and N9 as well as the preferentially enhanced SERS signals of Raman modes involving the external amino group and the nitrogen atom N7, it is suggested that the interaction between adenine and the silver surface takes place via the external amino group and N7. Furthermore, out-of-plane modes appear strongly weakened in the SERS spectrum but do not disappear completely. Thus, a slightly tilted orientation of the adenine molecule to the metal surface is probable. In further studies, the orientation of adenine and its derivatives polyadenine single stranded DNA (polyA) and adenosine monophosphate (AMP) were investigated at different pH values using SERS as well as surface enhanced IR absorption (SEIRA) on gold nanoshell particles [67]. Due to the protonation of adenine at various pH values, relative changes in the band intensity are found. The recorded SERS spectra of adenine and its investigated derivatives polyA and AMP are dominated by the adenine ring breathing mode at 735 cm^-1 which is in consistency to other studies. Based on a detailed vibrational analysis of the recorded SERS as well as SEIRA spectra, the ‘end-on’ binding of adenine via the nitrogen atom N3 with the C-NH₂ bond normal to the surface is suggested as the presumed orientation relative to the gold nanoshell surface. In the case of polyA and AMP, an adsorption via N3 is sterically hindered due to substituents bound at N9 and a binding via the external amino group is more likely. In order to increase the sensitivity for the detection of the nucleobases cytosine, adenine, thymine and guanine, the automated SERS detection at different pH values is developed [68] since the pH-sensitive SERS enhancement is known from various studies [65, 67, 69, 70]. As an example, the influence of the experimental conditions, like type of colloid, adenine concentration and pH value on the recorded SERS spectra is investigated [65]. It was found, that the SERS spectra are in agreement with the N1-protonated form of adenine at acidic pH values applying both silver and gold colloids. In contrast to previous studies, the recorded spectra at neutral and alkaline pH are assigned to the N9-deprotonated form rather than the neutral adenine molecule. Thus, the authors concluded that the ‘normal’ spectrum of adenine is attributed to the deprotonated form, similar to guanine and uracil. For low adenine concentrations applying silver colloids under neutral and alkaline conditions, the detected SERS spectra are attributed to different silver complexes of adenine. The high cross section of the silver complexes might be an explanation for the observed and difficult to interpret changes in intensity with varying the adenine concentrations. In addition, the SERS spectra of desoxyadenosine and 5′-desoxyadenosine monophosphate (5′-dAMP) are also dependent on the experimental conditions and the results indicate that both protonated and neutral forms of desoxyadenosine and 5′-dAMP are detectable as function of the pH value [70]. Since the ribose unit is substituted via the position N9, a deprotonated analogue to adenine is not detectable. Based on the weakened SERS intensity of the in-plane breathing modes, a much flatter orientation to the metal surface of desoxyadenosine is found for both the neutral and protonated forms compared to that of the corresponding forms of adenine. In the case of 5′-dAMP, a reorientation of the molecule on the metallic surface is observed as function of the concentration, pH and the used metal colloid. In summary, all introduced studies show that the SERS spectrum of adenine is dominated by the breathing mode of the entire molecule at around 730 cm^-1, that the attachment of adenine is at least via the external amino group and moreover, hints are found for a N9-deprotonated form of the free adenine under normal conditions at neutral pH values.

Figure 1

Illustration of the molecular structure of adenine.

In addition to the detailed investigation of nucleobases – especially adenine, also DNA and RNA are characterized by means of SERS. The here presented results are the starting point for a SERS-based application in label-free DNA and RNA analytics. In order to record reliable SERS spectra of nucleic acids, the interaction time between the molecules of interest and the metallic surface as well as the amount of molecules within the sample volume should be chosen with caution due to strong influences on the SERS signal [71]. A detailed analysis on the correlation of the molecular orientation and packing density of double-stranded DNA adsorbed on a metallic surface was performed [72]. In Figure 2, the detection strategy as well as the recorded SERS spectra is depicted. The SERS spectra were analyzed regarding their peak ratio of adenine and guanine vibrational modes as function of the DNA concentration. For high DNA concentrations which correspond to a high packing density, the adenine peak is more intense in comparison to guanine. In the case of low DNA concentrations and thus low packing densities, the guanine peak is increased with respect to the adenine vibrational mode. Based on these studies, higher adenine signal intensity indicates a less tilted orientation of the DNA molecule relative to the metal surface. A reorientation of double-stranded DNA towards an upright position was further done by means of insertion of polythymine single stranded DNA (polyT) which is detectable via an increased adenine peak intensity. Guanine-rich nucleic acid sequences are known to form a four-stranded DNA structure. The formation of these so-called G quadruplexes was characterized by means of SERS as a label-free analytical method [73]. The fluctuation in SERS intensity is quantitatively investigated before and after the quadruplex formation. Since the single DNA strands show a random orientation relative to the metal surface, the detailed analysis of the quadruplex SERS spectra suggests a perpendicular orientation of the G quadruplexes with respect to the metal surface. The characterization of the SERS signal as function of the numbers of G planes illustrates the improved stability of the quadruplex structure with an increasing number of G planes. In addition, the SERS technique is applied for the characterization of RNA. Adenine-containing microRNA chains adsorbed on a silver surface were investigated regarding their spectral features and moreover the structural arrangement relative to the metal surface [74]. The recorded SERS spectra, which are dominated by Raman modes of adenine, were analyzed in comparison with the spectral fingerprint of adenine, adenosine and the silver-adenine complex structure. Based on SERS and DFT results for adenine and adenosine, an interaction of microRNA via the N3 atom of adenine is proposed. Furthermore, the aromatic character of the pyrimidinic ring of adenine might favor a stronger metal-molecule interaction. Since the SERS signal is proportional to the amount of free residues interacting with the metallic surface, this technique was applied to monitor the catalysis of ribozyme cleavages – catalytic active hairpin structures found within RNA molecules [75]. In further studies, the interaction of small molecules containing three imidazole as well as three pyridine rings with single-stranded RNA polynucleotides, double-stranded DNA polynucleotides and calf thymus DNA was subject of research [76]. Due to the wavenumber downshift of imidazole and pyridine ring vibrations, an aromatic stacking structure of imidazole and pyridine aromatic moieties and DNA base-pairs is concluded. In summary, the results presented within this paragraph open the way to label-free DNA and RNA SERS-based detection schemes and moreover allow the investigation of interactions between small molecules and nucleic acids adsorbed on metallic surfaces. As a consequence of surface selection rules, Raman modes perpendicular to the surface are dominating the SERS spectrum. Due to the evanescent field on the metal surface, only Raman modes in close vicinity are observable under SERS conditions. Furthermore, vibrational modes of chemical groups which bind preferably to the metal are dominating the SERS spectrum. Thus, a change in the structural arrangement (reorientation) of nucleic acids with respect to the surface due to attachment of other molecule will cause a significant change in SERS intensity and band ratios of the Raman modes of the molecular compounds.

Figure 2

Characterization of the DNA orientation towards the metal surface. (A) Illustration of the SERS-based detection scheme on the basis of the double-stranded DNA tilt angle. (B) SERS response of double-stranded DNA for various concentrations (spectra 1–5 are related to the concentrations 40, 20, 10, 5 and 1.25 μm). Reprinted with permission from Barhoumi et al. [72]. Copyright 2008 American Chemical Society.

