MazF-qPCR m6A Detection Service: Single-Nucleotide Precision Without Antibodies
Validate and quantify m6A modifications at specific ACA motifs with unmatched clarity—ideal for researchers who need site-specific insights beyond broad m6A peaks.
Key Highlights:
Single-nucleotide resolution – quantify methylation ratios at individual m6ACA sites.
When studying RNA modifications, researchers often face the same problem: resolution.
Conventional m6A-seq or MeRIP-seq highlights regions of enrichment, but these peaks usually span hundreds of nucleotides. For functional studies, this is not enough—you need to know which exact base is methylated.
Antibody-based assays add another layer of complexity. Variability in antibody quality can generate background noise, batch effects, and uncertain reproducibility.
For validation experiments, researchers need a direct, quantitative, and site-specific tool that is both efficient and reliable.
MazF-qPCR meets this exact demand.
By leveraging the natural property of the MazF endonuclease—its ability to cut only at unmodified ACA motifs—this method distinguishes between methylated and unmethylated sites with single-nucleotide precision. The result is a quantitative methylation ratio at the locus you care about, achieved through a streamlined qPCR workflow.
For researchers, this means:
A clear answer to whether your candidate site is methylated.
Direct numbers (% methylation) instead of indirect enrichment signals.
A validation method that integrates seamlessly after transcriptome-wide profiling.
How MazF-qPCR Works: Technical Insight
At the core of this service lies the MazF endonuclease, a bacterial RNA-cleaving enzyme that recognizes the trinucleotide motif ACA. Its unique property is that methylation at the N6 position of adenine (m6A) blocks the cleavage reaction.
Here is how the workflow unfolds:
1. Identify candidate ACA sites – based on prior prediction or high-throughput mapping (e.g., MeRIP-seq).
2. Split your RNA sample – one aliquot undergoes MazF treatment, the other remains untreated as a control.
3. Enzyme action – MazF cleaves RNA at unmethylated ACA sites, while m6ACA motifs remain intact.
4. Reverse transcription to cDNA – both treated and untreated RNAs are converted to cDNA.
5. qPCR quantification – specific primers amplify the target locus. A methylated site produces similar Ct values in both reactions, while an unmethylated site shows delayed amplification after MazF digestion.
6. Data interpretation – ΔCt between treated and untreated samples is converted into a methylation percentage, giving a direct numerical value for each site.
Schematic diagram of the MazF-qPCR principle
Key advantage: Unlike antibody-based assays that provide "peak-level" enrichment, MazF-qPCR generates single-nucleotide resolution and quantitative output at the exact ACA motif.
This approach is especially useful when you need to:
Verify a specific candidate m6A site after discovery studies.
Track methylation changes under different experimental conditions.
Compare methylation ratios across RNA species such as mRNA, lncRNA, and circRNA.
Advantages
What Makes CD Genomics' MazF-qPCR Service Unique
While the MazF principle is published and widely recognized, turning it into a reliable, reproducible service requires much more than enzyme digestion and qPCR. At CD Genomics, we refine every step to make sure researchers receive trustworthy data that can be used directly for downstream analysis or publication.
1. True Single-Site Resolution
We design and validate primers that specifically target your candidate ACA motifs. This ensures amplification comes only from the intended site, eliminating off-target amplification and false positives.
2. Antibody-Free, Bias-Free
Because the method relies on enzymatic cleavage rather than antibodies, it avoids common issues such as cross-reactivity and batch-to-batch variability. The result is a clean signal that reflects true methylation status.
3. Optimized for Multiple RNA Types
mRNA and lncRNA: direct total RNA workflow.
circRNA: integration of an RNase R digestion step ensures that only circular transcripts are retained before MazF treatment and qPCR.
4. Low Input, High Sensitivity
Even with limited RNA material, the assay produces robust results. This makes it especially useful for precious or difficult-to-obtain samples.
5. Seamless Data Delivery
We don't just provide raw Ct values—we calculate methylation ratios, provide visual data summaries, and supply all necessary files so you can integrate results into your ongoing research pipeline.
