AutoMate Express Nucleic Acid Extraction SystemIntroductionBiopharmaceuticals produced in live-cell systems such as CHO cells need to be tested for contaminants and impurities that originate from the process or from the host cell line. Testing for bacterial and viral contaminants such as mycoplasmas, mouse minute virus (MMV), and vesiviruses is performed during the upstream cell culture process, whereas host cell–derived impurities such as residual DNA need to be tested for as part of downstream process characterization. The availability of rapid and accurate testing methods is key to enabling in-process testing during manufacturing, and the results from those tests can then be used to make fact-based, go or no-go forward processing decisions.

The Applied Biosystems™ AutoMate Express™ Nucleic Acid Extraction System is an easy-to-use benchtop instrument that enables hands-free automation of the nucleic acid extraction process for contaminant and impurity testing. The instrument uses the established Applied Biosystems™ PrepSEQ™ nucleic acid extraction chemistry for quantitative recovery of DNA and RNA from diverse samples types, including cell culture, raw material (i.e., serum), and in-process downstream purification samples such as column purification or bulk drug substance (BDS) samples.

AutoMate Express Nucleic Acid Extraction System• Time-saving, cost-effective DNA extraction for

mycoplasma, MMV, vesivirus, and residual DNA quantitation

• Quantitative and reproducible recovery of DNA from complex samples

• Out-of-the-box automation with prefilled PrepSEQ™ express cartridges and ready-to-run protocols

• Closed system minimizes the risk of contamination

• Ideal for in-process testing of contaminant and impurities

APPLICATION NOTE Automate Express Nucleic Acid Extraction System

Three-in-one extraction of cell culture contaminantsThe AutoMate Express™ platform can be used to perform nucleic acid extraction of the common contaminants for mammalian cell culture manufacturing, i.e., mycoplasmas, MMV, and vesiviruses. Flexible protocols are available to isolate DNA and RNA from a single organism, or a 3-in-1

Figure 1. Detection of (A) mycoplasma DNA and (B) MMV DNA spiked into PBS (blue), fetal calf serum (black), CHO medium (gray), and CHO–conditioned medium (orange). For each matrix, a recovery control (RC) was used to assess extraction effi ciency.

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Figure 2. Detection of DNA from (A) M. arginini and (B) MMV spiked into PBS (blue), fetal calf serum (black), CHO medium (gray), and CHO– conditioned medium (orange). For each plate, control reactions were run with 500, 1,000, and 2,000 copies of the mycoplasma discriminatory positive control or MMV positive control in the real-time PCR assay (green).

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surveillance panel protocol can simultaneously extract mycoplasma, MMV, and vesivirus nucleic acid from a single sample. Figures 1 and 2 demonstrate recovery of DNA from spikes of DNA, or from cells or viruses of mycoplasmas and MMV into typical cell culture matrices, extracted using the AutoMate Express™ system.

Quantitative recovery for residual DNA applicationsThe AutoMate Express system is also designed for highly efficient recovery of host cell residual DNA from complex samples typically recovered during biopharmaceutical purification processes. When used together with the AutoMate Express system, the Applied Biosystems™

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M4 Protein A 100 mM sodium citrate (pH 3.0) 10 mg/mL

M5 Purified drug substance 3% mannitol, 2% sucrose,10 mM L-arginine, 0.01% Tween™ 20

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Figure 3. Recovery from 10 pg of (A) CHO genomic DNA and (B) Vero genomic DNA spiked into five different matrices. Panel (C) shows the composition of each of the five matrices.

PrepSEQ™ Express kits enable quantitative and consistent recovery of DNA from challenging matrices, including samples that have high protein concentration, low pH, or high salt. Figure 3 shows recovery of CHO and Vero cell line–derived genomic DNA spiked into five diverse matrices. The data demonstrate the quantitative recovery and reproducibility of the system.

Closed system with walk-away automation The AutoMate Express platform automatically performs all steps for effi cient nucleic acid extraction from contaminants and impurities in a closed system. The system uses PrepSEQ Express kits that contain sealed cartridges with extraction reagents, and plastics, including tips, and sample, lysis, and elution tubes. The workfl ow (Figure 4)

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For Research Use Only. Not for use in diagnostic procedures. © 2016 Thermo Fisher Scientifi c Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientifi c and its subsidiaries unless otherwise specifi ed. TWEEN is a trademark of Croda International PLC. COL21130 0516

has been designed for a completely hands-free operation enabling reproducible extraction effi ciencies and reduced time-to-results. The small footprint of the instrument enables easy integration into an existing lab setup. Up to 13 samples can be processed in under an hour, and the eluates from the extraction can be used directly in real-time PCR-Seq analytics assays.

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Centrifuge sample tubes to pellet cells or debris

Load tubes and cartridges ino the instrument

Start the protocol Use the eluate for real-time PCR

Figure 4. One-hour workfl ow for the AutoMate Express system.

Ordering information

Product Cat. No.

AutoMate Express Nucleic Acid Extraction System 4467754

PrepSEQ Express Nucleic Acid Extraction Kit 4466351

AutoMate Express IQOQ, SVC 4470470

Mycoplasma Detection Assay, with discriminatory positive control (does not include protocol and quick reference card) 4460623

Mycoplasma Detection Assay, with discriminatory positive control (includes protocol and quick reference card) 4460625

resDNASEQ CHO Quantitative DNA kit (does not include protocol and quick reference card) 4402085

resDNASEQ CHO Quantitative DNA kit (includes protocol and quick reference card) 4442731

resDNASEQ E. coli Quantitative DNA kit (does not include protocol and quick reference card) 4458435

resDNASEQ NS0 Quantitative DNA kit (does not include protocol and quick reference card) 4458441

resDNASEQ Vero Quantitative DNA kit (does not include protocol and quick reference card) 4458444

resDNASEQ Pichia pastoris Quantitative DNA kit (does not include protocol and quick reference card) 4464336

resDNASEQ MDCK Quantitative DNA kit (does not include protocol and quick reference card) 4464335