Miscellaneous proof-of-principle assays demonstrated the applicability of the SERS technique for the detection of adenine and its derivative as well as DNA or even RNA. As mentioned previously, adenine is one of the four RNA/DNA bases and therefore a main constituent of the nucleic acid metabolism in living organisms. Moreover adenine derivatives have pivotal roles in the cellular respiratory chain (e.g., adenosine triphosphate – ATP, nicotinamide adenine dinucleotide – NAD, flavin adenine dinucleotide – FAD) as well as second messengers in signal transduction processes (cyclic adenosine monophosphate – cAMP). Thus, the SERS-based detection of adenine or derivatives is addressed in recent articles. A planar chitosan-Ag SERS substrate was used for the quantification of adenine [77], whereas adenosine monophosphate (AMP) or deoxyadenosine monophosphate (dAMP) was detected by mean of SERS with noble metal particles [67, 78]. Also, DNA-aptamer biosensors were successfully used for analyzing adenosine/adenosine triphosphate [79–82]. Various papers introduced the applicability of the SERS-approach for the label-free detection of RNA or DNA molecules [83–85]. The successful use of SERS as a biosensor for DNA hybridization events with synthetic DNA or peptide nucleic acids (PNA) was described by several research groups [86–90]. Additionally, several sandwich hybridization assays concomitant with SERS detection were discussed in the literature [91–94]. The prominent spectral feature of adenine can also serve as an endogenous marker for a label-free SERS detection of DNA hybridization. As demonstrated in Figure 3 a DNA capture probe that harbors 2-aminopurine (2-AP) instead of adenine, which already preserved an adenine-like hybridization characteristic but lacked the 736 cm^-1 breathing mode, was immobilized on a gold surface [64]. After the successful hybridization with the unlabeled complementary target DNA, that brought adenine within the sequence, the characteristic adenine peak was detectable. Another interesting tool for monitoring DNA hybridization was emphasized by dendrimer formation as a signal amplification strategy [95].

Figure 3

Label-free DNA detection applying SERS for read-out. Recorded SERS spectra of (A) adenine containing and (B) adenine non-containing DNA sequence are shown. Within the inset, the hybridization model between probe DNA having 2-aminopurine substituted for adenine and unlabeled target DNA is illustrated. Reprinted with permission from Barhoumi et al. [64]. Copyright 2010 American Chemical Society.

Damaged DNA, more precisely oxidized and UV-light exposed genomic DNA isolated from human cell lines, is detectable by label-free SERS [96]. The SERS community also implemented novel trends from the field of nucleic acid diagnostics, namely isothermal DNA amplification and microarray-based detection schemes. Rolling circle amplification, as one isothermal amplification strategy, allows the accumulation of target DNA and significantly improves the resulting SERS signal [97–99]. The creation of SERS substrates in array format on planar surfaces opens the possibility for multiplex detection by a plethora of dye-labeled oligonucleotides [100]. After the detailed discussion about the characterization as well detection of nucleotides and nucleic acids, innovative approaches related to the characterization of amino acids and their macromolecules peptides and proteins as well as promising detection schemes will be introduced within the next paragraph.

3.2 Amino acids and peptides/proteins

Amino acids are molecules containing an amine and a carboxylic group as well as a side-chain that specifies each amino acid. Amino acids itself are the most versatile group of biomolecules. They possess a variety of important biological function, which include precursors of hormones or neurotransmitters and, in particular, they serve as the building blocks of peptides and proteins. There are 22 proteinogenic amino acids which can be linked together to form a variety of smaller peptides or complex proteins. Within this paragraph, the characterization of amino acids, small peptides and proteins under SERS conditions is introduced. The following chapter includes the discussion about the preferred binding sites of amino acids relative to the metal surface which are important in spectral analysis, since the vibrational modes of these surface-binding moieties are dominating the SERS response. Moreover, the influences on the SERS signature of peptides and proteins are discussed and innovative detection schemes of these biomolecules are introduced.

In detailed studies by various research groups, the characteristic Raman modes of amino acids under SERS conditions and their dependencies as well as the adsorption behavior and orientation relative to the metallic surface was investigated. Applying SERS as analytical tool in combination with supporting DFT (density functional theory) calculations, the adsorption of the zwitterionic L-cysteine on the silver surface via the carboxylate, ammonium and sulphydryl groups is concluded [101]. Furthermore, it is found, that cysteine shows the tendency to form the corresponding dipeptide in solution. The characterization of L-tryptophan by means of SERS on silver nanoparticles shows the result that Raman modes of carboxylate and amino groups become strong under SERS conditions [102]. A time-dependent SERS study shows a unique spectral response, related with the most stable configuration and orientation to the metal surface, after a stabilization period [103]. Overall, it is concluded, that the attachment of this amino acid is preferably via the carboxylate and amino groups of L-tryptophan [102, 103]. A study on L-lysine attached to silver colloidal surfaces indicates no unique conformation and orientation relative to the metal surface [104]. Within the study, no identical SERS spectra were recorded under neutral pH conditions indicating various conformation of L-lysine with respect to the metal surface. In general, L-lysine interacts via the carboxylate and amino groups with the silver surface, which is also found for other amino acids. In the case of arginine, the preferably interaction between the amino acid and the silver surface is verified to be conducted through the guanidinium moiety and not via the carboxylate and amino groups [105]. Reorientation of amino acids adsorbed on silver surfaces is achieved by adding cations which becomes visible within the SERS response. It is found, that Ce³⁺ affects the structure of N-acetylalanine self-assembled at silver surfaces due to a binding reaction between Ce³⁺ and the carbonyl as well as the amino moieties [106]. The same is true for the effect of Pb²⁺ influencing the structure of L-glutathione due to the binding possibly occurring between the cation and the carboxyl and amino groups of the amino acids [107]. The adsorption behavior of enantiomeric and racemic forms of an amino acid was investigated by using methionine and collecting SERS spectra as function of pH value and electrode potential [108]. Non negligible spectral differences are found by comparing the SERS response of D-methionine and a racemic mixture of D- and L-methionine under acidic conditions for different electrode potentials. In comparison, in alkaline medium where both carboxylate and amino groups are responsible for the interaction with the electrode surface, no differences in spectral response are found in contrast to the observations under acidic conditions. Thus, indications are found for a chirality-dependent interaction based on intermolecular hydrogen bonds between adjacent molecules at pH 3. A further study shows the stereoselective interaction between phenylalanine and monolayers of cysteine adsorbed on rough silver surfaces [109]. Significant changes in SERS intensity were established for the interaction of L-phenylalanine with L-cysteine monolayer adsorbed on silver surfaces as well as for D-phenylalanine interacting with D-cysteine monolayers. This effect is attributed to variations in hydrogen bonding between the ammonium groups of the adsorbed cysteine molecule with the carboxylate groups of the phenylalanine. In summary, applying SERS for characterization of amino acids, a preferably binding via the carboxylate and amino moieties is found through the enhancement of the Raman intensity of vibrations which are influenced by the nature of the binding to the metal surface. A reorientation of amino acids is found for adding cations. Finally, indications are found that SERS is sensitive to the chirality of amino acids.

