Mass Spectrometry (LC-MS)
LC-MS Based tRNA Modification Analysis Service
Arraystar LC-MS tRNA Modification Analysis Service analyzes 55 nucleoside modifications and characterizes global modification profile of tRNAs as tRNA biochemical properties vital to tRNA biogenesis, structure, functioning and implication in diseases.
Benefits
• Quantitative analysis of complex tRNA modifications from total RNA samples.
• Full service sample-to-data – from sample QC, tRNA isolation, nucleoside analyte preparation, LC-MS/MS data acquisition, analysis to report.
• High Performance – Highly optimized experimental procedures, state-of-the-art LC-MS system, expertise in operation.
• Best analytical coverage – Simultaneous profiling of 55 nucleoside modifications in tRNAs.
Service Order Guide
1. Check if your modifications of interest are in our standard detection list.
2. If yes, please click “Request Quote” below, and our technical sales team will follow up shortly.
| Service Name | Catalog No | Size | Price |
|---|---|---|---|
| LC-MS tRNA Modification Analysis Service- Eukaryotic | AS-LC-t-S | 1 sample | |
| Total RNA Extraction Service | AS-RE-S | 1 sample |
tRNAs are the fundamental component of mRNA decoding and protein translation. tRNAs undergo by far the greatest number of and the most chemically diverse post-transcriptional modifications. These modifications are critical for all core aspects of tRNA function, such as folding, stability and decoding[1]. Typically, modifications in the main body of tRNA are crucial for tRNA structure folding, stability, rigidity and flexibility, whereas modifications in the anticodon loop affect decoding by open loop structure, codon-anticodon pairing, wobbling, and preventing translational frameshifts. Additionally, modified nucleosides serve as identity determinants for aminoacyl-tRNA synthetase (AARS) for extra amino acid recognition accuracy[2]. In general, hypomodified tRNAs are targeted for degradation. Studying tRNA modification is perhaps just as important as tRNA expression profiling.
Defects in tRNA modifications and modification enzymes are linked with human diseases such as cancers, diabetes, neurological syndromes, cardiac conditions, and mitochondrial-linked disorders (Fig. 1)[3]. Analysis of tRNA modification profiles is key to establish the link with the disease, tRNA modification enzymes, and tRNA molecular functioning.
Arraystar LC-MS tRNA Modification Analysis Service offers the sample-to-data solution for simultaneous profiling of 55 nucleosides modifications important to tRNA, using total RNA as the starting material. The service includes tRNA isolation from the total RNA, complete hydrolysis, and dephosphorylation to prepare single nucleosides. The state of the art, ultra high performance LC-MS system delivers a new level of sensitivity, precision, accuracy, dynamic range, and robustness of the quantification results.
Figure 1. tRNA modifications in human diseases
References
1. Kirchner S. and Z. Ignatova (2015) “Emerging roles of tRNA in adaptive translation, sig-nalling dynamics and disease.” Nat. Rev. Genet. 16(2):98-112 [PMID: 25534324]
2. El Yacoubi B. et al. (2012) “Biosynthesis and function of posttranscriptional modifications of transfer RNAs.” Annu. Rev. Genet. 46:69-95 [PMID: 22905870]
3. Torres A.G. et al. (2014) “Role of tRNA modifications in human diseases.” Trends Mol Med 20(6):306-14 [PMID: 24581449]
Table1. Nucleoside modifications profiled by Arraystar LC-MS tRNA Modification Analysis
| Number | Nucleoside | Symbol | Number | Nucleoside | Symbol |
| 1 | 3′-O-methyladenosine | 3′-OMeA | 2 | 3′-O-methyluridine | 3′-OMeU |
| 3 | 2′-O-methylcytidine | Cm | 4 | 5-methyl-2-thiouridine | m5s2U |
| 5 | 3-methylcytidine | m3C | 6 | 5-methoxyuridine | mo5U |