Service Workflow
Service Workflow – From RNA to Quantitative Result
Our MazF-qPCR service follows a clear and reliable process, ensuring accurate site-specific results:
1. Consultation & Target Selection – define candidate ACA motifs from your predictions or sequencing data.
2. RNA Quality Control – check concentration, purity, and integrity.
3. Sample Split – one aliquot treated with MazF, the other kept as control.
4. Reverse Transcription – both fractions converted to cDNA.
6. Data Interpretation – ΔCt converted into methylation percentage, delivered in a clear report with raw data.
Bioinformatics
Bioinformatics Analysis – From Ct Values to Biological Insight
Beyond raw qPCR output, we provide structured data analysis to help you interpret site-specific methylation with confidence:
ΔCt normalization between treated and untreated samples
Methylation percentage calculation for each targeted ACA site
Replicate consistency checks and error assessment
Optional integration with RNA-seq or MeRIP-seq datasets for biological context
Visual summaries such as bar plots or ratio tables for quick interpretation
Our goal is to give you numbers you can trust and figures you can use directly in your research or publications.
Deliverables
Deliverables – What You Receive
Ct Value Tables and Amplification Curves
Raw qPCR output from +MazF and –MazF reactions, including amplification plots for transparency and validation.
Methylation Ratio Report
Calculated methylation percentages at each targeted ACA site, presented in clear tables with replicate consistency checks.
Assay Quality and Validation Notes
Key QC metrics and assay performance summaries to confirm data reliability.
Optional Data Interpretation Outputs
Visual representations such as bar plots or comparative charts, and integration notes with sequencing datasets if requested.
Processed Data Files
Accessible files containing raw Ct values and processed results for archival and further analysis.
Sample Requirements
Sample Requirements
To ensure reliable and reproducible MazF-qPCR results, please prepare your samples according to the following guidelines:
Sample Type
Minimum Quantity
Concentration
Quality Criteria
Storage & Shipping
mRNA / lncRNA
≥ 2 µg total RNA
≥ 50 ng/µL
A260/A280: 1.9–2.2; DNA-free; intact RNA
Frozen in RNase-free vials, shipped on dry ice or liquid N₂
circRNA
≥ 10 µg total RNA
≥ 50 ng/µL
Same as above; RNase R digestion recommended
Tissues or Cells
Equivalent to required RNA yield
—
Fresh or properly preserved for extraction
Note: Please avoid repeated freeze–thaw cycles and ensure samples are free from contaminants that may inhibit enzymatic reactions.
Applications
Ideal Applications
MazF-qPCR is designed for researchers who require site-specific, quantitative validation of m6A modifications. Typical use cases include:
Validation of candidate sites
Confirm whether specific ACA motifs identified by MeRIP-seq, Nanopore sequencing, or predictive algorithms are truly methylated.
Functional epitranscriptomic studies
Quantify methylation changes at regulatory sites to link m6A status with RNA stability, splicing, translation, or cellular response.
Comparative methylation analysis
Assess differences in methylation ratios across conditions such as developmental stages, stress responses, or experimental treatments.
CircRNA modification profiling
Determine the presence and extent of m6A modifications in circular RNAs after RNase R enrichment.
Note: For broader profiling across hundreds of sites, consider high-throughput alternatives like MazF-based arrays or GLORI-seq.
Choosing the Right Tool for Your m6A Study
When deciding how to study m6A modifications, researchers often face a choice between targeted validation and transcriptome-wide profiling. The table below highlights the key differences between MazF-qPCR and other commonly used approaches:
In summary: MazF-qPCR is the most straightforward choice for site-specific validation when your research focus is on one or a few candidate sites. For transcriptome-wide discovery or absolute stoichiometry, sequencing-based alternatives may be more suitable.
FAQ
Your Questions on MazF-qPCR m6A Detection, Answered
Schematic diagram of the MazF-qPCR principle 