Within the following paragraph, the characterization of peptides, which are defined as small assemblies of amino acids, is introduced and the influences on the SERS response of peptides is discussed. The investigations are focused on studies of the orientation of peptides relative to the metallic surface and the therewith related marker modes within the SERS spectra. For L-carnosine an interaction primarily via the carboxylate group with the imidazole ring oriented perpendicular to the silver surface and the alanine moiety with parallel orientation having the amino group close to the silver surface is found [110]. A comprehensive study of alafosfalin and its analogs, which are phosphonodipeptides of alanine, was done by using colloidal silver particles as SERS platform supported by DFT calculations [111]. It is found, that these peptides adsorb as intact anionic species with the P-terminal acid group onto the silver surface. The detected SERS response indicate that both the constituent amino acids and the amide bond linking the N- and P-terminal residues interact with the metallic surface. Moreover, the adsorption mechanism of phosphonodipeptides containing N-terminal glycine on silver surface is subject of research [112]. Since a similar adsorption behavior is not found for all analogs, it is concluded, that the aliphatic spacer group play an important role within the interaction of these dipeptides with the silver surface. For dipeptides containing dehydroalanine and dehydrophenylalanine a strongly by dehydroresidues influenced SERS profile is detected [113]. Here, the most prominent SERS signal for the investigated dipeptides is attributed to the symmetric stretching vibration of the carboxylate group, which indicates the preferred adsorption via the deprotonated carboxyl group. Time-dependent and pH-dependent SERS studies were performed to characterize the binding characteristics of the homodipeptide diglycine to the silver surface [114]. A time-dependent increase in signal intensity is found for Raman modes representing the amino and amide moiety of the dipeptide. Furthermore, the pH value influences the way of adsorption due to the protonation as well as deprotonation of functional groups. Cysteine-containing aromatic peptides were characterized and the spectral response is compared with the SERS spectra of the cell-penetrating peptide oligomer penetratin [115]. It is concluded that, beside the protein backbone groups, aromatic amino acid residues provide the dominant features within the SERS spectra of peptides and proteins when present in the molecule of interest. In the case of phosphonate tripeptides, the adsorption on the metal surface is realized also via the phosphonate moiety which results in a reasonable SERS enhancement of the related vibrational modes [116]. Various studies are dealing with the characterization of bombesin, a 14-amino acid peptide, and its related fragments and analogues [117–121]. As a result of one of the comprehensive studies, the 8–14 bombesin fragment takes almost a parallel orientation with respect to the metal surface while the 1–5 peptide chain is orientated in a way, that it remains out of the range of the evanescent field caused by the metal surface [120]. Moreover, an effect on the orientation and adsorption mechanism is found when substituting amino acids within the chain. The same is true for fragments of human neurotensin and mutated analogues, where the SERS response indicates a slight influence on their adsorption behavior on silver surfaces due to the substitution of native amino acids in the investigated peptides [122]. When characterizing the bombesin subfamily peptides phyllolitorin and a peptide derived from Pseudophryne guntheri the moieties phenylalanine and tryptophan rings, the sulfur atom of methionine and the amide bond are in contact as well as in close vicinity to the metallic surface [123]. Comparative analysis of bombesin and five related peptides, among others a homolog in mammals known as neuromedin B, shows that the interaction between peptides and the metallic surface depends on the geometry of the tryptophan, amide bond, and S-C fragments of these molecules [121]. In a more detailed study, neuromedin B was investigated using different electrode materials and applied electrode potentials [124]. The authors demonstrated that the peptide adsorbs via the molecules backbone (including the phenylalanine and tryptophan rings) onto the silver, gold and copper electrode surfaces. Moreover, it is found, that the amide III mode, a typical Raman marker band of peptides and proteins, exhibit an electrochemical Stark effect which is reflected in potential depended frequencies. Furthermore, the carboxy terminal polypeptide of the β-subunit of human chorionic gonadotropin without carbohydrates moieties (P37) is characterized concerning the P37-metal interaction [125]. Here, the SERS analysis is performed based on the prior investigated oligopeptides with selected amino acid sequences MRKDV, ADEDRDA and LGRGISL [126, 127]. The SERS spectra of the investigated oligopeptides are dominated by the guanidinium moiety of the amino acid arginine which illustrates the orientation of the peptide relative to the metal surface that is driven by guanidinium [127]. In the case of ADEDRDA and LGRGISL, an additional interaction with the metal surface via other amino acids is found [126]. Based on these findings, the authors proposed the P37 metal interaction to be mediated via positively charged fragments of selected amino acids, mainly threonine, lysine and arginine [125]. Finally, evidences were found by means of SERS that the secondary structure of peptides is modified due to the adsorption on metallic surfaces [128]. To summarize, the SERS signature of peptides is not only depending on the orientation of the molecules to the metallic surface as well as on the chemical composition or more specifically the amino acid sequence of the peptide. Also the metal, pH value and electrode potential play a key role for the SERS spectrum. Finally, the paragraph illustrates how SERS spectra of peptides are influenced by various parameters. Thus the findings open a way to detect peptides in low concentrations and investigate interactions of peptides with other molecules.

The characterization of proteins, biological macromolecules consisting of one or more chains of amino acids, is in the focus of the next paragraph. Furthermore, approaches for an application of SERS as analytical tool for the detection of proteins are introduced. Fundamental studies on protein detection are introduced by investigation on the interaction of bovine serum albumin (BSA) with the surface of gold nanoparticles. The presence of the S-S stretching vibration bands of disulfide bridges indicates that the disulfide bonds are unbroken and the protein is not denatured at room temperature due to the attachment on the gold surface [129]. The adsorption of BSA to the metal surface is realized mainly via the tryptophan residue. Thus, BSA is specifically attached to the surface and undergoes only minor conformational changes when interacting with gold nanoparticles. In the case of lysozyme, the main Raman modes within the SERS spectrum are attributed to the amino acids tryptophan, tyrosine, phenylalanine and histidine, indicating the close vicinity of these moieties to the metal surface [130, 131]. In order to prevent spectral fluctuations due to reorientation of proteins during the analysis, an approach to bind proteins reproducible on silver surfaces is developed by fusing a silver-binding peptide to the C-terminus of maltose-binding protein [132]. Moreover, enzymes, which are selective catalysts and mostly proteins, were characterized by means of SERS. As a result of the orientation of coactivator-associated arginine methyltransferase 1 (CARM1) in relation to the nanostructured silver surface, strong Raman modes in the SERS spectrum occur which are attributed to amide vibrations and aromatic ring amino acids [133]. In the case of tyrosinase, the molecule is oriented in a way that the aromatic rings are parallel to the silver surface [134]. Furthermore, the adsorption behavior of the coenzyme Q₁₀ radical intermediate as function of the potential is characterized [135]. For an applied potential lower than -0.30 V vs. SCE, a perpendicular orientation is found. The quinone ring of the reduced form adopts a face-on configuration for more positive electrode potentials than -0.30 V vs. SCE. The impact of the metal surface on the adsorption behavior of the protein bovine pancreatic trypsin inhibitor (BPTI) was investigated by using cetyltrimethylammonium bromide (CTAB)-protected gold nanoparticles in comparison to bare gold substrates [136]. While the disulfide stretching vibration of the protein deposited on the roughened gold substrate shows a significant heterogeneity, the S-S stretching signal remains unchanged for the application of CTAB-protected gold nanoparticle arrays. Thus, the authors concluded that the adsorption of BPTI on the protected nanoparticle array increases the stability of the protein. Cytochrome c, a small heme protein, was immobilized on 2-mercaptoethanesulfonate (MES) monolayers on silver nanostructures based on electrostatic attraction between the protein and the MES layer [137]. The linkage is characterized by SERS studies and finally the change of heme orientation relative to the metal surface deduced from the SERS response allowed the authors to propose protein dynamics. Furthermore, SERS demonstrated its benefit for the investigation of proteins on the basis of the characterization of myeloperoxidase (MPO), its corresponding antibody and their immunocomplex [138]. Within the SERS response variations in peak position and intensity can be assigned to conformational changes due to the immunocomplex formation. Another possible application of SERS is demonstrated by means of the characterization of amyloid beta peptide aggregates, which are related to the formation of neutric plaque, one of the primary pathological hallmarks of Alzheimer’s disease [139]. The spectral analysis of samples prepared by various aggregation procedures shows, that the Amide III band provides information about the secondary structure (α-helix and β-sheet) which allows understanding the properties of the protein aggregates at very low concentrations down to the femtomolar range. Using silver colloids as SERS substrate the cancer-promoting protein S100A4 was characterized [140]. Here, the SERS response of the dimer, tetramer and twelvemer aggregates demonstrates the possible discriminability of these species. Since dimeric forms are found in benign tumors, whereas oligomeric species are related to a late stage of cancer, this SERS study illustrates a possible application field of SERS in the field of biomolecule detection. Finally, the conformational changes of the photoactive yellow protein (PYP) are characterized on the single molecule level illustrating the high potential of SERS as analytical tool in detecting biomolecules [141]. In the ground state of the molecule, PYP has a para-Coumaric Acid (pCA) chromophore and its deprotonated phenolic oxygen is stabilized by means of hydrogen bridges. When absorbing a photon around 450 nm, the photocycle of PYP is initiated and yields a cascade of conformational changes. The detected spectral changes are attributed to temporal single molecule spectra and were related with photoisomerization, protonation of the chromophore and the carbonyl flip in the context of breaking hydrogen bridges.

