N1-(1,1,1-Trifluoroethyl)pseudouridine: Properties & Lab Use Guide

N1-(1,1,1-Trifluoroethyl)pseudouridine is a synthetic, fluorine-bearing pseudouridine analogue designed for incorporation into modified RNA studies and nucleoside chemistry research.

Product Name

N1-(1,1,1-Trifluoroethyl)pseudouridine

SKU / Catalog Number

N1425742

Compound Class

Fluorinated pseudouridine analogue (modified nucleoside)

Core Scaffold

Pseudouridine (C-glycoside of uracil) with N1-trifluoroethyl substitution

Key Modification

1,1,1-Trifluoroethyl group at N1 of the uracil base

Primary Research Area

RNA biology, nucleoside analogue chemistry, mRNA therapeutics research

Supplier Reference

MCE-TJY: HY-152768

Chemical Identity and Structure

N1-(1,1,1-Trifluoroethyl)pseudouridine is a chemically modified nucleoside built on the pseudouridine scaffold. Unlike canonical uridine, pseudouridine features a C5-glycosidic bond rather than the conventional N1-glycosidic bond, making it one of the most abundant naturally occurring RNA modifications. In this analogue, a 1,1,1-trifluoroethyl group is introduced at the N1 position of the uracil base, imparting unique electronic and steric properties attributable to the strong electron-withdrawing character of the trifluoromethyl-bearing carbon.

The fluorine atoms in the trifluoroethyl moiety markedly influence the compound's physicochemical profile: they increase metabolic stability relative to non-fluorinated counterparts, modulate hydrogen-bonding capacity, and alter lipophilicity (logP). These properties make N1-(1,1,1-Trifluoroethyl)pseudouridine a valuable building block and probe in nucleoside analogue programmes.

Research Applications

Modified RNA and mRNA Therapeutics Research: Pseudouridine and its analogues have become central to mRNA therapeutic platforms because pseudouridine substitution is known to reduce innate immune recognition of synthetic mRNA. N1-substituted pseudouridine derivatives are investigated as tools to further fine-tune immune evasion, translational efficiency, and RNA stability. N1-(1,1,1-Trifluoroethyl)pseudouridine may serve as a reference compound or structural probe in studies comparing the biological effects of different N1-alkyl substitutions on pseudouridine.

Nucleoside Chemistry and Structure–Activity Relationship (SAR) Studies: The trifluoroethyl group provides a fluorine-rich handle useful in ¹⁹F NMR spectroscopy for direct, background-free monitoring of nucleoside interactions with enzymes, ribosomes, or binding proteins. Researchers can exploit the distinct ¹⁹F NMR chemical shift to track compound fate in complex biological matrices.

Biochemical Probes: As a pseudouridine analogue, this compound may be evaluated for incorporation by RNA polymerases or as an inhibitor/substrate of pseudouridine synthases and other RNA-modifying enzymes, supporting target identification and mechanistic studies.

Handling, Storage and Safety Guidelines

General Handling: Handle N1-(1,1,1-Trifluoroethyl)pseudouridine under standard laboratory conditions appropriate for research-grade organic compounds. Use personal protective equipment (PPE) including nitrile gloves, safety glasses, and a lab coat. Work in a well-ventilated area or fume hood when weighing or preparing stock solutions.

Solubility and Stock Solution Preparation: As a nucleoside analogue bearing a polar ribose moiety and a moderately lipophilic trifluoroethyl group, the compound is anticipated to show solubility in polar aprotic solvents such as DMSO or DMF, and potentially in aqueous buffers at moderate concentrations. Prepare fresh stock solutions where possible and use validated solubility data before preparing biological assay solutions. Filter-sterilise solutions intended for cell-based assays.

Storage: Store as recommended by the supplier — typically at −20 °C in a tightly sealed, desiccated container, protected from light and moisture. Verify specific storage conditions on the product datasheet provided with the shipment.

Disposal: Dispose of waste in accordance with institutional and local regulatory requirements for organic chemical waste. Do not dispose of via drain or general waste.

Quality, Purity and Procurement

Aladdin Scientific supplies N1-(1,1,1-Trifluoroethyl)pseudouridine (SKU: N1425742) as a research-grade reagent. Cross-reference supplier reference MCE-TJY HY-152768 confirms alignment with the compound identity documented in third-party databases. Researchers should request the Certificate of Analysis (CoA) and Safety Data Sheet (SDS) at the time of ordering to confirm:

• Purity (typically assessed by HPLC)
• Structural confirmation (NMR, MS)
• Appearance and physical state
• Lot-specific analytical data

For procurement inquiries, bulk quantities, or custom synthesis, contact Aladdin Scientific's technical sales team. Storage and shelf-life information will be provided on the CoA accompanying each lot.

Frequently asked questions

What is N1-(1,1,1-Trifluoroethyl)pseudouridine used for in research?

N1-(1,1,1-Trifluoroethyl)pseudouridine is used as a chemically modified nucleoside analogue in RNA biology and nucleoside chemistry research. It serves as a structural probe and reference compound for studying the effect of N1-substitution on pseudouridine's biological properties, relevant to mRNA therapeutic development and RNA modification studies. The fluorine atoms also enable 19F NMR-based tracking in biochemical assays.

How should I store N1-(1,1,1-Trifluoroethyl)pseudouridine to maintain stability?

This compound should generally be stored at −20 °C in a tightly sealed container with desiccant, protected from light and moisture. Always refer to the Certificate of Analysis (CoA) supplied with each specific lot for confirmed storage recommendations, as conditions may vary by formulation.

What solvents are suitable for preparing stock solutions of this compound?

Based on its structural features — a polar ribose unit combined with a moderately lipophilic trifluoroethyl group — DMSO or DMF are anticipated to be suitable solvents for stock solution preparation. Solubility in aqueous buffers should be experimentally verified before use in biological assays. Researchers should consult the CoA or conduct solubility testing to confirm optimal solvent choice for their specific application.

What is the catalog number for N1-(1,1,1-Trifluoroethyl)pseudouridine at Aladdin Scientific?

The catalog number (SKU) for N1-(1,1,1-Trifluoroethyl)pseudouridine at Aladdin Scientific is N1425742. This product is also cross-referenced with supplier code MCE-TJY HY-152768.

Why is pseudouridine modification important for mRNA therapeutics?

Pseudouridine substitution in synthetic mRNA reduces activation of innate immune sensors such as Toll-like receptors, leading to lower immunogenicity and improved tolerability in vivo. This modification also enhances translational efficiency and mRNA stability. N1-substituted pseudouridine analogues like N1-(1,1,1-Trifluoroethyl)pseudouridine are studied to understand how additional chemical modifications at N1 further modulate these properties.

References

1. Karikó, K. et al. Suppression of RNA recognition by Toll-like receptors: the impact of nucleoside modification and the evolutionary origin of RNA. Immunity. 2005;23(2):165-175. doi:10.1016/j.immuni.2005.06.008
2. Roundtree, I.A. et al. Dynamic RNA Modifications in Gene Expression Regulation. Cell. 2017;169(7):1187-1200. doi:10.1016/j.cell.2017.05.045
3. Charette, M. and Gray, M.W. Pseudouridine in RNA: what, where, how, and why. IUBMB Life. 2000;49(5):341-351. doi:10.1080/152165400410182

Products are supplied for research and development use only. Not for use in humans, animals, diagnosis, or therapy.