NM-seq resolves 2'-O-methylation (Nm) on tRNA through periodate chemistry: repeated oxidation–elimination–dephosphorylation cycles strip unmodified nucleotides while Nm positions survive, so each protected site is read at single-base precision.
Base-resolution mapping of 2'-O-methylation across tRNA
2'-O-methylation sits on the ribose 2'-hydroxyl rather than on a base, and it is placed by 2'-O-methyltransferases or by C/D-box snoRNPs. On tRNA the mark shapes the folded architecture and influences decoding, so which positions carry Nm matters as much as whether Nm is present at all.
Arraystar Single-Nucleotide tRNA 2'-O-Me Modification Seq(NM-seq) carries the whole chain: RNA quality control, OED enrichment of methylated fragments, library construction, sequencing and tRNA-aware bioinformatics. Every reported position is placed inside a mature tRNA transcript with its relative coordinate, host tRNA gene, anticodon and isotype, and structural domain.
NM-seq is an antibody-free chemical sequencing method for 2'-O-methylation on tRNA. Periodate-driven oxidation, elimination and dephosphorylation degrade unmodified nucleotides while 2'-O-methylated positions resist cleavage, so sequencing the surviving fragments maps each Nm site at single-base precision.
Standard tRNA 2'-O-methylation project — custom designs and add-on analyses available on request
| Service Name | Price |
|---|---|
| Single-Nucleotide tRNA 2'-O-Me Modification Seq(NM-seq) |
What Arraystar tRNA NM-seq gives you
Each 2'-O-methylated position is fixed to a single nucleotide because the readout depends on chemical resistance rather than on enrichment breadth.
Sites are reported with relative positions inside mature tRNA transcripts, host tRNA gene attribution, anticodon, isotype and structural-domain context.
Periodate chemistry removes the pull-down bias and cross-reactivity that antibody capture brings to compact, structured tRNA.
Iterative OED rounds concentrate methylated fragments so that lower-abundance Nm positions remain visible.
Positions can be compared across tRNA isotypes and isoacceptors within a single experiment.
RNA QC, tRNA processing, library preparation, sequencing and bioinformatics are delivered as a single project.
Why Nm on tRNA needs a chemistry-first readout
Nm modifies the 2'-hydroxyl of the ribose instead of the base, which leaves it invisible to base-modification assays and calls for a chemistry-sensitive approach. The mark is deposited by 2'-O-methyltransferases and by C/D-box snoRNPs, and in tRNA it reinforces the folded L-shaped architecture while tuning decoding (2).
Periodate reacts with the free 2'-hydroxyl of unmodified nucleotides and leaves 2'-O-methylated positions untouched. Cycling oxidation, elimination and dephosphorylation therefore erases the unmodified background and leaves Nm-bearing fragments to be sequenced; Arraystar applies this chemistry in a tRNA setting so that protection is scored inside mature transcripts (1).
From total RNA to a base-resolution Nm map
Four handling stages carry the sample to a base-resolution Nm dataset: RNA QC and tRNA processing, repeated OED enrichment of methylated fragments, adapter ligation and sequencing, then tRNA-aware alignment and site calling.
Bioinformatics for NM-seq
Reads are aligned against a curated tRNA reference and the positions that escaped OED degradation are called as Nm sites. Reporting covers per-position stoichiometry, motif context, differential modification between groups and browser-ready signal tracks.
Where tRNA Nm profiling fits
Relates 2'-O-methylated positions to the folded L-shaped architecture and to tRNA turnover.
Places Nm inside anticodon and wobble context to test its effect on decoding.
Compares Nm occupancy between tRNA isotypes and isoacceptors in the same run.
Finds differentially 2'-O-methylated tRNA positions between conditions.
Sits alongside other single-base tRNA assays when a modification landscape is being assembled.
Sample handling and submission for tRNA 2'-O-methylation
| 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 100–300 µg total RNA. |
Submit at least 100–300 µg total RNA per sample; the higher end covers samples with lower tRNA content. Questions: support@arraystar.com
Questions we are asked about tRNA NM-seq
Key references for tRNA 2'-O-methylation
Arraystar tRNA NM-seq pairs periodate chemistry with mature-tRNA annotation — send us the sample set and we will return a base-resolution Nm map with per-site stoichiometry.