Investigating protein detection with the SERS technique, the classical model thrombin is frequently chosen. Within this context, the measurement of free thrombin plasma levels represents a promising biomarker reflecting a patient’s individual hemostatic status to guide successful treatment decisions and to avoid bleeding or even thromboembolic complications [142]. Furthermore, thrombin is a useful marker for the diagnosis of pulmonary metastasis [143]. Aptamers, an alternative for antibodies, are artificial single-stranded oligonucleotides (ssRNA or ssDNA) that can bind to target molecules due to their specific three-dimensional structures [144]. Unsurprisingly, diverse aptamer-based immuno-SERS approaches for thrombin detection were published recently [145–151]. As an example, an aptamer-based detection scheme applying crystal violet as reporter molecule is depicted in Figure 4 [149]. The thrombin detection is performed according to the different amount of the reporter molecule crystal violet contributing to the overall SERS signal, based on electrostatic effects due to the changed structure of the thrombin-binding aptamer. A number of articles deal with the imaging of surface proteins by applying on-cell SERS. The purpose of one experimental setting was to elucidate the putative co-localization between the β₂-adrenergic receptor and caveolin-3 on rat cardiomyoctes [152]. To that end, 4-(mercaptomethyl)-benzonitrile and d₇-mercaptomethylbenzen are synthesized as Raman reporters for silver nanoparticle functionalization. Subsequently, 17% of the receptor co-localize with surface-exposed caveolin-3 protein. With the help of antibody-conjugated fluorescent SERS-dots the extracellular and respectively intracellular expression of CD34, Sca-1 and SP-C proteins are verified on bronchioveolar stem cell of the murine lung [153]. An immunolabeling process involving keratan-specific primary antibodies and Au-conjugated secondary antibodies that trigger silver particle localization is used for imaging of keratan sulfate within a corneal epithelium [154]. To understand mannoprotein membrane dynamics in a single living yeast cell, a SERS approach with silver nanoaggregates is employed [155].

Figure 4

Aptamer-based immuno-SERS detection scheme. (A) Using unmodified metallic nanostructured surfaces, a strong SERS signal of the positively charged reporter crystal violet is detected. (B) When binding a monolayer of aptamers, the amount of crystal violet molecules on the metal surface is decreased due to electrostatic effects. This results in a lower SERS signal. (C) In the case of thrombin binding to the aptamer structure, more crystal violet molecules are bound to the surface (B). Thus, the SERS signal increases after the thrombin binding, albeit to a lower level than in case (A). Reprinted with permission from Hu et al. [149]. Copyright 2009 American Chemical Society.

Furthermore, the determination of enzymatic protein activity by means of SERS is addressed in recent studies. The monitoring of enzyme kinetics is an important issue of biochemistry, especially in the context of metabolism. With respect to this, SERS is a novel tool for determining the catalytic activity of an isolated succinate dehydrogenase by a color change of a redox dye. The artificial electron acceptor 2,6-dichlorphenolindophenol becomes SERS active when oxidized [156]. A study claims the applicability of SERS to quantitatively determine the proteolytic activity of a bovine protease on glass-immobilized substrates and rule out a detection limit of 0.43 mU/ml [157]. To detect the cAMP-protein kinase activity and further enzyme inhibition kinetics by diverse inhibitors, a SERS approach using anti-phosphoserine antibodies and gold nanoparticles is presented [158]. Moreover, the feasibility of SERS-based detection of two pterin entities is characterized by analyzing the serum from pterin-spiked rats [159]. A cascade of signal amplification reactions allows the SERS detection of lysozyme with a limit of detection of 10^-15m [160]. These findings and results, which are summarized within the chapter, illustrate the potential of SERS for the detection of biomolecules. Since various detection schemes of biomolecules are often based on the interaction of a capture molecule with the biomolecule of interest, investigations regarding the interaction of various biomolecules are highlighted within the final section of this chapter.

3.3 Characterization of the interaction between biomolecules

The interaction of biomolecules due to the accumulation to affine groups is the basis of various detection schemes in bioanalytics. This section summarizes the recent findings regarding this important topic. Some immuno-SERS approaches, like the interaction of DNA-aptamers with target proteins and antigen-antibody recognition as specialized protein-protein interactions are highlighted in the relevant application chapters. The study of DNA-protein interaction in the background of transcription factor binding is characterized on the example of Wilms tumor 1 (WT1) [161]. Here, dye-labeled double-stranded DNA with a WT1 protein binding site is immobilized on metal nanoparticles and shows a significant SERS response dominated by the label molecule. The sequence-specific binding of the transcription factor to the DNA prevent the access of an exonuclease. Thus, the SERS signal of the dye label is still detectable. If no DNA-binding protein is present, the DNA gets accessible for the DNase, is exonucleolytic digested and the label molecule is released from the surface, which yields a lower SERS intensity. In a proof-of-principle approach, protein-protein and protein-small molecule interactions are detected on glass-surface immobilized human immunoglobulin G or avidin by the help of colloidal silver [162]. The combination of magnetic separation and SERS allows the detection of biotin-avidin interaction on Ag-coated magnetic particles [163]. Cell membranes are composed, amongst other biomolecules, of fatty acid chains that form a lipid bilayer. Since the incorporation of small molecules into cell membranes is of biological importance in terms of the characterization of drug effects, the insertion of ibuprofen into lipid layers is investigated [164]. Within these studies, a hybrid bilayer formed of dodecanethiol and phospholipids is prepared on the surface of gold nanoparticles. The intercalation of ibuprofen in the lipid structure is related to the enhancement of ibuprofen Raman marker modes showing a concentration dependency. On the basis of using silver nanoparticles as SERS substrate, the interaction of hypericin with low-density lipoproteins and phosphatidylcholine is characterized [165]. The authors observe that at high hypericin concentrations these molecules are placed in the outer shell of low-density lipoproteins forming aggregates. These results show the great potential of SERS for the investigation and detection of interactions between biomolecules. Within the next chapter which deals with cutting-edge application fields in bioanalytics of the SERS technique, the capability applying this method as analytical tool is demonstrated.

4.1 Pathogen sensing

The SERS technique is extensively studied since decades for the sensing of bacteria and viruses. This chapter gives an overview of the current SERS literature within this important biomedical field. A major challenge of modern medicine is a rapid and specific identification of bacterial pathogens in human body fluids. Efforts towards so-called point-of-care settings encompass the improvement of SERS with portable Raman microscopes, robust SERS substrates and even a simplification of sample preparation [166]. The current SERS publication activity points into the direction of an early diagnosis of bacteremia as well as urinary tract infections. Bacteremia, the presence of bacteria in the patient’s blood, resulted from severe infections at sites in the body, surgical wounds, or contaminated implanted devices and may lead to a sepsis. Sepsis is a cause of considerable mortality, morbidity, cost and health care utilization [167]. Urinary tract infections are common, with 50% of all women experiencing at least one in their lifetime. The rate of infection leads to high economic costs as well as patient morbidity [168]. The current gold standard for testing in hospitals is based on culturing and normally takes up to three days [169]. Due to our scope, that covers the SERS-based identification of biomolecules, the plethora of great publications that address whole bacteria capturing and detection is excluded from this review.

