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

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

SERRS dyes. Part I. Synthesis of benzotriazole monoazo dyes as model analytes for surface enhanced resonance Raman scattering

The synthesis of seven monoazo benzotriazole dyes for use in surface enhanced resonance Raman scattering, SERRS, is reported. The dyes are all capable of complexing to the silver surface used to provide the surface enhancement found in SERRS and hence act as 'model' analytes. One dye was examined in detail and showed a quantitative relationship between concentration and signal intensity.     

A new approach to oligonucleotide labelling using Diels-Alder cycloadditions and detection by SERRS

Diels-Alder cycloaddition has been used to add a benzotriazole azo dye to a diene tagged oligonucleotide to generate unique SERRS signals at 10 attomoles.     

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

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

DNA detection by surface enhanced resonance Raman scattering (SERRS)

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

Mechanically facilitated retro [4+2] cycloadditions

Poly(methyl acrylate)s (PMAs) of varying molecular weights were grown from a [4+2] cycloaddition adduct of maleimide with furan containing two polymerization initiators. Subjecting the corresponding PMA (>30 kDa) chains to ultrasound at 0 °C resulted in a retro [4+2] cycloaddition reaction, as observed by gel permeation chromatography (GPC) and UV-vis spectroscopy, as well as labeling of the liberated maleimide and furan moieties with appropriate chromophores featuring complementary functional groups. Similar results were obtained by sonicating analogous polymers that were grown from a thermally robust [4+2] cycloaddition adduct of maleimide with anthracene. The generation of anthracenyl species from these latter adducts allowed for the rate of the corresponding mechanically activated retro [4+2] cycloaddition reaction to be measured. No reduction in the number average molecular weight (M(n)) or liberation of the maleimide, furan, or anthracene moieties was observed (i) for polymers containing the cycloaddition adducts with M(n) < 20 kDa, (ii) for high molecular weight PMAs (M(n) > 60 kDa) featuring terminal cycloaddition adducts, or (iii) when the cycloaddition adducts were not covalently linked to a high molecular weight PMA. Collectively, these results support the notion that the aforementioned retro [4+2] cycloaddition processes were derived from a vectorially opposed mechanical force applied to adducts embedded within the polymer chains.     

Oligonucleotide conjugation to a cell-penetrating (TAT) peptide by Diels-Alder cycloaddition

Modifed oligonucleotides are routinely employed as analytical probes for use in diagnostics, e.g. in the examination of specific RNA sequences for infectious diseases, however, a major limiting factor in oligonucleotide-based diagnostics is poor cellular uptake of naked oligonucleotides. This problem can be overcome by covalent attachment of a so-called 'cell-penetrating peptide' to form an oligonucleotide peptide conjugate. Stepwise solid phase synthesis of such a conjugate is difficult and expensive due to the conflicting chemistries of oligonucleotides and peptides. A simple approach to overcome this is post-synthetic conjugation. Diels-Alder cycloaddition is an attractive methodology for oligonucleotide peptide conjugation; the reaction is fast, chemoselective and the reaction rate is greatly enhanced in aqueous media - ideal conditions for biological moieties. An oligodeoxyribonucleotide sequence has been derivatised with a series of dienes at the 5'-terminus, using a series of unique dienyl-modified phosphoramidites, and investigation into the effect of diene type on the efficiency of conjugation, using Diels-Alder cycloaddition with a maleimido-derivatised cell-penetrating (TAT) peptide, has been performed. This led to the observation that the optimal diene for conjugation was cyclohexadiene, allowing conjugation of oligodeoxyribonucleotides to a cell-penetrating peptide by Diels-Alder cycloaddition for the first time.     

Interfacing capillary electrophoresis and surface-enhanced resonance Raman spectroscopy for the determination of dye compounds

