Benchtop PAGE mRNA QC is the New LC/MS

Tired of wait times and costs associated with outsourcing your mRNA for liquid chromatography/mass spectrometry (LC/MS) 5’ capping efficiency and 3’ tail length analyses? Now you can easily perform precise quantitative mRNA 5’ capping efficiency and 3’ poly(A) tail length assessments using standard lab equipment with the EZ-QC™ mRNA Assay Kits.

Discover quantitative fluorescence-based benchtop polyacrylamide gel electrophoresis (PAGE) assays for accurate and cost-effective QC of mRNA 5’ capping and 3’ poly(A) tail length analysis in a single day. Accelerate your mRNA research with the EZ-QC™ Kits for a fraction of the cost of LC/MS.

Benefits:

Fast benchtop 5’ capping and 3’ tailing QC analyses
Low-input mRNA (picomoles, not micromoles!)
Uses common polyacrylamide gel electrophoresis (PAGE) equipment
Cost-effective – stretch your budget for more experiments

How Our EZ-QC™ mRNA Assays Work

EZ-QC™ mRNA Capping Efficiency Assay Kits
Quantitate total capping efficiency (% capped vs uncapped RNA) of synthesized mRNA

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How they work:

A chimeric RNA-DNA-RNA Targeting Oligonucleotide hybridizes to the 5′ end of synthesized mRNA.
- The EZ-QC™ XBG mRNA Capping Efficiency Assay Kit supplies an XBG 5′ UTR Targeting Oligo for mRNA with an XBG 5′ UTR.
- The EZ-QC™ mRNA Capping Efficiency Assay Kit requires a user-provided Targeting Oligo for mRNA with any known 5′ UTR sequence.
The hybridization complex undergoes RNase H cleavage, releasing capped and uncapped 5′-end fragments.
Released capped and uncapped 5′-end fragments are resolved using PAGE and quantitated by fluorescence-based gel band analysis.

EZ-QC™ mRNA Cap 1 Efficiency Assay Kit
Quantitates the percentage of Cap 1 vs Cap 0 caps of synthesized mRNA

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How it works:

5′ ends of a synthesized mRNA sample are labeled fluorescently with cyanine5 hydrazide (Cy5).
Hydrolysis of the Cy5-labeled mRNA mixture releases Cy5-labeled Cap 1 and Cap 0 caps.
Size resolution by PAGE and fluorescence-based gel imaging is used to determine percentage of Cap 1 vs Cap 0.
Note: The EZ-QC™ mRNA Cap 1 Efficiency Assay labeling chemistry is not compatible with cap structures that contain a 3′-O-methyl group on the capping G nucleotide such as Anti Reverse Cap Analog (ARCA) or some versions of GpppAG cap analogs.

EZ-QC™ mRNA Poly(A) Tail Length Assay Kit
Quantitates poly(A) tail length of synthesized mRNA

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How it works:

RNase A is used to digest the synthesized mRNA, leaving only intact Poly(A) tails.
Poly(A) tails are stained with fluorescent dyes (e.g., SYBR Gold Nucleic Acid Gel Stain (Invitrogen) + provided poly(A) fluorescence enhancer).
Poly(A) tail lengths (from 20 to >300 A’s) are resolved using PAGE with our proprietary Poly(A) 20-mer Ladder and quantitated by fluorescence-based gel band analysis.

Webinar

Exploring mRNA quality assessment using electrophoretic separation methods.

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In this webinar we present new accurate same-day methods we have developed for measuring mRNA characteristics using simple benchtop electrophoretic separation formats. Join this webinar to learn how to shorten your workflow time and reduce costs while obtaining precise 5’ capping efficiency and 3’ poly(A) tail length data.

Gain insights into the importance of 5’ capping and 3’ poly(A) tail length and current QC methods used to assess these characteristics.
Identify the challenges of the current mRNA QC methods.
Learn about three new QC assays to evaluate 5’ capping and 3’ poly(A) tailing of synthesized mRNA for stability and efficient translation.

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Presenter:

Chateen Krueger
Senior R&D Scientist
CELLSCRIPT™

Host:

Roisin McGuigan
Editor
BioInsights

Scientific Poster Presentation

mRNA Developmental Analytics and Quality Control Summit
Boston, MA Feb 25-27, 2025

Download the poster that Kari Weber, PhD, CELLSCRIPT™ Director, Assay and Process Development, presented at the 2025 mRNA Developmental Analytics and Quality Control Summit in Boston on February 27 entitled “Assessing mRNA Capping Efficiency and Poly(A) Tail Length by Simple Electrophoretic Separation”.

Download the Poster