A whole bunch of articles reports a nucleic acid based identification of pathogens in conjunction with SERS. The advantages in this context are the capability of multiplexing and the improved sensitivity. Some proof-of-principle publications demonstrate the proper identification of various pathogens by using synthetic oligonucleotides. For example, the omp A gene of Clamydia trachomatis, a sexually transmitted bacteria, is used within an elegant exo-SERS assay [170]. Here, a sandwich-hybridization is performed with a magnetic bead immobilized capture probe, the target DNA and terminal phosphate/TAMRA-modified reporter probe. The 5′-phosphorylated reporter probe allow the partial degradation after the sequence-specific hybridization by a lambda-exonuclease [171]. Eventually, the shortened reporter probe is coated with silver nanoparticles and SERS spectra were recorded. Another sandwich hybridization assay highlight the usage of oligonucleotide-gold and oligonucleotide-silver nanoparticles for the probing of Staphylococcus aureus [172]. Two studies claim multiplexed detection of several E. coli strains by using either different dye-labeled reporter probes or even Ag/Au-colloids and multivariate data analysis [173, 174]. The diagnosis of pathogens is also presented in conjunction with the amplification of organism’s genomic DNA and SERS measurements. A multiplexed gold particle-on-wire sensor allowed the identification of Staphylococcus aureus and Vibrio vulnificus, which are causatives for severe human diseases like sepsis or gastroenteritis [175]. The detection limit of this sensor is depicted as 10 pM. The usability of SERS for the multiplexed detection of hospital-acquired methicillin-resistant Staphylococcus aureus is addressed [176]. To that end target genes are amplified by PCR. In case of hybridization with the complementary fluorescence-probe, the formed dsDNA did not adsorb on the surface of silver nanoparticles which result in a SERS signal reduction. Another assay based on SERS-primers and silver nanoparticles for the identification of Staphylococcus epidermis is depicted in Figure 5 [177]. In case of the absence of target DNA the SERS primer is closed, thus the DNA is predominantly double-stranded and has a lower affinity to adsorb to the nanoparticles, resulting in a low SERS response. The improved SERS assay using PCR and enzyme digestion to generate dye-labeled single-stranded DNA to detect pathogens like Staphylococcus aureus is highlighted in a recent article [178]. A specific detection of Staphylococcus aureus DNA through the combination of TaqMan assay with SERS is also realizable [179]. A successful multiplexed SERS detection of Mycoplasma mycoides, the causative agent of contagious bovine pleuropneumonia, is realized via combining magnetic nanoparticles and DNA hybridization [180]. SERS is able to provide a vibrational spectrum of the diverse cell wall molecules of a single bacterium within a few seconds. A fingerprint bacterial identification via their O-antigens, a part of the lipopolysaccharides that are exposed on the outer bacterial wall, is described [181]. In the proof-of-principle paper the reliable differentiation between Salmonella typhimurium and E. coli O16 is enabled by characteristic vibrational modes in the spectral regions 1250–1130 cm^-1, 1030–730 cm^-1 and 650–430 cm^-1 that represented carbohydrates, most probably O-antigens. Using a liquid core photonic crystal fiber a detection limit of 10⁶Shewanella oneides bacteria is achieved [182]. For an immuno-SERS approach metallic nanoparticles were functionalized with ligands like antibodies or aptamers that recognize target biomolecules on the surface of the pathogen [183]. The simultaneous detection of three different bacteria is accomplished by using gold, silver and Ag-Au core shell nanoparticles co-immobilized with anti-Salmonella typhimurium aptamers, anti-Staphylococcus aureus and anti-Escherichia coli O157:H7 antibodies respectively and unique Raman reporter molecules [184]. Gold nanoparticles with a coat of anti-protein A and DTNB as Raman reporter could be used for identification of Staphylococcus aureus via the bacterial surface antigen. A detection limit of 1 pg/ml of protein A is achieved [185]. Gold nanoparticles are coated with DSNB and antibodies, which are generated against a surface antigen of Mycobacterium avium subsp. paratuberculosis [186]. This bacillus is the causative of a cattle disease, which is responsible for devastating losses in the worldwide dairy production. The sandwich immuno-SERS assay allows the quantification of 500 mycobacteria/ml milk.

Figure 5

Illustration of the detection scheme of DNA based on the application of silver nanoparticles (labeled as Ag NP in the figure). (A) When no target DNA is present, the SERS primer is closed, which results in a low SERS signal. (B) In the case of the presence of complementary DNA, the loop structure is opened. Thus, the dye label is free to adsorb on the silver nanoparticle surface producing a high SERS signal. Reprinted with permission from van Lierop et al. [177]. Copyright 2011 American Chemical Society.

Similar to bacterial sensing, the fast diagnosis and therapy of viral infections is of great importance. The West Nile virus (WNV), a pathogen with a RNA genome, is the causative of West Nile fever and encephalitis. WNV is transmitted to its vertebrate hosts by an infected mosquito during blood feeding. The replication of the virus was documented in human monocytes in vitro, which could lead to transmission via blood transfusion [187]. Thus, the screening of donor blood is desirable and SERS techniques were implemented to identify WNV. Various sandwich hybridization assays, that utilize synthetic target DNA sequence instead of the WNV-RNA, are applied on either gold or paramagnetic iron nanoparticles [188, 189]. These approaches enable a limit of detection for WNV target nucleic acid of 10 pM and the authors claim a future adaption to a clinical detection or on-site platform using low-cost, handheld Raman instrumentation. A multiplexed immuno-SERS detection addressing envelope and capsid antigens of WNV is also realized [190]. The identification of new infections with human immunodeficiency virus (HIV) is crucial to prevent transmission as well as slowing disease progression by early medical intervention. Thus, HIV RNA-based tests may allow a very early diagnosis even before a common antibody test may become positive. In clinical laboratories the assessment of HI virus load is done by so-called branched DNA technologies [191]. A SERS-approach use HIV-1 DNA sequence for sandwich hybridization that induced the formation of a molecular junction based biosensor [192]. With regard to this platform, a concentration as low as 10^-19 M HIV-1 DNA is detectable. An interesting experimental setup was invented to detect dengue virus sequences by on-chip SERS [193]. To date, the diagnosis of dengue, the most common mosquito-borne global disease, remains challenging. Infection by the RNA virus could lead to dengue fever or severe dengue illness [194]. Applying a microfluidic SERS assay, synthetic DNA sequences that mimic viral dengue serotypes are used as TAMRA-labeled targets. The complementary capture probes are immobilized on gold nanoparticles and the SERS measurement is performed within the optofluidic SERS-chip. Characteristic peaks are found at 1653 cm^-1, 1360 cm^-1 and 1219 cm^-1 [193]. Of further clinical importance is the fast and reliable detection of influenza viruses. Nowadays an extensive menu of diagnostic tools is available [195]. Within this diagnostic topic a SERS immunosensor experiment is conducted [196]. Gold binding polypetides with hemagglutinin H1 antigen are immobilized on a nanoforest-structured substrate, followed by an immersion with anti-H1 detection antibodies. The relevant SERS peaks are found at 993 cm^-1 and 1525 cm^-1, which correspond to phenylalanine and tryptophan peaks, respectively. Moreover, within a short communication an aptamer-based detection of influenza nucleoproteins is presented on the basis of silver nanorods [197]. A label-free detection of DNA hybridization limited to short oligonucleotides is introduced for the analysis of the respiratory syncytial virus (RSV) [198]. This pathogen is the major causative of lower respiratory tract infections prevalent among infants and elderly [199]. The Epstein-Barr virus (EBV)-associated expression of latent membrane protein 1 (LMP1), a tumor marker for nasopharyngeal carcinoma, is addressed by immuno-SERS [200]. Au/Ag core-shell nanoparticles coated with LMP1-specific antibody and 4-MBA as a Raman reporter are used for the detection of LMP1 in paraffin-embedded nasopharyngeal carcinoma tissues of patients, that were EBV-positive and healthy volunteers. The authors claim that with the LMP1-SERS, 97.1% of the cancer patients are tested positive for the virus-encoded protein, whereas only in 64.7% the protein was detectable when conventional immunohistochemical staining technique was applied.

To summarize, the SERS technique is successfully applied to detect pathogen contamination on the basis of their building blocks such as DNA or proteins. Various detection schemes are introduced to open the way towards point-of-care applications of the SERS technique.

4.2 Cancer diagnosis and prognosis

Nowadays, cancer belongs like every other disease to the risks of life of every person. Everyone has to deal with a cancer diagnosis or treatment either in the personal life, via family members or within the circle of friends. Often the person affected ask “why me” and moreover a late diagnosis has the consequence of a high mortality. Thus, a reliable method for cancer diagnosis and prognosis is of great importance. Within this chapter we address important SERS activities in the field of cancer diagnosis/prognosis in conjunction with the terms non-invasive cancer detection, splice variants and single nucleotide polymorphisms, epigenetics, chemotherapeutics as well as theranostics.

