SERRS immunoassay for quantitative human CRP analysis

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

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.     

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

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

Detection of DNA probes using Diels Alder cycloaddition and SERRS

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

Quantitative predictions for DNA two-dimensional display according to size and nucleotide sequence composition

2-D DNA display is a simple separation method that provides a fast and economical way of visualizing polymorphism and comparing genomes. The DNA fragments are separated first according to their size by standard gel electrophoresis and then according to their sequence composition using denaturing gradient gel electrophoresis. First developed by Fischer and Lerman (Cell 1979, 16, 191-200), this method has recently been used to distinguish strains within a bacterial species. The genomic restriction fragments are displayed as spots on a 2-D surface. Although most of the relevant physical mechanisms are understood, this technique is mostly empirical and remains essentially qualitative. In view of optimizing this procedure, we combine our understanding of the different physical mechanisms at play to develop a complete numerical model to predict the relative coordinates of the spots as a function of the corresponding DNA sequence and of the experimental conditions. We experimentally validate our model by predicting the outcome of a 2-D display of the lambda phage genome. It thus becomes possible to optimize in silico the experimental parameters, to predict whether specific mutations as well as yet undescribed genetic polymorphisms can be resolved, and to assist in interpreting the experimental data.     

铜(Ⅱ)、镍(Ⅱ)的新卟啉配合物的SERRS谱及DNA的影响

铜（Ⅱ）、镍（Ⅱ）的新卟啉配合物的ＳＥＲＲＳ谱及ＤＮＡ的影响周光明,盛蓉生,熊亚,徐知三,王小华,曾云鹗（武汉大学化学系、分析测试中心,武汉,４３００７２）关键词ＳＥＲＲＳ,卟啉,ＤＮＡ从分子水平上认识卟啉的生物学过程一直是人们感兴趣的研究领域,表面...     

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.     

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.     

A multivariate representation and analysis of DNA sequence data

A new way to represent and analyze DNA sequence data is described. This approach complements methods currently used, in that it allows the systematic part of the variation between different sequences to be modeled. This can prove as informative as absence of variation (homology), which is the most widely used criterion for comparing sequence data. A multivariate sequence-activity model (SAM), for DNA-promoter sequences is presented, by which the relative promoter strength is modeled in terms of the primary DNA-sequence. The model is shown to have a good predictive capability. The coefficients from the model are interpreted, and used to design new structures predicted to be strong promoters in the system investigated. The approach described is also applicable to other kinds of sequence data, e.g. RNAs, proteins or peptides.     

Characteristic sequences for DNA primary sequence

A DNA sequence can be identified with a word over an alphabet N = [A, C, G, T]. Characteristic sequences of a DNA sequence are given in term of classifications of bases of nucleic acids. Using the characteristic sequences, we construct a set of 2 x 2 matrices to represent DNA primary sequences, which are based on counting of the frequency of occurrence of all (0,1) triplets of characteristic sequences. Furthermore, the leading eigenvalues of these matrices are computed and considered as invariants for the DNA primary sequences. Similarity and dissimilarity analysis based on the characteristic sequences are given for eight exon-1 genes of beta-globin about eight species.     

Quantitative analysis and characterization of DNA immobilized on gold

We describe the complementary use of X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared (FTIR) spectroscopy to quantitatively characterize the immobilization of thiolated (dT)(25) single-stranded DNA (ssDNA) on gold. When electron attenuation effects are accurately accounted for in the XPS analysis, the relative coverage values obtained by the two methods are in excellent agreement, and the absolute coverage can be calculated on the basis of the XPS data. The evolution of chemically specific spectral signatures during immobilization indicates that at lower coverages much of the DNA lies flat on the surface, with a substantial fraction of the thymine bases chemisorbed. At higher immobilization densities, the (dT)(25) film consists of randomly coiled ssDNA molecules each anchored via the thiol group and at possibly one or two other bases. We use two examples to demonstrate how the quantitative analysis can be applied to practical problems: the effects of different buffer salts on the immobilization efficiency; the immobilization kinetics. Buffers with divalent salts dramatically increase the efficiency of immobilization and result in very high surface densities (>5 x 10(13)/ cm(2)), densities that may only be possible if the divalent counterions induce strong attractive intermolecular interactions. In contrast with previous reports of alkanethiol adsorption kinetics on gold, ssDNA immobilization in 1 M phosphate buffer does not occur with Langmuir kinetics, a result attributable to rearrangement within the film that follows the initial adsorption.     

Selective functionalisation of TNT for sensitive detection by SERRS

Selective chemical functionalisation of 2,4,6-trinitrotoluene to a surface enhanced resonance Raman active species for sensitive detection.     

