Highly sensitive detection of dye-labelled DNA using nanostructured gold surfaces

SERS in 3D cell models: a powerful tool in cancer research

Unraveling the cellular and molecular mechanisms underlying tumoral processes is fundamental for the diagnosis and treatment of cancer. In this regard, three-dimensional (3D) cancer cell models more realistically mimic tumors compared to conventional 2D cell cultures and are more attractive for performing such studies. Nonetheless, the analysis of such architectures is challenging because most available techniques are destructive, resulting in the loss of biochemical information. On the contrary, surface-enhanced Raman spectroscopy (SERS) is a non-invasive analytical tool that can record the structural fingerprint of molecules present in complex biological environments. The implementation of SERS in 3D cancer models can be leveraged to track therapeutics, the production of cancer-related metabolites, different signaling and communication pathways, and to image the different cellular components and structural features. In this review, we highlight recent progress in the use of SERS for the evaluation of cancer diagnosis and therapy in 3D tumoral models. We outline strategies for the delivery and design of SERS tags and shed light on the possibilities this technique offers for studying different cellular processes, through either biosensing or bioimaging modalities. Finally, we address current challenges and future directions, such as overcoming the limitations of SERS and the need for the development of user-friendly and robust data analysis methods. Continued development of SERS 3D bioimaging and biosensing systems, techniques, and analytical strategies, can provide significant contributions for early disease detection, novel cancer therapies, and the realization of patient-tailored medicine.

Electrochemical and in vitro neuronal recording characteristics of multi-electrode arrays surface-modified with electro-co-deposited gold-platinum nanoparticles

In order to complement the high impedance electrical property of gold nanoparticles (Au NPs) we have performed electro-co-deposition of gold-platinum nanoparticles (Au-Pt NPs) onto the Au multi-electrode array (MEA) and modified the Au-Pt NPs surface with cell adhesive poly-D-lysine via thiol chemistry based covalent binding. The Au-Pt NPs were analyzed to have bimetallic nature not the mixture of Au NPs and Pt NPs by X-ray diffraction analysis and to have impedance value (4.0 × 10(4) Ω (at 1 kHz)) comparable to that of Pt NPs. The performance of Au-Pt NP-modified MEAs was also checked in relation to neuronal signal recording. The noise level in Au-Pt NP-modified MEAs was lower than in that of Au NP-modified MEA.

Single-molecule force spectroscopic study on chiral recognition of cysteine derivatives immobilized on a gold substrate by using AFM tips chemically modified with optically active crown ethers

The chiral recognition of cysteine derivatives on a gold substrate was investigated using AFM tips modified with optically active crown ethers.

Photocaging strategy for functionalisation of oligonucleotides and its applications for oligonucleotide labelling and cyclisation

We have used a photocaging strategy to develop novel phosphoramidites and expand the repertoire of protecting groups for modification of oligonucleotides by solid-phase synthesis. We synthesised five photolabile phosphoramidites and four new photolabile controlled pore glasses (CPGs). By using these photolabile phosphoramidites and CPGs, modified oligodeoxynucleotides (ODNs) with phosphate, amine, acid, thiol and carbonyl moieties at 5' and/or 3' ends were readily synthesised. To the best of our knowledge, this is the first report of introducing a carbonyl at the 5' end and thiol groups at both ends of ODNs with photolabile modifiers. Terminal labelling was also easily realised in solution or by on-column solid-phase synthesis. By using the photolabile amine modifier and the photolabile acid CPG, cyclisation of an oligodeoxynucleotide was achieved with good yields. This study provides an alternative way to introduce functional groups into oligonucleotides and expand the scope of oligonucleotide bio-orthogonal labelling.

Combined SPR and SERS microscopy in the Kretschmann configuration

A novel hybrid spectroscopic technique is proposed, combining surface plasmon resonance (SPR) with surface-enhanced Raman scattering (SERS) microscopy. A standard Raman microscope is modified to accommodate the excitation of surface plasmon-polaritons (SPPs) on flat metallic surfaces in the Kretschmann configuration, while retaining the capabilities of Raman microscopy. The excitation of SPPs is performed as in standard SPR-microscopy; namely, a beam with TM-polarization traverses off-axis a high numerical aperture oil immersion objective, illuminating at an angle the metallic film from the (glass) substrate side. The same objective is used to collect the full Kretschmann cone containing the SERS emission on the substrate side. The angular dispersion of the plasmon resonance is measured in reflectivity for different coupling conditions and, simultaneously, SERS spectra are recorded from Nile Blue (NB) molecules adsorbed onto the surface. A trade-off is identified between the conditions of optimum coupling to SPPs and the spot size (which is related to the spatial resolution). This technique opens new horizons for SERS microscopy with uniform enhancement on flat surfaces.

Recent progress in SERS biosensing

This perspective gives an overview of recent developments in surface-enhanced Raman scattering (SERS) for biosensing. We focus this review on SERS papers published in the last 10 years and to specific applications of detecting biological analytes. Both intrinsic and extrinsic SERS biosensing schemes have been employed to detect and identify small molecules, nucleic acids, lipids, peptides, and proteins, as well as for in vivo and cellular sensing. Current SERS substrate technologies along with a series of advancements in surface chemistry, sample preparation, intrinsic/extrinsic signal transduction schemes, and tip-enhanced Raman spectroscopy are discussed. The progress covered herein shows great promise for widespread adoption of SERS biosensing.