The chances of curing cancer often correlate with the time of diagnosis. The earlier cancer is detected the better is the patient’s chance to be cured by an early treatment. In addition the risk for metastasis is reduced by early detection. Much effort has been made to develop rapid and non-invasive cancer screening tests. The preferable material for such a non-invasive diagnosis is blood plasma or serum and the sample preparation is simple during initial screening as well as following the patient’s treatment. This non-invasive cancer detection in conjunction with SERS includes the analysis of circulating nucleic acids, circulating tumor cells, immunophenotyping of cancer cells as well as the detection of various tumor markers and paves the way towards personalized medicine. Recently, a combination of membrane electrophoresis and SERS is applied for the optical detection of gastric and nasopharyngeal cancer [201, 202]. To that end, blood plasma from cancer patients and healthy volunteers is collected; the albumin and globulin protein fractions are separated by membrane electrophoresis, eluted and mixed with silver nanoparticles. A PCA reveals that the cancer and healthy group form distinct non-overlapping clusters. Again, silver nanoparticles are used as SERS substrate and directly mixed with blood plasma of gastric cancer patients or healthy subjects [203]. A subsequent PCA-LDA multivariate analysis point out that distinctive spectral SERS features and intensity differences between the two groups could reflect cellular changes associated with malignant transformation. The authors found for instance that the SERS peak at 725 cm^-1 corresponding to the C-H in-plane bending mode of adenine exhibits higher signal in the cancer panel, indicating that there is an increase in the relative amount of nucleic acids in blood of cancer patient. This finding is matching reports that so-called circulating nucleic acids are found in higher concentrations when subjects are affected by a neoplastic disease [204]. Further cancer entities, namely nasopharyngeal, colorectal, esophageal and cervical cancer are analyzed using silver or gold colloids and blood plasma samples [205–208]. An increase of distinct SERS signals are observed for patients with pathologically confirmed carcinoma that indicate an abnormal nucleic acid metabolism. The reasons for an increase in the relative amount of cell-free nucleic acids in cancer patients’ blood have been proposed in the literature by cell death-related cell disintegration or release of intact cells in the blood stream followed by their lysis [209]. On the other hand a decrease of signal intensities for SERS-bands, which originate from tyrosine, serine, galactosamine and mannose reflects a higher tumor metabolism [206–208]. An overall decrease of the 1400 cm^-1 peak intensity in the cancer patient’s plasma, reflecting the CH₂ bending mode of collagen might account for elevated concentrations of matrix metalloproteinases that cleave the structure protein in cancer dysplasia [208]. A label-free serum RNA analysis enabled the detection of colorectal cancer by using 3D silver nanofilm as a SERS-active substrate [210]. The authors describe that RNA-SERS combined with PCA-LDA multivariate analysis was applicable for the differentiation of colorectal cancer patients from healthy subjects with a diagnostic sensitivity of 89.1% and a specificity of 95.6%. These results employing the SERS technique put forward the possibility of detecting circulating nucleic acids from blood plasma samples as biomarkers for monitoring cancer occurrence. Malignant cells can disseminate from the solid tumor and float as so called circulating tumor cells (CTCs) in the bloodstream of patients, potentially manifesting a metastasis [211]. The capturing from patient’s blood and the analysis of these rare cancer cells is of great importance for treatment decisions and monitoring. SERS is successfully applied for the detection of CTCs, even in complex matrices like blood [212, 213]. Magnetic beads functionalized with anti-epithelial cell adhesion molecule (EpCAM) antibodies are used for the capturing of SKBR3 cells, which mimic CTCs, spiked in human blood. Subsequent, the captured EpCAM-overexpessing cancer cells are detected with Nanoplex SERS tags [213]. Another experimental setting uses gold nanoparticles coated with antibodies against epidermal growth factor (EGF) to specifically capture CTCs in the blood of patients with head-and-neck cancer [212]. Here, 1–720 CTCs per ml of white blood cells get enriched. The diagnostic immunophenotyping of cancer cells is an important issue concerning the identification and of subpopulations and has a great value in predicting the invasiveness and metastatic potential of a tumor. In general, the amount of surface marker proteins, the cluster of differentiation (CD), is evaluated by flow cytometry. Antibodies against CD24 and CD44 antigens immobilized on gold nanoparticles enable the SERS-subtyping of three breast cancer cell populations [214]. The non-invasive but selective targeting of hematologic malignancies, e.g., chronic lymphocytic leukemia (CLL) using SERS gold nanoparticles is recently reported [215, 216]. To that end, e.g. anti-CD19 antibodies are conjugated covalently to gold nanoparticles. The antibodies recognize the CD19 surface antigen on CLL cells prepared from leukemia patients. The growing amount of publications which deals with cancer biomarker detection in patient’s blood/serum or on target cells by means of SERS reflects the efforts that are made within this field. Well characterized tumor markers are two ErbB family members: epidermal growth factor receptor (EGFR, ErbB-1) and human epidermal growth factor receptor 2 (HER2, ErbB-2). The EGFR is significantly overexpressed in aberrant crypt foci, which represent putative colon cancer precursors [217]. Immuno-SERS techniques using antibody- or affibody-conjugated SERS nanoparticles are applied to monitor the presence of EGFR in vivo [218, 219]. The authors conclude that the approach is capable of targeting EGFR biomarker in human cancer cells as well as in xenograft mouse tumor models. The Olivo group uses photonic crystal fibers filled with lysate of cancer cell lines to immobilize the target protein EGFR [220]. Then anti-EGFR-antibody conjugated SERS nanotags are flown through the hollow fiber and specifically bind to their target protein. An antibody-based SERS platform allows the multiplex detection of EGFR and HER2 on cancer cell lines [221]. Various publications report the identification of HER2-positive breast cancer cell lines by means of immuno-SERS [222–224]. The sequence-specific DNA analysis using sentinel nanoprobes is exemplarily demonstrated for the breast cancer marker HER2 and the proliferation marker Ki-67 [225]. The researchers use two different DNA-aptamer structures conjugated to silver nanoparticles for sensing the presence of synthetic HER2/Ki-67 target DNA. A well-known marker for tumor-associated angiogenesis is the vascular endothelial growth factor (VEGF) [226]. The functionality of a sandwich immunoassay is documented by the combination of the target VEGF immobilization on the gold array via antibodies and the detection by VEGF-aptamer-nanoparticles [227]. VEGF is also detectable by an immunosensor setting in blood plasma from breast cancer patients [228]. Hybrid Ag-Au-aptamer structures labeled with Rhodamine 6G are constructed that are capable of recognizing mucin 1 (MUC1) [229]. The transmembrane protein MUC1 is overexpressed in primary and metastatic breast cancers [230]. In their experimental section the authors demonstrate that MUC1-positive MCF-7 cells show a characteristic SERS signal, whereas MUC1-negative HepG2 or MCF-10A cells did not show any signal of the reporter. The screening for the cancer biomarker mucin 4 (MUC4) in the blood serum of patients can help to early diagnose pancreatic cancer [231]. Within this project, an immuno-SERS principle is performed to monitor the presence of MUC4 in various serum samples. The results indicate that sera from patients with prostate cancer produce significantly higher SERS response for MUC4 compared to sera from healthy subjects. Also, an antibody-based recognition of two important markers in routine cancer diagnosis, namely carcinoembryonic antigen (CEA) and α-fetoprotein (AFP), respectively, is demonstrated recently by means of SERS [232]. Here, a duplex SERS nanoprobe is created by coupling two antibodies against the cancer biomarkers on magnetic beads that allow the simultaneous detection of both markers in blood serum with a single exitation wavelength. A gold patterned microarray is used as a matrix for the immuno-based detection of AFP and angiogenin, the latter one seems to have an important role in tumor angiogenesis [233–235]. The multiplexed detection of the prostate specific antigen (PSA) in paraffin prostate cancer sections is investigated with antibody-conjugated nanoparticles or the antibody-fluorochrome-conjugate [236]. Both detection reagents possess similar performance in the tissue, supporting the development of Raman probes for PSA tumor marker screening in situ. Soluble PSA as a target protein is also detectable by antibody-conjugated hybrid Fe₃O₄/Au nanoparticles, emphasizing the advantages of magnetic particles in the bioassays [237]. Two further serum biomarkers, matrix metalloproteinase 7 (MMP-7) and carbohydrate antigen 19-9 (CA 19-9) are suitable for the diagnosis of early stage pancreatic cancer [238]. To that end, human serum was spiked with the recombinant proteins and the subsequent immuno-SERS allowed the measurement of these biomarkers. A biorecognition between the bacterial redox protein azurin and human p53 is exploited to realize a SERS-based detection of the tumor suppressor at concentrations of 500 fM in human serum [239, 240]. It is well documented in the literature that wild-type as well as mutant p53 protein is found in elevated levels in tumor cells concomitant with altered levels in the blood serum [241–243]. The SERS approaches for ultrasensitive detection of p53 involve a coupling of the protein via the interaction with 4-amithiophenol to gold nanoparticles and the subsequent interaction with immobilized azurin molecules on a glass surface [239, 240]. Azurin exhibit strong association with both, the wild-type as well as the mutated p53 protein and represents due its combination with SERS a promising approach for future tumor marker screenings. Another member of the p53 tumor suppressor family, p65, is addressed by an immuno-SERS approach together with the cyclin-dependent kinase inhibitor p21cip [244]. Here, the two proteins are spiked into human blood serum and are detected in a multiplexed fashion by antibody-functionalized Au-Ag nanorods. Immuno-SERS microscopy is applied for the fast detection of p63 in paraffin-embedded prostate biopsies [245, 246].

