scholarly journals Quantitative surface-enhanced Raman spectroscopy of single bases in oligodeoxynucleotides

2017 ◽  
Vol 205 ◽  
pp. 517-536 ◽  
Author(s):  
S. Dick ◽  
S. E. J. Bell
Keyword(s):  
Secondary Structure ◽  
Dna Sequences ◽  
Positional Information ◽  
Surface Enhanced Raman Spectroscopy ◽  
Test Sequence ◽  
Structural Variations ◽  
Difference Spectra ◽  
Surface Enhanced Raman ◽  
Pre Treatment ◽  
The Individual

To address the question of whether the SERS signals of ss-DNA are simply combinations of the signals from the individual bases that comprise the sequence, SERS spectra of unmodified ss-DNA sequences were obtained using a hydroxylamine-reduced Ag colloid aggregated with MgSO4. Initially, synthetic oligodeoxynucleotides with systematic structural variations were used to investigate the effect of adding single nucleobases to the 3′ terminus of 10-mer and 20-mer sequences. It was found that the resulting SERS difference spectra could be used to identify the added nucleobases since they closely matched reference spectra of the same nucleobase. Investigation of the variation in intensity of an adenine probe which was moved along a test sequence showed there was a small end effect where nucleobases near the 3′ terminus gave slightly larger signals but the effect was minor (30%). More significantly, in a sample set comprising 25-mer sequences where A, T or G nucleobases were substituted either near the centres of the sequences or the 5′ or 3′ ends, the SERS difference spectra only matched the expected form in approximately half the cases tested. This variation appeared to be due to changes in secondary structure induced by altering the sequences since uncoiling the sequences in a thermal pre-treatment step gave difference spectra which in all cases matched the expected form. Multivariate analysis of the set of substitution data showed that 99% of the variance could be accounted for in a model with just three factors whose loadings matched the spectra of the A, T, and G nucleobases and which contained no positional information. This suggests that aside from the differences in secondary structure which can be eliminated by thermal pre-treatment, the SERS spectra of the 25-mers studied here are simply the sum of their component parts. Although this means that SERS provides very little information on the primary sequence it should be excellent for the detection of post-transcription modifications to DNA which can occur at multiple positions along a given sequence.

scholarly journals Spectroelectrochemical Investigation of the Interaction of Adenine with Pyridoxine at Physiological pH

2019 ◽  
Vol 2019 ◽  
pp. 1-12
Author(s):  
Yasmin Roye ◽  
Uche Udeochu ◽  
Maraizu Ukaegbu ◽  
Jonathan Onuegbu
Keyword(s):  
Raman Band ◽  
Bathochromic Shift ◽  
Surface Enhanced Raman Spectroscopy ◽  
Raman Shift ◽  
Sers Spectrum ◽  
Visible Absorption ◽  
Adenine Ring ◽  
Surface Enhanced ◽  
Surface Enhanced Raman ◽  
The Individual

Spectroelectrochemical techniques were used to probe the interaction of adenine with pyridoxine at pH 7.0. Analysis of UV-visible absorption of the adenine-pyridoxine complex at 260 nm using the Lineweaver–Burk double reciprocal plot produced a linear graph indicating a 1 : 1 mode of interaction between the compounds and a binding constant of 29.1. Change in the background current and broadening of adenine and pyridoxine cyclic voltammetry (CV) oxidation peaks at 1.0 V and 0.8 V, respectively, compared to the CV of the individual compounds is indicative of an interaction. The Raman shift of the coupled –C(11)H2-OH bending and in-plane N(7)-H mode at 1235 cm−1 to 1215 cm−1 of pyridoxine and the shift to the lower wavenumber of the adenine –N(10)H2 rocking band from 942 to 906 cm−1 confirm that the adenine exocyclic amino group and its purine nitrogen atom N(7) interacts with pyridoxine O(12) via the formation of hydrogen bonds. Strong enhancement of surface-enhanced Raman spectroscopy (SERS) bands pertaining to adenine and the bathochromic shift of the normal Raman band due to the adenine ring breathing mode observed at 722 cm−1 in the spectrum of adenine, to 732 cm−1 in the SERS spectrum of aqueous adenine-pyridoxine indicates that the complex adsorbs onto the Ag nanoparticle surface with the adenine portion possessing a perpendicular orientation.