The at-line coupling of capillary electrophoresis (CE) and surface-enhanced resonance Raman spectroscopy (SERRS) was optimized for the separation and subsequent spectroscopic identification of charged analytes (dye compounds). Raman spectra were recorded following deposition of the electropherogram onto a moving substrate. To this end a new interface was developed using a stainless steel needle as a (grounded) cathode. The outlet end of the CE capillary was inserted into this metal needle; CE buffer touching the needle tip served as the electrical connection for the CE separation. A translation table was used to move the TLC plate at a constant speed during the deposition. The distance between the tip of the fused silica column and the TLC plate was kept as small as possible in order to establish a constant bridge-flow, while avoiding direct contact. The dyes Basic Red 9 (BR9), Acid Orange 7 (AO7) and Food Yellow 3 (FY3) were used as test compounds. After CE separation in a 20 mM borate buffer at pH 10, after deposition, concentrated silver colloid was added to each analyte spot, followed by irradiation with 514.5 nm light from an argon ion laser to record the SERRS signal using a Raman microscope. Different types of silver colloids were tested: Lee–Meisel type (citrate), borate, and gold-coated silver. BR9 (positively charged) gave much more intense SERRS spectra than the two negatively charged dyes. For BR9 and AO7 the citrate-coated Lee–Meisel colloid yielded the most intense SERRS spectra. The CE–SERRS system was used to separate and detect the negatively charged dyes. Silver colloid and nitric acid (to improve adsorption) were added post-deposition. Even though their chemical structures are very similar, AO7 and FY3 could be readily distinguished based on their SERRS spectra. The limits of detection (S/N=3) of the CE–SERRS system ranged from 6.7×10^–5 M (2.6×10^–12 mol injected) for FY3 down to 1.8×10^–6 M (7.0×10^–14 mol injected) for BR9.D. Arráez Román and E. Efremov contributed equally to this work.     

Electrochemical pathway for the quantification of SERS enhancement factor

This communication presents a new pathway for the more precise quantification of surface-enhanced Raman scattering (SERS) enhancement factor via deducing resonance Raman scattering (RRS) effect from surface-enhanced resonance Raman scattering (SERRS). To achieve this, a self-assembled monolayer of 1,8,15,22-tetraaminophthalocyanatocobalt(II) (4α-Co^IITAPc) is formed on plasmon inactive glassy carbon (GC) and plasmon active GC/AuNP surface. The surfaces are subsequently used as common probes for electrochemical and Raman (RRS and SERRS) studies. The most crucial parameters required for the quantification of SERS substrate enhancement factor (SSEF) such as real surface area of GC/AuNPs substarte and the number of 4α-Co^IITAPc molecules contributing to RRS (on GC) and SERRS (on GC/AuNPs) are precisely estimated by cyclic voltammetry experiments. The present approach of SSEF quantification can be applied to varieties of surfaces by choosing an appropriate laser line and probe molecule for each surface.     

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

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

Squaraines as unique reporters for SERRS multiplexing

Modified anilino squaraine dyes provide unique SERRS spectra that can be identified at low concentrations within any mixture of current reporters using longer, biologically compatible wavelengths of excitation.     

The observation of high order overtones and combinations in the SERRS spectra of a perylene dye spin coated onto silver island films

The intensity of high harmonics and the background observed in the SERRS spectra of the bis(4-chlorbenzylimido)perylene (CLPTCD), spin-coated onto silver nanostructures are discussed. The SERRS spectra of an Ag island film spin coated with 50 muL of a 8.7 x 10(-7) M of CLPTCD in CH(2)Cl(2) excited at 514.5 nm show signals from the first to the third overtones and combinations of fundamental vibrational modes observed between 1200 and 1600 cm(-1). SERRS spectra were obtained where 2nd overtones were seen with relative intensity equal to that of the 1st overtones and in other SERRS spectra the 3rd overtones were more intense than the 2nd overtones. These varying intensity patterns are seen at submonolayer coverage where there is a breakdown of statistical average, and the spatial distribution of enhancement factors becomes evident. The apparent correlation between the background intensity profile and the enhancement of the overtones and combinations is also discussed.     

Study of Regiochemical Trends During the Synthesis of Furan and 5‐(p‐chlorophenyl)Furan Containing Novel Spiropyrrolidine Library Through 1,3‐dipolar Cycloaddition Reactions

A new class of functionalized furan and 5‐(p‐chlorophenyl)furan containing spiropyrrolidines has been synthesized in moderate to excellent yields by the one‐pot, three‐component 1,3‐dipolar cycloaddition reaction of in situ generated azomethine ylides with various furan/aryl furan‐substituted chalcones as dipolarophiles. The effect of electron deficient substituents at the fifth position of the furan ring in the chalcone on the regiochemistry of the cycloaddition formed was studied. The structures of the newly synthesized cycloaddicts were proved by analytical and spectral data.     

Synthesis and evaluation of a new non-fluorescent quencher in fluorogenic oligonucleotide probes for real-time PCR

A non-fluorescent quencher, based on the diaminoanthraquinone Disperse Blue 3, has been incorporated into oligonucleotides at the 5'-end, the 3'-end and internally as a thymidine derivative. Fluorimetry and fluorogenic real-time PCR experiments demonstrate that the quencher is effective with a wide range of fluorescent dyes. The anthraquinone moiety increases the melting temperature of DNA duplexes, thus allowing shorter, more discriminatory probes to be used. The quencher has been used in Scorpion primers and TaqMan probes for human DNA sequence recognition and mutation detection.     