Nanoscale in situ morphological study of proteins immobilized on gold thin films

The nanoscale organization of acetylcholinesterase (AChE) and of its polyclonal antibody immobilized on gold thin films was studied by means of Energy Dispersive X-ray Reflectometry (EDXR) and Atomic Force Microscopy (AFM). The macromolecules were alternatively deposited over a self-assembled monolayer (SAM) of N-hydroxysuccinimide esters of thioctic acid. The measurements, collected in situ at subsequent deposition stages of the device, gave information on the distribution of the macromolecules on the surface showing that both the proteins can bind covalently to the SAM. In addition to this, we demonstrated that the antigen-antibody reaction takes place when one of the two reactants is anchored to the surface.

PCR-free quantification of multiple splice variants in a cancer gene by surface-enhanced Raman spectroscopy

We demonstrate a surface-enhanced Raman spectroscopy (SERS) based array platform to monitor gene expression in cancer cells in a multiplex and quantitative format without amplification steps. A strategy comprising DNA/RNA hybridization, S1 nuclease digestion, and alkaline hydrolysis was adopted to obtain DNA targets specific to two splice junction variants, Delta(9,10) and Delta(5), of the breast cancer susceptibility gene 1 from MCF-7 and MDA-MB-231 breast cancer cell lines. These two targets were identified simultaneously, and their absolute quantities were estimated by a SERS strategy utilizing the inherent plasmon-phonon Raman mode of gold nanoparticle probes as a self-referencing standard to correct for the variability in surface enhancement. The results were then validated by reverse-transcription polymerase chain reaction. Our proposed methodology could be expanded to a higher level of multiplexing for quantitative gene expression analysis of any gene without any amplification steps.

Quantitative surface-enhanced Raman for gene expression estimation

We demonstrate for the first time, to our knowledge, a unique gene expression assay by surface-enhanced Raman scattering (SERS) using nonfluorescent Raman labels to quantify gene expression at the resolution of alternative splicing using RNA extracted from cancer cells without any amplification steps. Our approach capitalizes on the inherent plasmon-phonon mode of SERS substrates as a self-referencing standard for the detection and quantification of genetic materials. A strategy integrating S1 nuclease digestion with SERS detection was developed to quantify the expression levels of splice junction Delta(9,10), a segment of the breast cancer susceptibility gene 1 (BRCA1) from MCF-7 and MDA-MB-231 cells. Quantification results were cross-validated using two Raman tags and qualitatively confirmed by RT-PCR. Our methodology based on SERS technology provides reliable gene expression data with high sensitivity, bypassing the intricacies involved in fabricating a consistent SERS substrate.

Advances in Nucleic Acid Detection and Quantification

The last decade has seen many changes in molecular biology at the bench, as we have moved away from a primary goal of cataloguing genes and mRNA towards techniques that detect and quantify nucleic acid molecules even within single cells. With the invention of the polymerase chain reaction (PCR), a nucleic acid sequence could now be amplified to generate a large number of identical copies, and this launched a new era in genetic research. PCR has developed in parallel to fluorescent hybridization probing to provide low-, medium- and high-throughput detection methods. However, PCR and hybridization detection have significant drawbacks as long-term solutions for routine research and diagnostics assays. Therefore many novel methods are being developed independently, but as yet no one technique has emerged as a clear replacement for PCR, microarrays or even sequencing. In order to examine the technological horizon in this area, around 90 delegates assembled at Hinxton Hall, Cambridge, U.K. on 28 and 29 October 2008 for a Biochemical Society/Wellcome Trust Focused Meeting sponsored by Thermo Fisher Scientific and the British Library. The title of the meeting was ‘Advances in Nucleic Acid Detection and Quantification’, and the primary aim was to bring together scientists from different disciplines who nevertheless are trying to develop reliable methods for the quantification or detection of RNA and DNA molecules. This meant that physical and organic chemists, microbial ecologists and clinicians appeared alongside molecular biologists. An introductory session on general nucleic acid detection technologies was initiated with a fascinating insight into single-molecule, singlecell hybridization from Professor Sir Edwin Southern. This served as an ideal base for sessions on single-cell molecular biology and an examination of current applications of emerging technology. This issue of Biochemical Society Transactions contains some of the papers prepared by speakers at the meeting, and highlights not only how PCR and microarrays are already being replaced, but also which methods are likely to replace them.

Functionalized nanoparticles for nucleic acid sequence analysis using optical spectroscopies

SERRS (surface-enhanced resonance Raman scattering) is a vibrational spectroscopy which allows extremely sensitive and selective detection of labelled DNA sequences with detection limits which rival, and in most cases surpass, that of fluorescence. SERRS relies on a visible chromophore adsorbing on to an enhancing surface. DNA itself is not SERRS-active, as it lacks a suitable visible chromophore and has poor adsorption properties on to the surfaces used for enhancement. The surface normally used for enhancement in these sorts of studies are metallic nanoparticles and, through modification of DNA probes by the addition of suitable SERRS labels, signals can be obtained that are highly sensitive and very selective. The aggregation state of the nanoparticles is critical to the sensitivity, and, in the present paper, we show how straightforward detection of labelled DNA probes can be achieved using SERRS in a quantitative manner and with a variety of different commercially available labels. In a second approach, we show how the properties of aggregation to turn on the SERRS effect can be exploited through DNA hybridization to give identification of a particular DNA sequence. This approach lends itself to closed-tube formats and is a promising way forward for molecular diagnostics using SERRS.