Single nucleotide polymorphisms (SNPs) are single base pair differences in the DNA among individuals that account for more than 90% of all sequence variations [247, 248]. Roughly one of every 100–300 bases in the human genome is a SNP [248, 249]. Numerous SNPs are detected as reliable diagnostic biomarkers for selection of appropriate drug therapies in the upcoming field of personalized medicine. For instance, a single nucleotide substitution in different codon positions of the proto-oncogenic Kirsten rat sarcoma (KRAS) is responsible for an activating mutation. Thus patients with this type of mutations will not respond to certain therapies [250]. An expansion of the SNP screening method repertoire is facilitated by SERS. A midsequence SNP discrimination by using synthetic oligonucleotides and gold nanoparticles is realized as dye-label-free SERS [251]. Another interesting approach utilizing sequence-specific hybridization and the ligase detection reaction (LDR) is introduced for discriminating KRAS SNPs [252, 253]. When the SNP sequence matches the discriminating primer, two adjacent oligonucleotide sequences get ligated and a SERS active product result. With the help of this LDR-SERS method a multiplexed SNP genotyping of the KRAS oncogene is possible down to a limit of detection of 10 pM [252]. A further SNP-related study depicts the application of gold nanowire/nanofilm-hybrids and a S1 nuclease digestion for assaying Wilson disease [254]. The SNP at codon 504 of the breast cancer 1 (BRCA1) gene is chosen to be detected by SERS [255]. The authors demonstrate the usability of a SERS molecular sentinel that comprises a silver nanoparticle plus the associated DNA hairpin structure that gets opened when the target DNA hybridizes to it. Thus the Raman label is physically separated from the particle and quenches the SERS signal.

In addition to SNP analysis, the detection of BRCA1 splice variants is of great importance. Changes in the alternative mRNA splicing profile of the BRCA1 gene is associated with malignant transformation in breast cancer [256]. The identification of cell and tissue specific splicing patterns helps to unravel the role of such genes in tumor development. In two proof-of-concept papers a SERS approach for a multiplexed detection of BRCA1 splice variants through nanoparticle-DNA-Raman-tag setup is presented with synthetic DNA [257, 258]. An advanced gene expression assay by SERS, involving the isolation of RNA from breast cancer cell lines followed by an translation into complementary DNA, sensitively quantify the expression levels of splice junction, skipping exon 9 and 10, of the BRCA1 gene [259, 260]. Moreover, SERS experiments are conducted that allowed the screening for wild-type and mutated BRCA1 peptides involving gold nanocuboids [261].

The SERS technique is also introduced by numerous groups to detect epigenetic modifications in the context of cancer diagnosis and prognosis. Epigenetic variations within the human genome are realized by means of non-coding RNAs or covalent DNA modifications. Micro RNAs (miRNAs) are small non-coding RNA molecules that regulate eukaryotic gene expression by mRNA degradation or inhibition of translation [262, 263]. It has been suggested that up to 30% of the human genome may be regulated by miRNAs [264]. Of further importance is the fact, that miRNA expression profiling can serve as diagnostic/prognostic biomarker of human cancers. Recent studies highlight the frequent downregulation of miR-15/16 in chronic lymphocytic leukemia [265, 266]. In addition, a reduced expression of multiple let-7 miRNA members has been found to be associated with human cancers [267]. Emerging techniques for the detection of miRNA alterations are bead-based flow cytometry and RNA-primed array-based Klenow extention (RAKE) that significantly reduced assay time [268, 269]. Nevertheless, the requirement of a hybridization step remained. To further accelerate analysis time, SERS is introduced as a label-free method for the detection and classification of miRNA. The applicability of SERS for miRNA analysis is demonstrated using silver nanorods and synthetic human miRNAs, like the pathogenic relevant miR-16 or let-7f [270–273]. The findings indicate that miRNA sequences could be accurately discriminated and quantified even in multicomponent mixtures. The fact, that let-7 miRNA family members produced SERS spectra very similar to one other in number and location of peaks is remarkable. But the spectra differed significantly in the relative intensities of some bands [270]. The SERS-based approaches enable rapid as well as quantitative miRNA detection using minimal sample volumes concomitant with an elimination of probe labeling and hybridization steps. Thus, the SERS technique is successfully adopted for the growing field of miRNA expression profiling. In eukaryotic cells methylated cytosine (mC) in so called CpG islands is the most common epigenetic mark [274]. More recently, hydroxymethylcytosine (hmC) was discovered as a novel DNA methylation tag [275, 276]. Methylated DNA represents an important epigenetic modification that provides information for altering the gene expression. Moreover, aberrant DNA methylation has been found to strongly correlate with human cancer. In that context the relationship of hypermethylation of CpG islands in the promotor regions of tumor-suppressor genes like p16^INK4A and the promotion of tumor progression is reported [277, 278]. New scientific findings point in the direction of using methylation profiles as diagnostic or predictive biomarkers [278–280]. So far, a whole bunch of techniques have been developed for DNA methylation screening [281]. Recently, an article claims the single base extension reaction-based SERS for the detection of methylated p16^INK4A-DNA [282]. Additionally, a SERS-based analysis enables the differentiation of the post-replicative DNA modifications mC and hmC [283]. The spectral variations between normal and hydroxymethylated DNA are significant, so an increase in the 665 cm^-1 peak is an obvious marker of the presence of hmC. The acquired data point into the direction that SERS is a reliable method for discrimination between mC and hmC.

Besides the usefullness of the SERS technique for cancer diagnosis and prognosis, it can also be successfully exerted for monitoring the effect of anticancer drugs on target cells. With the help of a gold nanoflower-array the immobilization of living HepG2 liver cells is realized and this cell-based chip is used for studying the various effects of anticancer drugs on the cell behavior [284]. The chosen drugs are 5-fluorouracil and hydroxyurea which both interfere with DNA synthesis and cyclophosphamide, a DNA damaging agent. The recorded Raman spectra reflect a significant change in the cellular composition of nucleic acids and even proteins after the chemotherapeutical treatment. The measurement of drug concentrations in patient saliva instead of blood is a further non-invasive option to monitor drug metabolism and regulate drug dosage administration. In a proof-of-principle experiment disposable SERS-active capillaries filled with silver layers are tested for evaluation of 5-fluorouracil and its metabolite concentrations in saliva [285]. Furthermore, a DNA approach is performed to illuminate the interaction with the chemotherapy agent cisplatin [286]. After incubation of dsDNA with cisplatin the resulting intrastrand and interstrand adducts evoke spectral changes. These characteristic time-dependent spectra variations are caused by conformational distortions due to the ligand binding. The intracellular release of the chemotherapeutic agent 6-mercaptopurine, which is coupled to gold nanoparticles, can be triggered by glutathione. The release monitoring is performed by using SERS [287].

Within the emerging field of personalized medicine the development of so called theranostics is of great interest. Theranostics is referred to as a treatment combining therapeutics and diagnostics [288]. The aim is to integrate diagnostic approach and therapeutic intervention, allowing a simultaneous diagnosis, treatment as well as efficacy monitoring [289]. The earlier mentioned report about the binding of SERS-active nanostructures to MUC1-expressing cancer cell lines has also outlined the capability of absorbing near-infrared irradiation. They are therefore eligible for the photothermal therapy to selectively induce cell death of the targeted cancer cells without destroying surrounding tissues [230]. Further reports on photodynamic tumor therapy implementing SERS are presented in the literature [290, 291]. In general the photodynamic therapy (PDT) involves the selective uptake and accumulation of a photosensitizing agent in the target cells and the subsequent irradiation with light. The induced generation of reactive oxygen species (ROS) causes damaging of intracellular biomolecules, leading to cell death by apoptotic processes [292]. The intracellular accumulation of the photosensitizer-coated nanoparticles in cancer cells is realizable by either the use of cell-penetrating peptides [291] or enhanced permeability and retention (EPR) [290]. The latter EPR effect accounts for the uptake of gold nanorods by tumor cells and a large area of dead cells could be clearly seen in PDT-treated tumors. A non-invasive in situ release monitoring possibility is introduced very recently by the help of SERS [293]. The authors demonstrate the controlled release of the cargo doxorubicin from gold nanocages by applying heating, pointing into the direction of controlled drug delivery. The development of plasmonic vesicles assembled from SERS-active gold nanoparticles for targeted drug delivery, which can be tracked by Raman spectroscopy is reported [294]. The gold particles contain the Raman reporter BGLA, mixed brushes of hydrophilic poly ethylene glycol (PEG) and pH-sensitive hydrophobic copolymers of methyl methacrylate and 4-vinylpyridine (PMMAVP) to allow drug release, HER2 antibodies for cancer cell targeting and encapsulated doxorubicin as an anticancer drug. To verify the targeting properties concomitant with pH-triggered payload release, studies with HER2-overexpressing breast cancer cells were performed. The vesicle-coated cancer cells display a strong fingerprint Raman signal of the BGLA probe that gradually decrease with time caused by acidic driven disruption of the vesicles and a drug release. The entire strategy of this approach is depicted in Figure 6.

