scholarly journals Parallel RNA extraction using magnetic beads and a droplet array

Lab on a Chip ◽  
2015 ◽  
Vol 15 (4) ◽  
pp. 1059-1065 ◽  
Author(s):  
Xu Shi ◽  
Chun-Hong Chen ◽  
Weimin Gao ◽  
Shih-hui Chao ◽  
Deirdre R. Meldrum
Keyword(s):  
Nucleic Acid ◽  
Magnetic Beads ◽  
Rna Extraction ◽  
Lab On A Chip ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Droplet Array

Nucleic acid extraction is a necessary step for most genomic/transcriptomic analyses, but it often requires complicated mechanisms to be integrated into a lab-on-a-chip device.

scholarly journals Evaluation of an Automated High-Throughput Liquid-Based RNA Extraction Platform on Pooled Nasopharyngeal or Saliva Specimens for SARS-CoV-2 RT-PCR

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 615
Author(s):  
Allen Wing-Ho Chu ◽  
Cyril Chik-Yan Yip ◽  
Wan-Mui Chan ◽  
Anthony Chin-Ki Ng ◽  
Dream Lok-Sze Chan ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
High Throughput ◽  
Rna Extraction ◽  
Nasopharyngeal Swab ◽  
Acid Extraction ◽  
Rt Pcr ◽  
Nucleic Acid Extraction ◽  
Suitable Alternative ◽  
Pcr Inhibitors ◽  
Pcr Targeting

SARS-CoV-2 RT-PCR with pooled specimens has been implemented during the COVID-19 pandemic as a cost- and manpower-saving strategy for large-scale testing. However, there is a paucity of data on the efficiency of different nucleic acid extraction platforms on pooled specimens. This study compared a novel automated high-throughput liquid-based RNA extraction (LRE) platform (PHASIFYTM) with a widely used magnetic bead-based total nucleic acid extraction (MBTE) platform (NucliSENS® easyMAG®). A total of 60 pools of nasopharyngeal swab and 60 pools of posterior oropharyngeal saliva specimens, each consisting of 1 SARS-CoV-2 positive and 9 SARS-CoV-2 negative specimens, were included for the comparison. Real-time RT-PCR targeting the SARS-CoV-2 RdRp/Hel gene was performed, and GAPDH RT-PCR was used to detect RT-PCR inhibitors. No significant differences were observed in the Ct values and overall RT-PCR positive rates between LRE and MBTE platforms (92.5% (111/120] vs 90% (108/120]), but there was a slightly higher positive rate for LRE (88.3% (53/60]) than MBTE (81.7% (49/60]) among pooled saliva. The automated LRE method is comparable to a standard MBTE method for the detection of SAR-CoV-2 in pooled specimens, providing a suitable alternative automated extraction platform. Furthermore, LRE may be better suited for pooled saliva specimens due to more efficient removal of RT-PCR inhibitors.

Functional Magnetite Nanoparticle: A Review on the Particles Lysis and Nucleic Acid Separation

2021 ◽  
Vol 33 ◽  
pp. 13-27
Author(s):  
Puspita Nurlilasari ◽  
Camellia Panatarani ◽  
Mia Miranti ◽  
Savira Ekawardhani ◽  
Ferry Faizal ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Magnetite Nanoparticles ◽  
Magnetic Beads ◽  
Functional Materials ◽  
Cell Lysis ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Coating Materials ◽  
Magnetite Nanoparticle ◽  
Separation Cell

The functional magnetite nanoparticles are one of the most important functional materials for nucleic acid separation. Cell lysis and magnetic separation are two essential steps involve in optimizing nucleic acid extraction using the magnetic beads method. Many coating materials, coupling agents, chemical cell lysis, and several methods have been proposed to produce the specific desired properties for nucleic acid extraction. The important properties, such as biocompatibility, stability, linking ability, hydrophobicity, and biodegradable, were considered. The appropriate coating material of magnetite core and coupling agent are necessary to give biomolecules a possibility to link with each other through chemical conjugation. In this review, progress in functional magnetite nanoparticles to optimize the high binding performance in nucleic acid extraction is discussed.

scholarly journals Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extraction and manipulation

PLoS Biology ◽  
2019 ◽  
Vol 17 (1) ◽  
pp. e3000107 ◽  
Author(s):  
Phil Oberacker ◽  
Peter Stepper ◽  
Donna M. Bond ◽  
Sven Höhn ◽  
Jule Focken ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
High Throughput ◽  
Magnetic Beads ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Open Platform

scholarly journals Robotic RNA extraction for SARS-CoV-2 surveillance using saliva samples

2021 ◽  
Author(s):  
Jennifer R. Hamilton ◽  
Elizabeth C. Stahl ◽  
Connor A. Tsuchida ◽  
Enrique Lin-Shiao ◽  
C. Kimberly Tsui ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Rna Extraction ◽  
Detection Sensitivity ◽  
Nasopharyngeal Swab ◽  
Infection Prevalence ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Rapid Pcr ◽  
Large Populations ◽  
Asymptomatic Individuals