Quantitative analysis of DNA methylation in chronic lymphocytic leukemia patients

Changes in the genomic DNA methylation level have been found to be closely associated with tumorigenesis. In order to analyze the relation of aberrant DNA methylation to clinical and biological risk factors, we have determined the cytosine methylation level of 81 patients diagnosed with chronic lymphocytic leukemia (CLL). The analysis was based on DNA hydrolysis followed by derivatization of the 2'-desoxyribonucleoside-3'-monophosphates with BODIPY FL EDA. Derivatives were separated by micellar electrokinetic chromatography, and laser-induced fluorescence was used for detection. We analyzed potential correlations between DNA methylation levels and numerous patient parameters, including clinical observations and biological data. As a result, we observed a significant correlation with the immunoglobulin variable heavy chain gene (VH) mutation status. This factor has been repeatedly proposed as a reliable prognostic marker for CLL, which suggests that the methylation level might be a valuable factor in determining the prognostic outcome of CLL. We are now in the process of refining our method to broaden its application potential. In this context, we show here that the oxidation of the fluorescence marker in the samples and the evaporation of methanol in the electrolytes can be prevented by a film of paraffin oil. In summary, our results thus establish capillary electrophoresis as a valuable tool for analyzing the DNA methylation status of clinical samples.     

酞菁化合物LB单分子膜的SERRS

酞菁类化合物具有优良的光电特性,选择适当的取代侧链可得到稳定的LB成膜材料,可望在微电子器件等方面获得重要的应用.本工作观测了四-4-(2,4-二特戊基苯氧基)酞菁铜(CuPc(Dt-PP)_4)在银岛膜上的LB单分子层的表面增强共振拉曼散射(SERRS)光谱。比较其固体粉末的共振拉曼散射(RRS)光谱,讨论了酞菁铜分子大环在载片表面的取向及其可能的原因。1 实验CuPc(Dt-PP)_4样品由陈文启等合成,经元素分析、IR、NMR、色谱等研究确认其结构如图1所示.银岛膜用真空蒸镀法制备在玻璃载片上。用同时蒸镀在铜网上的银膜的透射电     

Reproducible SERRS from structured gold surfaces

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

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

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

Separation and analysis of DNA sequence reaction products by capillary gel electrophoresis

This paper demonstrates the potential of capillary gel electrophoresis with laser induced fluorescence detection as a tool for DNA sequence determination. Both synthetic oligonucleotides and single-stranded phage DNA were utilized as templates in the standard chain termination procedure. Primer molecules were tagged at the 5' end with the fluorescent dye, JOE. First, baseline resolution of a dA extended primer from 18 to 81 bases long, a total of 64 fragments, was observed. A second synthetic template was designed to yield alternating stretches of dA and dT extensions of the primer. Thirdly, the sequence reaction products from a synthetic oligonucleotide template containing all four bases was analyzed in four independent runs, one for each of the four base-specific reactions. In all cases, the expected number and patterns of peaks were observed by capillary gel electrophoretic analysis. Finally, separation of sequence reaction products generated with single-strand M13mp18 phage DNA as template exhibited baseline resolution of fragments differing in length by a single nucleotide and from 18 to greater than 330 bases total length.     

Quantitative analysis of specific target DNA oligomers using a DNA-immobilized packed-column system

Although a DNA-immobilized packed-column (DNA-packed column), which relies on sequence-dependent interactions of target DNA or mRNA (in the mobile phase) with DNA probes (on the silica particle) in a continuous flow process, could be considered as an alternative platform for quantitative analysis of specific DNA to DNA chip methodology, the performance in practice has not been satisfactory. In this study, we set up a more efficient quantitative analysis system based on a DNA-packed column by employing a temperature-gradient strategy and DMSO-containing mobile phase. Using a temperature-gradient strategy based on T _m values of probe/target DNA hybridizations and DMSO (5%)-containing mobile phase, we succeeded in the quantitative analysis of a specific complementary target distinguishable from non-complementary DNA oligomers or other similar DNA samples. In addition, two different target DNA oligomers even with similar T _m values were separated and detected quantitatively by using a packed column carrying two different DNA probes.     

TNT stilbene derivatives as SERRS active species

Synthesis of four trinitrotoluene stilbene derivatives and assessment for SERRS activity is reported.     

New graphical representation of a DNA sequence based on the ordered dinucleotides and its application to sequence analysis

Graphical representation of a DNA sequence is a powerful tool for basic biological research. Based on the ordered dinucleotides, we propose a novel three dimensional (3D) graphical representation without circuit or degeneracy. Simultaneously, we derive the projection curve of the 3D graph. These two curves have good visualization for longer DNA sequences. The utility of the proposed curves is illustrated by mutation analysis, similarity analysis, and evolutionary relationships of different species. The results indicate that our method is efficient and powerful. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012