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

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

Efficient reverse click labeling of azide oligonucleotides with multiple alkynyl Cy-Dyes applied to the synthesis of HyBeacon probes for genetic analysis

A convenient method of oligonucleotide labeling using click chemistry has been developed. A 2′-mesyloxyethyl ribothymidine phosphoramidite monomer was incorporated into DNA at several loci during solid phase oligonucleotide synthesis and converted to 2′-azidoethyl ribothymidine in high yield on the synthesis resin. The resultant azide oligonucleotides were doubly and triply labeled with alkyne-modified cyanine dyes and their biophysical properties were studied. The influence of the dye structures and method of labeling on the fluorescence properties of the DNA probes is discussed and compared with a standard labeling method using active esters of Cy-Dyes.     

荧光标记寡核苷酸的反相离子对色谱分析

建立荧光标记寡核苷酸反相离子对色谱分析方法,优化了流动相醋酸三乙胺浓度(0～0.15 mol/L), pH 4.5～7.0和洗脱强度等色谱条件.对5-mer, 10-mer和15-mer非标记和5'-羧基荧光素(5'FAM)标记寡核苷酸的保留进行比较分析,研究荧光标记寡核苷酸的保留机理,并分离TaqMan~(TM)探针等多种常用荧光标记寡核苷酸.结果显示,不同长度荧光标记寡核苷酸在0.01 mol/L醋酸三乙胺,pH 7.0的条件下获得最大分离.荧光标记寡核苷酸的保留与非标记寡核苷酸有明显差异,两者可完全分离.在一定长度范围内非标记寡核苷酸随长度的增加,保留时间增长;相反,荧光标记寡核苷酸的长度增加,保留时间减短.荧光染料疏水性对其标记的寡核苷酸在反相柱中的保留有较大影响,荧光染料疏水性越强,其标记寡核苷酸保留时间越长.但疏水性的影响程度随标记寡核苷酸长度增加而逐渐变小.     

Development of a Wavelength-Shifting Fluorescent Module for the Adenosine Aptamer Using Photostable Cyanine Dyes

DNA-based aptamers are commonly used recognition elements in biosensors for a range of target molecules. Here, the development of a wavelength-shifting optical module for a DNA-based adenosine-binding aptamer is described. It applies the combination of two photostable cyanine-styryl dyes as covalent modifications. This energy-transfer pair is postsynthetically attached to oligonucleotides via a copper(I)-catalyzed azide–alkyne cycloaddition by two structurally different approaches: 1) as nucleotide modifications at the 2′-position of uridines and 2) as nucleotide substitutions using (S)-amino-1,2-propanediol as acyclic linker between the phosphodiester bridges. Both dyes exhibit a remarkable photostability. A library of DNA aptamers consisting of different combinations of the two dyes in diagonal orientations were evaluated by their emission color contrast as readout. Further optimization led to aptasensors with improved fluorescent readout as compared with previously reported aptasensors. This approach described is synthetically facile using simple propargylated phosphoramidites as DNA building blocks. As such, this approach could be applied for other dyes and other chemical/biological applications.     

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

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

Tuning the Electrical and Optical Properties of Diketopyrrolopyrrole Complexes for Panchromatic Dye‐Sensitized Solar Cells

A series of metal‐free organic dyes that were bridged by a diketopyrrolopyrrole moiety and were composed of indoline and triphenylamine as donor groups and furan and benzene as conjugated spacer groups were designed and synthesized for use in dye‐sensitized solar cells (DSCs). The photophysical properties, electrochemical properties, and performance of the DSCs were related to the structure of their corresponding dyes. Their absorption spectra broadened upon the introduction of the indoline and heterocyclic furan moieties through fine‐tuning of their molecular configuration. The overall conversion efficiencies of DSCs that were based on these dyes ranged from 5.14–6.53 %. Among the four dyes that were tested, indoline‐based ID01 and ID02 showed higher efficiencies (6.35 % and 6.53 %) as a result of their improved light‐harvesting efficiency and larger electron driving force. The ID01 dye, which contained an indoline moiety as an electron donor and a furan group as a π‐conjugated linker, showed an excellent monochromatic incident‐photon‐to‐current‐conversion efficiency (IPCE) spectrum (350–650 nm) with a maximum value of 78 % in the high plateau region and an onset value close to 800 nm. Intensity‐modulated photovoltage spectroscopy (IMVS) and impedance spectroscopy (IS) revealed that dyes that contained benzene conjugation spacers suppressed the charge‐recombination rate more efficiently than dyes that contained furan spacers, thereby resulting in improved photovoltage.