Figure 6

Theranostics strategy based on plasmonic vesicles built of gold nanoparticles. (A) Scheme of the applied gold nanoparticles coated with mixed polymer brushes and a Raman reporter as well as the drug-loaded plasmonic vesicle coated with antibodies for cancer cell targeting. (B) Illustration of the plasmonic vesicle’s attachment to the outer cell membrane, their uptake and finally the disruption of the SERS-active, pH-sensitive vesicle structure. Reprinted with permission from Song et al. [294]. Copyright 2012 American Chemical Society.

This chapter summarizes innovative strategies based on the SERS application in cancer diagnostics and prognosis. It is shown, that the SERS technique is used by various detection schemes based on silver and gold nanoparticles to contribute to the research field of non-invasive cancer detection, which includes the detection of circulating nucleic acids and tumor markers. Moreover, the sequence specific DNA detection to investigate splice variants and single nucleotide polymorphisms as well as the contribution to the research on epigenetics is highlighted by using SERS as analytical tool. The detection of chemotherapeutics is of great importance in terms of personalized medicine and drug treatment. Finally, the findings within the research field theranostics illustrate the great capability of SERS to detect and to release drugs within cancer cells.

4.3 Further SERS-based application strategies in biomedicine and biomolecule detection

As described in the previous paragraphs, SERS is an alternative method to detect pathogens and cancer alterations. In addition, SERS can be applied in other important biomedical fields. Thus, the following overview summarizes SERS applications concerning disease-related mutation detection, cell death and differentiation verification, forensics, drug and neurotransmitter screening, metabolism monitoring, prion protein detection in neurons, oxygen-binding protein sensing as well as targeting of immunoglobulins in blood. By employing SERS, the discrimination between single nucleotide and triplet deletion mutations as well as wild type of cystic fibrosis transmembrane regulator (CFTR) gene is accomplished [295, 296]. CFTR mutations cause cystic fibrosis, which is one of the most common life-threatening inherited diseases in Caucasians [297]. The use of an electroactive label for so-called SERS-E-melting experiments that enable the CTFR gene discrimination at the attomole level is reported [295]. A further SERS-E-melting approach is introduced for the discrimination of short tandem repeats [298]. These polymorphic short sequences are commonly used to determine genetic profiles for forensic individual identifications. Programmed cell death, alias apoptosis, is a highly important cellular process in vivo and the selective induction of apoptosis in cancer tissue is an established chemotherapeutic strategy. A label-free detection of apoptosis at the single-cell level is realized by silver nanoparticles [299]. After apoptosis induction by detergents only a weak SERS signal of DNA is observed due to specific cleavage of DNA strands as a late apoptotic event. The verification of cell differentiation is also accomplished by SERS [300, 301]. The in vitro differentiation of neuronal progenitor cells into terminal differentiated neurons is realized by staurosporine. To record SERS spectra corresponding to nucleic acids, the accumulation of gold nanoparticles within the nucleus of the different cell types is done by using the nuclear localization signal of the SV40-large T antigen [301]. The tracking of differentiation of mouse embryonic stem cells by intracellular nanoparticles show the following results: SERS peaks derived from undifferentiated cells are mostly attributed to nucleic acids (high proliferation rate) whereas the SERS peak at 1604 cm^-1 originated from mitochondria of the terminally differentiated cardiomyocytes (high metabolic activity) [300]. As mentioned earlier, aptamers are a versatile tool for bioanalytical purposes. In conjunction with SERS the conformational changes in the aptamers induced by target molecule interaction are monitored on a label-free level. To that end the drug cocaine is chosen as a model substance [302, 303]. An antibody-based immuno-SERS approach use silver-coated carbon nanotubes for the detection of the major cocaine metabolite benzoylecgonine [304]. Serotonin, a ubiquitous neurotransmitter is quantified in a background of other indoles using SERS [305]. Lastly, SERS assisted ultra-fast peptide screening is described as a novel promising tool for drug discovery [306]. The authors claim the usability of microbeads with Au-Ag nanoparticle coat as a solid support for the synthesis of combinatorial peptide libraries. The subsequent SERS analysis enables the identification of several tripeptide combinations as a consequence of the unique vibrational signature of each amino acid. A transcutaneous in vivo glucose measurement in a rat model is realized by SERS [307]. This work represents a significant step towards an implantable, real time glucose SERS-sensor. Another example of metabolism monitoring is the detection of lactic acid at physiological concentrations in blood samples [308]. The study of prion proteins is performed by several SERS approaches [309–312]. The focus lay on the native cellular prion protein (PrP^c), which is mainly expressed on the cell surface of neurons. The physiological function of PrP^c remains elusive, although it has been related to copper metabolism [313]. SERS allow the tracking of PrP^c-Cu²⁺ interaction on the cell membrane of different neuronal cells [309, 312]. The detection of PrP^c either in bovine serum or in blood samples with silver nanorods is displayed [310, 311]. A proof-of-concept paper focuses on the combination of isotachophoretic flow electrophoresis on a chip-device and SERS for the detection of myoglobin, an abundant oxygen-binding protein in muscle cells [314]. To gain relevant information about putative drug effects on different hemoglobin subpopulations in intact erythrocytes, SERS based on silver colloids is performed [315]. The group shows that submembrane and cytosolic hemoglobin molecules display significant conformation differences. Beyond that, an immuno-SERS approach is applied to detect immunoglobulin E (IgE) in blood serum of rabbits [316]. Gold nanoparticles are coated with protein A/G and malachite green as a Raman tag. The formed immuncomplex allow the monitoring of rabbit serum IgEs by SERS and represents an alternative to classical ELISA formats. Mouse or human IgG is chosen as a model protein to demonstrate the feasibility of SERS as a novel spectroscopic technique in clinical diagnostics [317, 318].

Finally, novel strategies regarding SERS for toxin monitoring in water and food, identification of genetically modified organisms, extraterrestrial life sensing and even art evaluation are presented. As an example, ricin, a potential bioterrorism agent, is successfully quantified by either an aptamer-based SERS approach or a pre-immunomagnetic separation, respectively [319, 320]. At least 100 ng/ml ricin B is detectable in complex matrices like milk. This highlighted the promising potential of the SERS technique for bioweapon screening and the feasibility of using portable Raman instruments for on-site detection [319]. The assembly of gold nanorods is used for the principle detection of microcystin, an algae toxin pollution in drinking water reservoirs [321]. The presence of the toxin interfered with the antibody-antigen triggered assembly of nanorod chains, thus significantly reducing the SERS signal for 4-ATP. In a study, the screening for genetically modified organisms is performed by combining magnetic pre-concentration of the target DNA, which was the 35S gene promoter, with further SERS measurements. A real sample analysis with Bt-176 maize DNA demonstrates the feasibility of the assay concept [322]. Surprisingly, SERS was utilized for analyzing nucleobases that mimic microbial life on pyroxene rocks [323]. The authors depict that the experimental procedure could be easily adapted for in situ recognition of life traces in extraterrestrial environments, mainly detecting the marker band of adenine at 735 cm^-1. Moreover, SERS is introduced in artworks. Here, the precise identification and localization of proteins, such as ovalbumin, collagen or casein is demonstrated by indirect immuno-SERS in multilayered paintings [324].

In addition to the application fields of SERS pathogen sensing and cancer diagnostics, this section shows the potential of SERS in further research areas. The innovative, here described approaches might be the starting point for the establishment of new application schemes employing the SERS technique.