CRISPR/Cas9 analysis

Set your own schedule for CRISPR/Cas9 gene editing with innovative, intuitive analytical solutions. 

Unleash the potential of your Cas9 messenger RNA (mRNA), single guide RNA (sgRNA) and Cas9 proteins by understanding quality, purity and safety and assessing on/off target effects.

Overview

The development of novel gene-editing approaches goes beyond the treatment of diseases or their symptoms. However, analytical solutions for CRISPR/Cas9 analysis need to keep up with the demands of these new approa

Leverage highly sensitive techniques for characterizing large synthetic guide RNAs and in vitro transcribed RNA products, and understand low-abundance post-translational modifications (PTMs) of Cas9 proteins and CRISPR/Cas9 effects on the proteome. With dedicated analytical solutions, personalized medicine is only a step away.

Size and integrity of sgRNA and mRNA

Workflow

The latest gene-editing approaches require overcoming new analytical challenges. Confirmation of the size, integrity and purity of large synthetic guiding RNAs (sgRNA and pegRNA) and confident analysis of Cas9 mRNA require the highest data quality over a wide size range. 

Move past analytical challenges with high separation quality, sensitivity and superior reproducibility. Reclaim your time with intuitive software and kit-based workflows that are compatible with compliant data systems.

  • Simultaneous, high-resolution measurement of sgRNA and Cas9 mRNA over a wide size range
  • High repeatability and minimized secondary structure formation with stable temperature control of the capillary and cartridge
  • High-sensitivity detection of analytes and low-abundance impurities
  • Easy assay transfer to regulated environments due to compatibility with the Empower Chromatography Data System (CDS)

Size and integrity of sgRNA and mRNA

Suited for:

  • High-quality resolution and sizing of RNAs and impurities
  • Medium to large sample batches
BioPhase 8800 system

Purpose-built for the biopharmaceutical scientist for efficiency and quality, enabling multiple samples to be run in parallel.

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RNA 9000 Purity & Integrity kit

Purity and integrity analysis of RNA therapeutics, vaccines and single stranded oligos.

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BioPhase BFS capillary cartridge

Pre-assembled bare-fused silica 8-capillary cartridge for the BioPhase 8800 system.

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Size and integrity of sgRNA and mRNA

Suited for:

  • High-quality resolution and sizing of RNAs and impurities
  • Smaller sample sets
PA 800 Plus system

Characterize therapeutic molecules with confidence with the kit-based system.

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RNA 9000 Purity & Integrity kit

Purity and integrity analysis of RNA therapeutics, vaccines and single stranded oligos.

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BFS capillary cartridge for the PA 800 Plus system

Pre-assembled bare-fused silica capillary cartridge for the PA 800 Plus system.

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Cas9 protein characterization with peptide mapping

Workflow

A deeper understanding of gene-editing mechanisms paves the way for higher target specificity and minimized side effects. Engineering Cas9 proteins with improved binding and stability can be one approach. However, ensuring the correct function requires comprehensive characterization of the Cas9 proteins.

Obtain high-quality, comprehensive sequence and fragment coverage with advanced MS/MS sensitivity. Explore how to elucidate the position and identity of amino acid substitutions/isomers and other challenging PTMs with confidence.

  • High sequence coverage and comprehensive PTM determination with high-quality MS/MS collision-induced dissociation (CID)
  • Identification of low-abundance amino acid mutations using the Zeno trap
  • Determination of identity and position of amino acid isomers and other challenging PTMs with electron activated dissociation (EAD)
  • High fragment coverage for long, difficult-to-fragment peptides using Zeno EAD
  • High fragment coverage for long, difficult-to-fragment peptides using Zeno EAD

Cas9 protein characterization with peptide mapping

Suited for:

  • Differentiation of amino acid isomers and identification of challenging PTMs
  • Most sensitive detection of low abundance PTMs and impurities
  • Meeting flexibility needs to perform a range of additional workflows
ZenoTOF 7600 system

A high-resolution mass spectrometry solution that combines powerful MS/MS sensitivity, fragmentation technology and a step-change in data independent acquisition.

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Biologics Explorer software

Be empowered with highly accurate and informative workflows for fully characterizing protein therapeutics and viral vector proteins.

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SCIEX OS software

Unleash the analytical power of the next-generation software platform for data acquisition and processing.

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Cas9 protein characterization with peptide mapping

Suited for:

  • Straightforward confirmation of sequence and identification of PTMs
  • Robust, analytical flow setup
ExionLC AE system

Reproducibility, reliability and carryover performance to match your quantitative workflows. Dependability you can count on, from injection to injection and batch after batch.

