m1A-Quant-seq passes an engineered reverse transcriptase across N1-methyladenosine in tRNA, so each modified position emits a discrete mutation signature. That signature both locates the site and reports its fraction, at single-base resolution and without disturbing the surrounding sequence.
Per-site m1A values inside the tRNA transcriptome
N1-methyladenosine organises the folded tRNA architecture and stabilises codon–anticodon pairing. It sits at conserved positions such as 9, 14 and 58, where it tunes aminoacylation and decoding fidelity, so the useful measurement is the modification level at a named tRNA position rather than a bulk signal.
Arraystar runs m1A-Quant-seq as a complete tRNA project: sample QC, tRNA enrichment, reverse transcription, library preparation, sequencing and tRNA-aware bioinformatics. You receive per-site m1A values with absolute stoichiometry, so the analysis can go straight to the biology instead of stopping at assay assembly.
m1A-Quant-seq is an antibody-free, base-resolution method for N1-methyladenosine on tRNA. An engineered reverse transcriptase reads through m1A and records a reproducible mutation signature at that position; the mutation rate at the site equals the m1A fraction, giving absolute stoichiometry.
Standard tRNA m1A project — custom designs and add-on analyses available on request
| Service Name | Price |
|---|---|
| Single-Nucleotide tRNA m1A Modification Seq(m1A-Quant-seq) |
Why m1A-Quant-seq is used for tRNA
The engineered enzyme keeps moving through modified, tightly folded tRNA regions instead of stalling before the mark.
The proportion of mutation signal at a position converts directly into the m1A fraction, which supports quantitative comparison across samples.
No enrichment step means no pull-down bias and no cross-reactivity inside compact tRNA.
Every site is mapped within a mature tRNA with anticodon, isodecoder and isotype assignment plus structural-domain context.
The chemistry tolerates small inputs, which matters when tRNA from primary cells or clinical material is scarce.
A demethylase-treated aliquot provides the baseline against which native signal is scored.
m1A at conserved positions and how it is read
The N1-methyladenosine mark at conserved tRNA positions stabilises the L-shaped fold and fine-tunes aminoacylation and decoding fidelity. Losing or gaining those sites disturbs translation and has been linked to developmental defects and cancer phenotypes, which is why the level at each position is worth measuring (1,2).
Antibody-capture strategies give coarse resolution and struggle with the dense structure of tRNA. m1A-Quant-seq instead relies on reverse transcriptase processivity: as the enzyme crosses the modified base it leaves a reproducible mismatch, and the mutation proportion at that position reports the modification level (1).
From total RNA to per-site m1A stoichiometry
Total RNA is cleared of ribosomal and messenger transcripts, sized into uniform fragments and split into two arms. One arm is demethylated with AlkB as a baseline and the other is left native; both are copied by the engineered enzyme into libraries, sequenced and mapped so that m1A is scored and quantified.
Bioinformatics for m1A-Quant-seq
The tRNA-aware pipeline maps m1A at base resolution, quantifies per-site stoichiometry and flags differential modification. Every site is assigned to the reference tRNA library with anticodon, isodecoder, isotype and structural-domain context, and results arrive as tables, distribution and motif figures and browser-ready tracks.
Where tRNA m1A quantification fits
Profiles m1A occupancy on individual tRNAs and compares it with codon-biased translation.
Links m1A levels at conserved positions to folding and to tRNA stability.
Maps m1A changes on the tRNA isotypes that participate in tumour or developmental programmes.
Tests whether m1A stoichiometry shifts when cells are challenged.
Uses anticodon and isodecoder assignment to separate closely related tRNA genes.
Sample handling and submission for tRNA m1A
| Sample Type | Notes |
|---|---|
| Whole blood | Use EDTA tubes only; heparin is not compatible with subsequent analytical procedures. |
| Cultured cells | Cell pellets are preferred to ensure high-quality material for processing. |
| Tissue | Provide fresh or frozen specimens and avoid necrotic material. |
| Total RNA | Maintain an OD 260/280 ratio ≥ 1.8 and RIN ≥ 7 with no visible degradation. Submit at least 10 µg total RNA. |
Submit at least 10 µg total RNA per sample; smaller amounts can be discussed with support@arraystar.com before submission. Questions: support@arraystar.com
Questions we are asked about tRNA m1A quantification
Key references for tRNA m1A
Arraystar tRNA m1A-Quant-seq returns absolute modification levels at named tRNA positions — get in touch and we will scope the project around your sample set.