| 7 | 5-methylcytidine | m5C | 8 | pseudouridine |  |
| 9 | N6-isopentenyladenosine | i6A | 10 | 2′-O-methylinosine | Im |
| 11 | 5,2′-O-dimethylcytidine | m5Cm | 12 | 3-methyluridine | m3U |
| 13 | 1-methyladenosine | m1A | 14 | 1-methylpseudouridine | m1 |
| 15 | 2-thiocytidine | s2C | 16 | 5-hydroxymethylcytidine | hm5C |
| 17 | N2, N2, 7-trimethylguanosine | m2,2,7G | 18 | 5,2′-O-dimethyluridine | m5Um |
| 19 | N4-acetyl-2′-O-methylcytidine | ac4Cm | 20 | N6-threonylcarbamoyladenosine | t6A |
| 21 | N6-methyladenosine | m6A | 22 | 2-methylthio-N6-threonylcarbamoyladenosine | ms2t6A |
| 23 | 3′-O-methylcytidine | 3′-OmeC | 24 | 5-carboxymethyluridine | cm5U |
| 25 | 2′-O-methyladenosine | Am | 26 | 5-methoxycarbonylmethyl-2-thiouridine | mcm5s2U |
| 27 | N2, N2-dimethylguanosine | m22G | 28 | 5-Methoxycarbonylmethyluridine | mcm5U |
| 29 | 5′-O-methylthymidine | 5′-OMeT | 30 | 2-methylthio-N6-isopentenyladenosine | ms2i6A |
| 31 | 2′-O-methyluridine | Um | 32 | Peroxywybutosine | o2w |
| 33 | inosine | I | 34 | 5-taurinomethyl-2-thiouridine | tm5s2U |
| 35 | 2′-O-methylguanosine | Gm | 36 | 5-oxyacetic acid uridine | cmo5U |
| 37 | 1-methylguanosine | m1G | 38 | 5-carbamoylmethyuridine | ncm5U |
| 39 | 7-methylguanosine | m7G | 40 | Queuosine | Q |
| 41 | N2-methylguanosin | m2G | 42 | 5-taurinomethyluridine | tm5U |
| 43 | 3′-O-methylinosine | 3′-OMeI | 44 | 5-formyl-2′-O-methylcytidine | f5Cm |
| 45 | 2-thiouridine | s2U | 46 | dihydrouridine | D |
| 47 | 4-thiouridine | s4U | 48 | 5-formylcytidine | f5c |
| 49 | 5-methyluridine | m5U | 50 | wybutosine | W |
| 51 | N4-acetylcytidine | ac4C | 52 | 5-methoxycarbonylmethyl-2′-o-methyluridine | mcm5Um |
| 53 | N6, O2′-methyladenosine | m6Am | 54 | 5-methylaminomethyl-2-thiouridine | mnm5s2U |
| 55 | 5-hydroxyuridine | ho5U |
Workflow of Arraystar LC-MS tRNA Modification Analysis.
• Raw and normalized peak data
• Total Ion Current chromatogram of nucleosides
• Differential modification of nucleosides among samples
References
1. Kirchner S, Ignatova Z. Emerging roles of tRNA in adaptive translation, signalling dynamics and disease. Nature reviews Genetics 2015;16:98-112.
2. El Yacoubi B, Bailly M, de Crecy-Lagard V. Biosynthesis and function of posttranscriptional modifications of transfer RNAs. Annual review of genetics 2012;46:69-95.
3. Torres AG, Batlle E, Ribas de Pouplana L. Role of tRNA modifications in human diseases. Trends in molecular medicine 2014;20:306-14.
Loss of Elp1 in cerebellar granule cell progenitors models ataxia phenotype of Familial Dysautonomia. Arnskötter F, et al. Neurobiology of Disease, 2024
Unconventional secretion of Magnaporthe oryzae effectors in rice cells is regulated by tRNA modification and codon usage control. Li G, et al. Nature Microbiology, 2023
Elp3-mediated codon-dependent translation promotes mTORC2 activation and regulates macrophage polarization. Chen D,et al. The EMBO Journal, 2022
Phytophthora capsici infection causes dynamic alterations in tRNA modifications and their associated gene candidates in black pepper. Usha A,et al. Computational and Structural Biotechnology Journal, 2022
Loss of tRNA-modifying enzyme Elp3 activates a p53-dependent antitumor checkpoint in hematopoiesis. Rosu A, et al. Journal of Experimental Medicine, 2021
Elongator Subunit 3 (Elp3) Is Required for Zebrafish Trunk Development. Rojas-Benítez D, et al. International Journal of Molecular Sciences, 2020
Papillary Renal Cell Carcinomas Rewire Glutathione Metabolism and Are Deficient in Both Anabolic Glucose Synthesis and Oxidative Phosphorylation. Ahmad A A, et al. Cancers, 2019
Elongator and codon bias regulate protein levels in mammalian peripheral neurons. Goffena J, et al. Nature Communications, 2018