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X500B QTOF system

A purpose-built QTOF system, designed specifically to accelerate everyday biologics characterization.

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Biologics Explorer software

Be empowered with highly accurate and informative workflows for fully characterizing protein therapeutics and viral vector proteins.

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SCIEX OS software

Unleash the analytical power of the next-generation software platform for data acquisition and processing.

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pegRNA analysis with CGE

Workflow

More sophisticated, chemically synthesized gRNAs are in development with the goal of increasing efficiency and specificity of CRISPR/Cas9 gene editing. One of these newly emerging classes is pegRNA with sizes ranging from around 120–250 nucleotides (nt). 

The length and associated risk of secondary structure formation, however, pose challenges for the analytical assessment of its purity. 

Move beyond these boundaries of CRISPR/Cas9 analysis and confirm size and purity for large pegRNA with confidence. Rely on high resolving power and repeatability to separate your products from impurities with similar properties.

  • Reliable purity assessment through high-resolution separation of full-length pegRNAs from their impurities
  • Control of secondary structures of chemically synthesized pegRNAs (>100 nt)
  • Excellent repeatability with accurate and stable temperature control
  • Easy assay transfer to regulated environments due to compatibility with the Empower CDS

Solution

pegRNA analysis with CGE

PA 800 Plus system

Characterize therapeutic molecules with confidence with the kit-based system.

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ssDNA 100-R kit

Kit with coated capillaries, gel, and standards to analyze single-stranded nucleic acids on the PA 800 Plus system.

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sgRNA intact mass analysis

Workflow

Oligonucleotides—such as guide RNAs, sgRNAs and pegRNAs—are prone to a high number of impurities due to their stepwise chemical synthesis. Obtaining molecular weight information to confirm the identity of the main product and quantitation of related impurities is key for quality assessment prior to performing lengthy cell-based assays. 

Take control of the purity of your products with high-quality, accurate mass data derived from intuitive solutions. Enable your team to gain key insights that are relevant for ensuring safety and efficacy.

  • Excellent spectra quality with superior ionization and declustering of salt adducts using the Turbo V ion source
  • A short learning curve with intuitive SCIEX OS software for acquisition and processing
  • Additional quantitation and deconvolution options with SCIEX OS software

sgRNA intact mass analysis

Suited for:

  • Straightforward molecular weight determination of sgRNAs and impurities
  • Robust, analytical flow setup
ExionLC AE system

Reproducibility, reliability and carryover performance to match your quantitative workflows. Dependability you can count on, from injection to injection and batch after batch.

Learn more
X500B QTOF system

A purpose-built QTOF system, designed specifically to accelerate everyday biologics characterization.

Learn more
SCIEX OS software

Unleash the analytical power of the next-generation software platform for data acquisition and processing.

Learn more

sgRNA intact mass analysis

Suited for:

  • Straightforward molecular weight determination of sgRNAs and impurities
  • Detection of low abundance impurities with superior linear dynamic range (LDR)
ExionLC AE system

Reproducibility, reliability and carryover performance to match your quantitative workflows. Dependability you can count on, from injection to injection and batch after batch.

Learn more
ZenoTOF 7600 system

A high-resolution mass spectrometry solution that combines powerful MS/MS sensitivity, fragmentation technology and a step-change in data independent acquisition.

Learn more
SCIEX OS software

Unleash the analytical power of the next-generation software platform for data acquisition and processing.

Learn more

On/off target effects

Workflow

Despite efforts to increase the specificity and efficiency of CRISPR/Cas9 gene editing, unexpected effects on the proteome can occur. Biochemistry-based assays are blind towards such changes, or they only provide limited information on affected proteins. 

Give your team the advantage of comprehensive unbiased characterization of proteome changes to streamline the development of gene-editing tools. Reach new milestones with the dynamic range, sensitivity and reproducibility needed to better understand on- and off-target effects of gene therapies while enabling simultaneous quantitation in samples with limited amounts.

  • A deeper understanding of CRISPR/Cas9 effects on the proteome with high MS/MS spectral quality
  • Confident identification of even low-abundance species with the Zeno trap
  • Identification of off-target effects for comprehensive characterization
  • A short learning curve with intuitive SCIEX OS software for acquisition

Solution

On/off target effects

M5 MicroLC system

Enjoy the perfect balance of sensitivity and robustness with a feature-rich microflow LC solution built for small and large molecule quantitation and characterization.

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ZenoTOF 7600 system

A high-resolution mass spectrometry solution that combines powerful MS/MS sensitivity, fragmentation technology and a step-change in data independent acquisition.

Learn more
SCIEX OS software

Unleash the analytical power of the next-generation software platform for data acquisition and processing.

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