scholarly journals A high-throughput fluorescent indicator displacement assay and principal component/cluster data analysis for determination of ligand-nucleic acid structural selectivity

2017 ◽  
Author(s):  
Rafael del Villar-Guerra ◽  
Robert D. Gray ◽  
John O. Trent ◽  
Jonathan B. Chaires
Keyword(s):  
Nucleic Acid ◽  
High Throughput ◽  
Principal Component ◽  
Binding Selectivity ◽  
Cluster Data ◽  
Structural Selectivity ◽  
Secondary Screen ◽  
Displacement Assay ◽  
Nucleic Acid Structures

ABSTRACTWe describe a high-throughput fluorescence indicator displacement assay (HT-FID) to evaluate the affinity and the selectivity of compounds binding to different DNA structures. We validated the assay using a library of 30 well-known nucleic acid binders containing a variety chemical scaffolds. We used a combination of principal component analysis and hierarchical clustering analysis to interpret the results obtained. This analysis classified compounds based on selectivity for AT-rich, GC-rich and G4 structures. We used the FID assay as a secondary screen to test the binding selectivity of an additional 20 compounds selected from the NCI diversity set III library that were identified as G4 binders using a thermal shift assay. The results showed G4 binding selectivity for only a few of the 20 compounds. Overall, we show that this HT-FID assay, coupled with PCA and HCA, provides a useful tool for the discovery of ligands selective for particular nucleic acid structures.

Imaging of ribosomal RNA-protein interactions by dark-field STEM

1989 ◽  
Vol 47 ◽  
pp. 250-251
Author(s):  
M. Boublik ◽  
V. Mandiyan ◽  
S. Tumminia ◽  
J.F. Hainfeld ◽  
J.S. Wall
Keyword(s):  
Nucleic Acid ◽  
16S Rrna ◽  
Dark Field ◽  
Radius Of Gyration ◽  
Central Domain ◽  
The Core ◽  
16S Rna ◽  
30S Subunit ◽  
Core Particles

Success in protein-free deposition of native nucleic acid molecules from solutions of selected ionic conditions prompted attempts for high resolution imaging of nucleic acid interactions with proteins, not attainable by conventional EM. Since the nucleic acid molecules can be visualized in the dark-field STEM mode without contrasting by heavy atoms, the established linearity between scattering cross-section and molecular weight can be applied to the determination of their molecular mass (M) linear density (M/L), mass distribution and radius of gyration (RG). Determination of these parameters promotes electron microscopic imaging of biological macromolecules by STEM to a quantitative analytical level. This technique is applied to study the mechanism of 16S rRNA folding during the assembly process of the 30S ribosomal subunit of E. coli. The sequential addition of protein S4 which binds to the 5'end of the 16S rRNA and S8 and S15 which bind to the central domain of the molecule leads to a corresponding increase of mass and increased coiling of the 16S rRNA in the core particles. This increased compactness is evident from the decrease in RG values from 114Å to 91Å (in “ribosomal” buffer consisting of 10 mM Hepes pH 7.6, 60 mM KCl, 2 m Mg(OAc)2, 1 mM DTT). The binding of S20, S17 and S7 which interact with the 5'domain, the central domain and the 3'domain, respectively, continues the trend of mass increase. However, the RG values of the core particles exhibit a reverse trend, an increase to 108Å. In addition, the binding of S7 leads to the formation of a globular mass cluster with a diameter of about 115Å and a mass of ∽300 kDa. The rest of the mass, about 330 kDa, remains loosely coiled giving the particle a “medusa-like” appearance. These results provide direct evidence that 16S RNA undergoes significant structural reorganization during the 30S subunit assembly and show that its interactions with the six primary binding proteins are not sufficient for 16S rRNA coiling into particles resembling the native 30S subunit, contrary to what has been reported in the literature.

Application of Ogur & Rosen's Method for the Determination of Nucleic Acid Content of Bacteria

1957 ◽  
Vol 12 (2) ◽  
pp. 125-129 ◽  
Author(s):  
Nobuyasu KAWASAKI ◽  
Ichiro TAKI ◽  
Chiaki WATANABE ◽  
Kiyoshi MATOBA ◽  
Mokichiro NISHIO ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Acid Content ◽  
Nucleic Acid Content

scholarly journals Application of Derivative, Derivative Ratio, and Multivariate Spectral Analysis and Thin-Layer Chomatography-Densitometry for Determination of a Ternary Mixture Containing Drotaverine Hydrochloride, Caffeine, and Paracetamol

2007 ◽  
Vol 90 (2) ◽  
pp. 391-404 ◽  
Author(s):  
Fadia H Metwally ◽  
Yasser S El-Saharty ◽  
Mohamed Refaat ◽  
Sonia Z El-Khateeb
Keyword(s):  
Thin Layer ◽  
Least Squares ◽  
Ternary Mixture ◽  
Principal Component Regression ◽  
Pharmaceutical Preparations ◽  
Principal Component ◽  
Standard Addition ◽  
Drotaverine Hydrochloride ◽  
Assay Precision

