If we could specifically label nascent RNA as it is being synthesized, we could distinguish ongoing transcriptional activity from pre-existing RNA in the cell.

This is the core idea of nascent RNA labeling technology.

By supplying cells with chemically modified nucleoside triphosphates that get incorporated into newly synthesized RNA strands during transcription, and then using specific chemical reactions for detection or enrichment, researchers can track RNA production, changes, and dynamic processes.

Among them, 5-Ethynyl-UTP is an important chemically modified nucleoside triphosphate that can be used for labeling nascent RNA, providing a chemical basis for subsequent detection, enrichment, and sequencing analysis.

Chinese Name: 5-Ethynyluridine 5'-(tetrahydrogen triphosphate)

English Name: 5-Ethynyluridine 5'-(tetrahydrogen triphosphate)

Abbreviation: 5-Ethynyl-UTP

CAS Number: 1004955-96-7

Molecular Formula: C11H15N2O15P3

Molecular Weight: 508.16

Specifications: 25 µl / 100 µl / 1 ml (Custom packaging supported)

Form: Aqueous solution

Product Number: G09010023

Stock: In stock

Concentration: ~100 mM in water

5-Ethynyl-UTP is a chemically modified nucleoside triphosphate that can be directly incorporated into RNA molecules, serving as a core raw material for nascent RNA labeling, detection, and enrichment.

To overcome this bottleneck, nascent RNA metabolic labeling technology emerged. The key to this technology is an efficient chemically modified nucleotide – 5-Ethynyl-UTP.

Its working principle is ingenious and efficient:

1. Precise incorporation: In in vitro transcription systems or permeabilized cell systems, RNA polymerase recognizes 5-Ethynyl-UTP as regular UTP and directly incorporates it into newly synthesized RNA strands. Thus, RNA that is synthesized and incorporates this nucleotide analog during the labeling window receives the corresponding chemical tag.

2. Click chemistry reaction: Using the alkynyl group (-C≡CH) at the end of 5-Ethynyl-UTP as a tiny "handle", subsequent labeling can be performed via the bioorthogonal reaction between the alkyne and azide groups.

3. Targeted tracking: Through this stable covalent linkage, the corresponding reporter group is introduced into the labeled nascent RNA, enabling subsequent detection or enrichment.

After labeling, what can we do? 5-Ethynyl-UTP is not just a chemical label; it is the key to unlocking the dynamic window of RNA life. In actual research, it can help you accomplish the following core tasks:

1. Detecting RNA synthesis rates and transcription kinetics

Dynamically monitor transient fluctuations in transcription levels in response to specific physiological, pathological, or microenvironmental stimuli (such as small molecule interventions, environmental stress, cell differentiation, etc.).

2. Elucidating transcription regulatory mechanisms and small molecule inhibitor effects

In transcription regulation and drug screening studies, 5-Ethynyl-UTP is a sensitive indicator for quantitatively evaluating the intervention effects of candidate compounds on the transcription system.

3. Specific enrichment and high-throughput sequencing of nascent RNA (EU-seq)

Using click chemistry to couple biotin-azide to nascent RNA, followed by streptavidin magnetic bead affinity purification, enables specific enrichment and high-throughput sequencing analysis of nascent RNA for studying non-coding RNA and precursor mRNA processing and degradation kinetics.

Compared to traditional radioisotope labeling (such as ³²P-UTP) or older antibody-based methods (such as Br-UTP), 5-Ethynyl-UTP exhibits significant technical advantages:

✅ Sensitive and low-noise: The click chemistry reaction is efficient, with clear signals and low background, suitable for labeling low-abundance nascent RNA and subsequent detection.

✅ Bioorthogonal specificity: The alkyne and azide groups have good bioorthogonality, helping to reduce non-specific reactions that could affect labeling results.

✅ RNA integrity protection: The reaction conditions are mild, causing minimal damage to RNA structure, and can be connected with downstream analysis workflows such as sequencing and qRT-PCR, providing a labeling foundation for nascent RNA research.

✅ No radioactive labeling required: No need for radioactive isotopes like ³²P, reducing the operational and management requirements associated with radioactive experiments.