Saliva is an attractive specimen type for asymptomatic surveillance of COVID-19 in large populations due to its ease of collection and its demonstrated utility for detecting RNA from SARS-CoV-2. Multiple saliva-based viral detection protocols use a direct-to-RT-qPCR approach that eliminates nucleic acid extraction but can reduce viral RNA detection sensitivity. To improve test sensitivity while maintaining speed, we developed a robotic nucleic acid extraction method for detecting SARS-CoV-2 RNA in saliva samples with high throughput. Using this assay, the Free Asymptomatic Saliva Testing (IGI-FAST) research study on the UC Berkeley campus conducted 11,971 tests on supervised self-collected saliva samples and identified rare positive specimens containing SARS-CoV-2 RNA during a time of low infection prevalence. In an attempt to increase testing capacity, we further adapted our robotic extraction assay to process pooled saliva samples. We also benchmarked our assay against the gold standard, nasopharyngeal swab specimens. Finally, we designed and validated a RT-qPCR test suitable for saliva self-collection. These results establish a robotic extraction-based procedure for rapid PCR-based saliva testing that is suitable for samples from both symptomatic and asymptomatic individuals.

Effects of diverse materials-based methods on DNA extraction for Clostridium difficle from stool samples

2019 ◽  
Vol 9 (5) ◽  
pp. 509-516 ◽  
Author(s):  
Ziqi Xiao ◽  
Gaojian Yang ◽  
Deng Yan ◽  
Song Li ◽  
Zhu Chen ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Dna Extraction ◽  
Magnetic Beads ◽  
Diagnostic Technique ◽  
Proteinase K ◽  
Molecular Diagnostic ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Spin Column ◽  
Stool Samples

Nosocomial infections, including Clostridium difficile infection (CDI), and their fatality rates have increased in the past few decades. Despite emerging molecular diagnostic technologies with rapid, accurate outcomes, nucleic acid extraction from stool samples remains the first limiting step before downstream applications. Commercial nucleic acid extraction kits greatly decrease labor and time requirements, and also provide nucleic acid preparations with higher quality and purity for enzyme digestion analysis or genotyping. The magnetic bead based technique is a novel method compared with the conventional spin-column method, and currently has widespread use in nucleic acid extraction. We evaluated five DNA extraction kits with magnetic beads using materials with various properties (particle size, concentration of magnetic beads, grinding beads) and reagents (proteinase K, lysozyme, isopropanol, and absolute ethanol) to determine the cost, hands-on time, number of essential operations, and quality and purity of the DNA preparations, compared with those obtained using the QIAamp Fast DNA Stool Mini Kit. The six DNA extraction kits yielded A260/280 ratios ranging from 0.85 to 1.9 (average 1.57), and concentrations from 3.70 to 108.09 ng/μL (average 34.64 ng/μL). All the DNA samples had acceptable downstream application effects, except for those obtained using the TIANGEN Magnetic Soil and Stool DNA Kit. However, gel electrophoresis analysis of the DNA samples resulted in a light strip on the gel, indicating that the proteinaceous contaminant may not have been removed completely. A rapid and accurate molecular diagnostic technique could allow for more suitable treatment and prognosis outcomes for inpatients, depending, in large part, on the quality and purity of DNA preparations, which are frequently neglected. Our study focused on the quality of commercial kits with a primary focus on the treatment of stool samples and molecular diagnostic applications.

scholarly journals Robotic RNA extraction for SARS-CoV-2 surveillance using saliva samples

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0255690
Author(s):  
Jennifer R. Hamilton ◽  
Elizabeth C. Stahl ◽  
Connor A. Tsuchida ◽  
Enrique Lin-Shiao ◽  
C. Kimberly Tsui ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Rna Extraction ◽  
Detection Sensitivity ◽  
Nasopharyngeal Swab ◽  
Infection Prevalence ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Rapid Pcr ◽  
Large Populations ◽  
Asymptomatic Individuals

Saliva is an attractive specimen type for asymptomatic surveillance of COVID-19 in large populations due to its ease of collection and its demonstrated utility for detecting RNA from SARS-CoV-2. Multiple saliva-based viral detection protocols use a direct-to-RT-qPCR approach that eliminates nucleic acid extraction but can reduce viral RNA detection sensitivity. To improve test sensitivity while maintaining speed, we developed a robotic nucleic acid extraction method for detecting SARS-CoV-2 RNA in saliva samples with high throughput. Using this assay, the Free Asymptomatic Saliva Testing (IGI FAST) research study on the UC Berkeley campus conducted 11,971 tests on supervised self-collected saliva samples and identified rare positive specimens containing SARS-CoV-2 RNA during a time of low infection prevalence. In an attempt to increase testing capacity, we further adapted our robotic extraction assay to process pooled saliva samples. We also benchmarked our assay against nasopharyngeal swab specimens and found saliva methods require further optimization to match this gold standard. Finally, we designed and validated a RT-qPCR test suitable for saliva self-collection. These results establish a robotic extraction-based procedure for rapid PCR-based saliva testing that is suitable for samples from both symptomatic and asymptomatic individuals.

