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Optimized and scalable synthesis of magnetic nanoparticles for RNA extraction in response to developing countries' needs for the detection and control of SARS-CoV-2.

Version
1
Resource Type
Dataset : images: photographs, drawings, graphical representations, observational data, other
Creator
  • Chacón-Torres, Julio C. (Yachay Tech University)
  • Reinoso, C. (Yachay Tech University)
  • Navas-Leon, Daniela G. (Yachay Tech University)
  • Briceño, Sarah (Yachay Tech University)
  • González, Gema (Yachay Tech University)
Publication Date
2020-07-17
Free Keywords
Nanoparticles; Physics; Materials Science; Health; COVID-19
Description
  • Abstract

    Database of experimental results along the synthesis of functionalized magnetic nanoparticles for the RNA magnetic extraction methodology in real time RT-PCR for the clinical diagnosis of COVID-19 including:
    • Scanning electron micrographs.
    • Raman spectra taken at 532nm excitation waveleght.
    • Optical micrographs.
    • Infrared spectra.
    • X-ray photoelectron spectra.
    • Real time RT-PCR amplification fluorescence spectra.
    • Laboratory pictures.
Temporal Coverage
  • 2020-04-03 / 2020-06-26
    Time Period: Fri Apr 03 00:00:00 EDT 2020--Fri Jun 26 00:00:00 EDT 2020
  • 2020-04-03 / 2020-06-26
    Collection Date(s): Fri Apr 03 00:00:00 EDT 2020--Fri Jun 26 00:00:00 EDT 2020
Geographic Coverage
  • Ecuador
  • Developing countries
  • Latin America
  • Worldwide
Sampled Universe
Synthesis and characterization of nanoparticles applied research.
Sampling
Infrared spectroscopy. The infrared analysis of the samples was done using an Agilent Technologies spectrometer Cary 360 with a diamond attenuated total reflectance (ATR) accessory and resolution of 4 cm-1. For each spectrum 32 scans  acquisitions were compiled in a range between 400 and 4000 cm-1.
Raman spectroscopy. The spectroscopic Raman detection was carried out under ambient conditions using a HORIBA LabRam spectrometer with a 514 nm and 633 nm excitation wavelengths at ~0.65 mW and 1.5 mW between -50 and 4,000 cm-1. To avoid laser-induced damage on the samples the laser power was kept below 1 mW. Raman measurements were carried out using a micro-Raman setup with a 100X short distance objective in backscattering geometry. A charge-coupled device is used to detect the signal after analyzing the signal via a monochromator similar to previous Raman spectroscopy studies we have conducted [13]. The spectrometer was calibrated in frequency with the Rayleigh peak to be set at 0 cm-1.
X-ray photoelectron spectroscopy. The surface chemistry characterization was recorded by using X-Ray Photoelectron Spectroscopy (XPS) PHI VersaProbe III (Physical-Electronics) equipped with a 180 hemispherical electron energy analyzer and excited by a monochromatized Al-K¿ source with an energy 1486.6 eV. Its energy analyzer operates in the pass energy mode at 280 eV for Survey and 55 eV for high resolution. The analysis spot had a diameter of 50 µm and 45° detection angle relative to the substrate surface. Atomic concentration for each element was calculated using Mutipak Version 9.8.0.19 (Ulvac-phi, Inc.) this software uses the peak intensity (peak area) in units of counts per second taking into account the specific relativity sensitivity factor for each element.25,26  Background subtraction was not necessary due the high intensity peaks and non important energy losses prior to emission from the sample.
RNA extraction and Real Time RT-PCR. To evaluate the effectiveness of the Poly-NH2-MNP, a commercial IVD kit was used with already standardized reagents and whose only differential variables were the Poly-NH2-MNP in different concentrations and in different extraction procedures.The steps of the kit extraction protocol were followed and 15, 20 and 25 µL (microliters) of Poly-NH2-MNP were added to our nasopharyngeal swab samples along with a positive control of a known sample with the presence of the SARS-CoV-2 virus.After obtaining the genetic material, 8 µL of extracted RNA (stored between 2-8 °C) was used to start the PCR with a final volume of 20 µL.The PCR was given under the following thermocycling from a commercial kit.
Collection Mode
  • ONELABT provided some chemicals for these experiments
    Claudio Maldonado conducted the RT-PCR tests.
    InnovativeHealth LATAM supported the RT-PCR collection tests.

Availability
Download
Relations
  • Is version of
    DOI: 10.3886/E120310
Publications
  • Chacón-Torres, Julio C., C. Reinoso, Daniela G. Navas-Leon, S. Briceño, and G. González. “Optimized and Scalable Synthesis of Magnetic Nanoparticles for RNA Extraction in Response to Developing Countries’ Needs in the Detection and Control of SARS-CoV-2.” Laboratory Diagnostics. Research Square, June 10, 2020. https://doi.org/10.21203/rs.3.rs-34552/v1.
    • ID: 10.21203/rs.3.rs-34552/v1 (DOI)

Update Metadata: 2020-07-17 | Issue Number: 1 | Registration Date: 2020-07-17

Chacón-Torres, Julio C.; Reinoso, C.; Navas-Leon, Daniela G.; Briceño, Sarah; González, Gema (2020): Optimized and scalable synthesis of magnetic nanoparticles for RNA extraction in response to developing countries' needs for the detection and control of SARS-CoV-2.. Version: 1. ICPSR - Interuniversity Consortium for Political and Social Research. Dataset. https://doi.org/10.3886/E120310V1