scholarly journals Rapid Detection and Identification of miRNAs by Surface-Enhanced Raman Spectroscopy Using Hollow Au Nanoflowers Substrates

2017 ◽  
Vol 2017 ◽  
pp. 1-11 ◽  
Author(s):  
Xiaowei Cao ◽  
Min Bao ◽  
Yibo Shan ◽  
Wei Li ◽  
Hongcan Shi
Keyword(s):  
Mirna Expression ◽  
Rapid Detection ◽  
Expression Patterns ◽  
Surface Enhanced Raman Spectroscopy ◽  
Label Free ◽  
Difference Spectra ◽  
Detection And Identification ◽  
Ito Glass ◽  
Surface Enhanced ◽  
Surface Enhanced Raman

MicroRNAs (miRNAs) are recognized as regulators of gene expression during the biological processes of cells as well as biomarkers of many diseases. Development of rapid and sensitive miRNA profiling methods is crucial for evaluating the pattern of miRNA expression related to normal and diseased states. This work presents a novel hollow Au nanoflowers (HAuNFs) substrate for rapid detection and identification of miRNAs by surface-enhanced Raman scattering (SERS) spectroscopy. We synthesized the HAuNFs by a seed-mediated growth approach. Then, HAuNFs substrates were fabricated by depositing HAuNFs onto the surfaces of (3-aminopropyl)triethoxysilane- (APTES-) functionalized ITO glass. The result demonstrated that HAuNFs substrates had very good reproducibility, homogeneous SERS activity, and high SERS effect. The substrates enabled us to successfully obtain the SERS spectra of miR-10a-5p, miR-125a-5p, and miR-196a-5p. The difference spectra among the three kinds of miRNAs were studied to better interpret the spectral differences and identify miRNA expression patterns with high accuracy. The principal component analysis (PCA) of the SERS spectra was used to distinguish among the three kinds of miRNAs. Considering its time efficiency, being label-free, and its sensitivity, the SERS based on HAuNFs substrates is very promising for miRNA research and plays an important role in early disease detection and prevention.

scholarly journals From Space to Sequence and Back Again: Iterative DNA Proximity Ligation and its Applications to DNA-Based Imaging

2018 ◽  
Author(s):  
Alexander A. Boulgakov ◽  
Erhu Xiong ◽  
Sanchita Bhadra ◽  
Andrew D. Ellington ◽  
Edward M. Marcotte
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Positional Information ◽  
Theoretical Work ◽  
Sequence Information ◽  
Sequencing Data ◽  
Experimental Proof ◽  
Proximity Ligation ◽  
Geometric Patterns ◽  
The Individual

AbstractWe extend the concept of DNA proximity ligation from a single readout per oligonucleotide pair to multiple reversible, iterative ligations re-using the same oligonucleotide molecules. Using iterative proximity ligation (IPL), we can in principle capture multiple ligation events between each oligonucleotide and its various neighbors and thus recover a far richer knowledge about their relative positions than single, irreversible ligation events. IPL would thus act to sample and record local molecular neighborhoods. By integrating a unique DNA barcode into each participating oligonucleotide, we can catalog the individual ligation events and thus capture the positional information contained therein in a high throughput manner using next-generation DNA sequencing. We propose that by interpreting IPL sequencing results in the context of graph theory and by applying spring layout algorithms, we can recover geometric patterns of objects labeled by DNA. Using simulations, we demonstrate that we can in principle recover letter patterns photolithographed onto slide surfaces using only IPL sequencing data, illustrating how our technique maps complex spatial configurations into DNA sequences and then – using only this sequence information – recovers them. We complement our theoretical work with an experimental proof-of-concept of iterative proximity ligation on an oligonucleotide population.

scholarly journals DeltaPCA: A Statistically Robust Method for Detecting Protein Analyte Binding to Aptamer-Functionalised Nanoparticles using Surface-Enhanced Raman Spectroscopy

2021 ◽  
Author(s):  
Fiona Given ◽  
Tamsyn Stanborough ◽  
Mark Waterland ◽  
Deborah Crittenden
Keyword(s):  
Raman Spectroscopy ◽  
Computational Analysis ◽  
Surface Enhanced Raman Spectroscopy ◽  
Analysis Procedure ◽  
Indirect Detection ◽  
Difference Spectra ◽  
Data Set ◽  
Technical Variability ◽  
Surface Enhanced ◽  
Surface Enhanced Raman

