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.

scholarly journals Surface-enhanced Raman spectroscopy for the characterization of Vaccinium myrtillus L. bilberries of the Baltic–Nordic regions

2021 ◽  
Author(s):  
Lina Traksele ◽  
Valentinas Snitka
Keyword(s):  
Raman Spectroscopy ◽  
Silver Nanoparticles ◽  
Principal Component ◽  
Surface Enhanced Raman Spectroscopy ◽  
Vaccinium Myrtillus ◽  
Spectral Variation ◽  
Data Set ◽  
Sers Substrates ◽  
Surface Enhanced ◽  
Surface Enhanced Raman

AbstractIn this study, an investigation of the wild bilberries (Vaccinium myrtillus L.) of the different Baltic–Nordic regions using surface-enhanced Raman spectroscopy (SERS) combined with principal component analysis (PCA) is presented. The bilberries were collected in Lithuania, Latvia, Finland and Norway. The set of the SERS spectra of the berry extracts (pH ~ 4) were recorded on the silver nanoparticles based SERS substrates. The SERS spectra of the extracts were acquired using 532 nm laser as an excitation source. The morphology of the SERS substrates was evaluated by scanning electron microscopy (SEM) and the presence of the silver nanoparticles was confirmed by the energy-dispersive X-ray spectroscopy (EDX). The enhancement factor (EF) of the silver SERS substrates was found to be 105. It has been shown that a strong fluorescence background, associated with the phenolic compounds found in bilberries, can be subtracted due to the fluorescence-quenching properties of the silver nanoparticles. Therefore, an application of the SERS technique allowed to observe the characteristic peaks of the bilberries and the PCA tool enabled to evaluate the spectral variation across the entire SERS data set. The results presented in this paper show that the SERS technique coupled with PCA chemometric analysis might serve as a complementary method that allows to identify the country of origin of the bilberries based on the spectral differences.

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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