Abstract New selective, precise, and accurate methods are described for the determination of a ternary mixture containing drotaverine hydrochloride (I), caffeine (II), and paracetamol (III). The first method uses the first (D1) and third (D3) derivative spectrophotometry at 331 and 315 nm for the determination of (I) and (III), respectively, without interference from (II). The second method depends on the simultaneous use of the first derivative of the ratio spectra (DD1) with measurement at 312.4 nm for determination of (I) using the spectrum of 40 μg/mL (III) as a divisor or measurement at 286.4 and 304 nm after using the spectrum of 4 μg/mL (I) as a divisor for the determination of (II) and (III), respectively. In the third method, the predictive abilities of the classical least-squares, principal component regression, and partial least-squares were examined for the simultaneous determination of the ternary mixture. The last method depends on thin-layer chromatography-densitometry after separation of the mixture on silica gel plates using ethyl acetatechloroformmethanol (16 + 3 + 1, v/v/v) as the mobile phase. The spots were scanned at 281, 272, and 248 nm for the determination of (I), (II), and (III), respectively. Regression analysis showed good correlation in the selected ranges with excellent percentage recoveries. The chemical variables affecting the analytical performance of the methodology were studied and optimized. The methods showed no significant interferences from excipients. Intraday and interday assay precision and accuracy values were within regulatory limits. The suggested procedures were checked using laboratory-prepared mixtures and were successfully applied for the analysis of their pharmaceutical preparations. The validity of the proposed methods was further assessed by applying a standard addition technique. The results obtained by applying the proposed methods were statistically analyzed and compared with those obtained by the manufacturer's method.

Multivariate Analysis Aided Surface-Enhanced Raman Spectroscopy (MVA-SERS) Multiplex Quantitative Detection of Trace Fentanyl in Illicit Drug Mixtures Using a Handheld Raman Spectrometer

2021 ◽  
pp. 000370282110329
Author(s):  
Ling Wang ◽  
Mario O. Vendrell-Dones ◽  
Chiara Deriu ◽  
Sevde Doğruer ◽  
Peter de B. Harrington ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Principal Component ◽  
Surface Enhanced Raman Spectroscopy ◽  
Quantitative Detection ◽  
Least Squares Regression ◽  
Surface Enhanced ◽  
Surface Enhanced Raman ◽  
Sers Detection ◽  
Current Screening

Recently there has been upsurge in reports that illicit seizures of cocaine and heroin have been adulterated with fentanyl. Surface-enhanced Raman spectroscopy (SERS) provides a useful alternative to current screening procedures that permits detection of trace levels of fentanyl in mixtures. Samples are solubilized and allowed to interact with aggregated colloidal nanostars to produce a rapid and sensitive assay. In this study, we present the quantitative determination of fentanyl in heroin and cocaine using SERS, using a point-and-shoot handheld Raman system. Our protocol is optimized to detect pure fentanyl down to 0.20 ± 0.06 ng/mL and can also distinguish pure cocaine and heroin at ng/mL levels. Multiplex analysis of mixtures is enabled by combining SERS detection with principal component analysis and super partial least squares regression discriminate analysis (SPLS-DA), which allow for the determination of fentanyl as low as 0.05% in simulated seized heroin and 0.10% in simulated seized cocaine samples.

scholarly journals Possibility of Human Gender Recognition Using Raman Spectra of Teeth

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3983
Author(s):  
Ozren Gamulin ◽  
Marko Škrabić ◽  
Kristina Serec ◽  
Matej Par ◽  
Marija Baković ◽  
...  
Keyword(s):  
Raman Spectra ◽  
Principal Component ◽  
Support Vector ◽  
Gender Recognition ◽  
Proof Of Concept ◽  
Male And Female ◽  
Tooth Type ◽  
Tooth Apex ◽  
The Difference

Gender determination of the human remains can be very challenging, especially in the case of incomplete ones. Herein, we report a proof-of-concept experiment where the possibility of gender recognition using Raman spectroscopy of teeth is investigated. Raman spectra were recorded from male and female molars and premolars on two distinct sites, tooth apex and anatomical neck. Recorded spectra were sorted into suitable datasets and initially analyzed with principal component analysis, which showed a distinction between spectra of male and female teeth. Then, reduced datasets with scores of the first 20 principal components were formed and two classification algorithms, support vector machine and artificial neural networks, were applied to form classification models for gender recognition. The obtained results showed that gender recognition with Raman spectra of teeth is possible but strongly depends both on the tooth type and spectrum recording site. The difference in classification accuracy between different tooth types and recording sites are discussed in terms of the molecular structure difference caused by the influence of masticatory loading or gender-dependent life events.

scholarly journals Full spectrum and genetic algorithm-selected spectrum-based chemometric methods for simultaneous determination of azilsartan medoxomil, chlorthalidone, and azilsartan: Development, validation, and application on commercial dosage form

2021 ◽  
Vol 19 (1) ◽  
pp. 205-213
Author(s):  
Hany W. Darwish ◽  
Abdulrahman A. Al Majed ◽  
Ibrahim A. Al-Suwaidan ◽  
Ibrahim A. Darwish ◽  
Ahmed H. Bakheit ◽  
...  
Keyword(s):  
Genetic Algorithm ◽  
Simultaneous Determination ◽  
Predictive Power ◽  
Principal Component Regression ◽  
Selection Procedure ◽  
Principal Component ◽  
Chemometric Methods ◽  
Full Spectrum ◽  
Azilsartan Medoxomil

Abstract Five various chemometric methods were established for the simultaneous determination of azilsartan medoxomil (AZM) and chlorthalidone in the presence of azilsartan which is the core impurity of AZM. The full spectrum-based chemometric techniques, namely partial least squares (PLS), principal component regression, and artificial neural networks (ANN), were among the applied methods. Besides, the ANN and PLS were the other two methods that were extended by genetic algorithm procedure (GA-PLS and GA-ANN) as a wavelength selection procedure. The models were developed by applying a multilevel multifactor experimental design. The predictive power of the suggested models was evaluated through a validation set containing nine mixtures with different ratios of the three analytes. For the analysis of Edarbyclor® tablets, all the proposed procedures were applied and the best results were achieved in the case of ANN, GA-ANN, and GA-PLS methods. The findings of the three methods were revealed as the quantitative tool for the analysis of the three components without any intrusion from the co-formulated excipient and without prior separation procedures. Moreover, the GA impact on strengthening the predictive power of ANN- and PLS-based models was also highlighted.

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