In this work, we introduce a novel joint experimental design and computational analysis procedure to reliably and reproducibly quantify protein analyte binding to DNA aptamer-functionalised silver nanoparticles using slippery surface-enhanced Raman spectroscopy. We employ an indirect detection approach, based upon monitoring spectral changes in the covalent bond-stretching region as intermolecular bonds are formed between the surface-immobilized probe biomolecule and its target analyte. Sample variability is minimized by preparing aptamer-only and aptamer-plus-analyte samples under the same conditions, and then analysing difference spectra. To account for technical variability, multiple spectra are recorded from the same sample. Our new DeltaPCA analysis procedure takes into account technical variability within each spectral data set while also extracting statistically robust difference spectra between data sets. Proof of principle experiments using thiolated aptamers to detect CoV-SARS-2 spike protein reveal that analyte binding is mediated through the formation of N-H...X and C-H...X hydrogen bonds between the aptamer (H-bond donor) and protein (H-bond acceptor). Our computational analysis code can be freely downloaded from https://github.com/dlc62/DeltaPCA.

Role of Transcriptional Read-Through in PRE Activity in Drosophila melanogaster

Acta Naturae ◽  
2016 ◽  
Vol 8 (2) ◽  
pp. 79-86 ◽  
Author(s):  
P. V. Elizar’ev ◽  
D. V. Lomaev ◽  
D. A. Chetverina ◽  
P. G. Georgiev ◽  
M. M. Erokhin
Keyword(s):  
Dna Sequences ◽  
Cell Types ◽  
Transcription Terminator ◽  
Response Elements ◽  
Polycomb Response Elements ◽  
The Individual ◽  
Multicellular Organisms ◽  
Different Cell Types ◽  
Main Factor

Maintenance of the individual patterns of gene expression in different cell types is required for the differentiation and development of multicellular organisms. Expression of many genes is controlled by Polycomb (PcG) and Trithorax (TrxG) group proteins that act through association with chromatin. PcG/TrxG are assembled on the DNA sequences termed PREs (Polycomb Response Elements), the activity of which can be modulated and switched from repression to activation. In this study, we analyzed the influence of transcriptional read-through on PRE activity switch mediated by the yeast activator GAL4. We show that a transcription terminator inserted between the promoter and PRE doesnt prevent switching of PRE activity from repression to activation. We demonstrate that, independently of PRE orientation, high levels of transcription fail to dislodge PcG/TrxG proteins from PRE in the absence of a terminator. Thus, transcription is not the main factor required for PRE activity switch.

Bacterial detection and differentiation via direct volatile organic compound sensing with surface enhanced Raman spectroscopy

2017 ◽  
Author(s):  
Caitlin S. DeJong ◽  
David I. Wang ◽  
Aleksandr Polyakov ◽  
Anita Rogacs ◽  
Steven J. Simske ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Bacterial Infections ◽  
Direct Detection ◽  
Point Of Care ◽  
Surface Enhanced Raman Spectroscopy ◽  
E Coli ◽  
Recent Emergence ◽  
Surface Enhanced ◽  
Volatile Organic ◽  
Surface Enhanced Raman

Through the direct detection of bacterial volatile organic compounds (VOCs), via surface enhanced Raman spectroscopy (SERS), we report here a reconfigurable assay for the identification and monitoring of bacteria. We demonstrate differentiation between highly clinically relevant organisms: <i>Escherichia coli</i>, <i>Enterobacter cloacae</i>, and <i>Serratia marcescens</i>. This is the first differentiation of bacteria via SERS of bacterial VOC signatures. The assay also detected as few as 10 CFU/ml of <i>E. coli</i> in under 12 hrs, and detected <i>E. coli</i> from whole human blood and human urine in 16 hrs at clinically relevant concentrations of 10<sup>3</sup> CFU/ml and 10<sup>4</sup> CFU/ml, respectively. In addition, the recent emergence of portable Raman spectrometers uniquely allows SERS to bring VOC detection to point-of-care settings for diagnosing bacterial infections.

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