Research note: Rapid isolation of total RNA and genomic DNA from Hakea actities

2002 ◽  
Vol 29 (8) ◽  
pp. 1015 ◽  
Author(s):  
Michael G. Mason ◽  
Susanne Schmidt
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Genomic Dna ◽  
Rna Extraction ◽  
Nutrient Concentrations ◽  
Cluster Roots ◽  
Acid Extraction ◽  
Native Plant ◽  
Nucleic Acid Extraction ◽  
Total Rna

Tissues of the Australian native plant species Hakea actities (Proteaceae) contain numerous metabolites and structural compounds that hinder the isolation of nucleic acids. Separate RNA and genomic DNA extraction procedures were developed to isolate high quality nucleic acids from H. actities. Total RNA was extracted from leaves, roots and cluster roots of H. actities grown in low nutrient levels. Cluster root formation in H. actities only occurs when the plants are grown in low nutrient concentrations. However, under these conditions, nucleic acid extraction becomes increasingly difficult. The new procedures are faster than many of the published nucleic acid extraction protocols, and avoid the use of hazardous chemicals. The RNA extraction method was used successfully on another Australian species and a crop species, suggesting that the procedure is useful for molecular studies of a broad range of plants.

scholarly journals Utility of Nucleic Acid Extraction Free COVID-19 Real Time PCR Protocol in Resource Limited Setting: A Pilot Study

2021 ◽  
Author(s):  
Santosh Karade ◽  
Pratik Thosani ◽  
Prashant Patil ◽  
Kavita Bala Anand ◽  
Sourav Sen ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Pilot Study ◽  
Real Time ◽  
Gold Standard ◽  
Rna Extraction ◽  
Molecular Diagnostic ◽  
Acid Extraction ◽  
Rt Pcr ◽  
Nucleic Acid Extraction ◽  
Resource Limited

Introduction: Coronavirus Disease (COVID-19), a respiratory infection, caused by severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2), was first identified in Wuhan, Hubei province, China in December 2019. Alarming increase in the number of cases has put tremendous pressure on existing health resources. Real Time Reverse Transcriptase Polymerase Chain Reaction (RT-PCR), a molecular diagnostic method, is considered gold standard for diagnosis of SARS-CoV-2 infection. It involves RNA extraction as the preliminary step. Innovations to cut down cost and time involved in SARS-CoV-2 testing are need of hour. Aim: The aim of this study was to assess the feasibility of Nucleic Acid Extraction Free (NEF) protocol for COVID-19 diagnosis in resource limited settings. Materials and Methods: In this pilot study a panel of 148 Nasopharyngeal (NP) samples was subjected to the novel NEF RT-PCR protocol and results were compared to gold standard RT-PCR on RNA extracted from NP specimen. The cycle threshold value for each target was tabulated in MS Excel Spreadsheet and data analysis was performed using Statistical Package for Social Sciences (SPSS) software version 15.0. Results: Out of 148 collected samples, 120 showed amplification of E and RdRp targets by RNA extraction-based RT-PCR. Overall sensitivity and specificity observed for NEF protocol was 43.94% and 96.42%, respectively. Conclusion: Further refinement in the protocol would be required to improve the sensitivity of NEF protocol and widespread use in laboratories.

scholarly journals An Automated and Miniaturized Rotating-Disk Device for Rapid Nucleic Acid Extraction

Micromachines ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 204 ◽  
Author(s):  
Rui Tong ◽  
Lijuan Zhang ◽  
Chuandeng Hu ◽  
Xuee Chen ◽  
Qi Song ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Sample Preparation ◽  
Magnetic Beads ◽  
Rotating Disk ◽  
Molecular Diagnostic ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Time Saving ◽  
Central Controller ◽  
Acid Sample

The result of molecular diagnostic and detection greatly dependent on the quality and integrity of the isolated nucleic acid. In this work, we developed an automated miniaturized nucleic acid extraction device based on magnetic beads method, consisting of four components including a sample processing disc and its associated rotary power output mechanism, a pipetting module, a magnet module and an external central controller to enable a customizable and automated robust nucleic acid sample preparation. The extracted nucleic acid using 293T cells were verified using real-time polymerase chain reaction (PCR) and the data implies a comparable efficiency to a manual process, with the advantages of performing a flexible, time-saving (~10 min), and simple nucleic acid sample preparation.

scholarly journals Correction: A lab-on-a-chip for preconcentration of bacteria and nucleic acid extraction

RSC Advances ◽  
2018 ◽  
Vol 8 (47) ◽  
pp. 26817-26817
Author(s):  
M. Hügle ◽  
G. Dame ◽  
O. Behrmann ◽  
R. Rietzel ◽  
D. Karthe ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Lab On A Chip ◽  
Acid Extraction ◽  
Nucleic Acid Extraction

Correction for ‘A lab-on-a-chip for preconcentration of bacteria and nucleic acid extraction’ by M. Hügle et al., RSC Adv., 2018, 8, 20124–20130.

Sign in / Sign up

Export Citation Format

Share Document