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Fluorophosphate-containing Cap

Background Fluorophosphate-containing Cap Services Highlights FAQs Published Data


A mature mRNA ready for efficient translation must contain two major modifications: a 5' cap structure and a poly(A) tail. The core structural feature of the cap is an N7-methylguanosine moiety linked by a 5'-5' triphosphate chain (m7G cap). This characteristic structure is involved in numerous interactions required for cellular functions. As an undoubted leader in mRNA services, Creative Biolabs is uniquely positioned to address mRNA synthesis & modification & applications with our unparalleled, multiplexed mRNA platform. We now offer different options for mRNA capping, such as fluorophosphate-containing capping, to meet specific demands.

  • Introduction of Fluorophosphate-containing Cap

mRNA cap is a methylated modification with a 7-methylguanosine moiety connected to the mRNA via a triphosphate linkage, referred to as m7GpppG cap. It is an important modification and specifically interacts with numerous cellular proteins to involve in pre-mRNA splicing, RNA export, translation initiation and RNA turnover. Fluorophosphate is one important capping moiety that has been widely used in mRNA modification. Cap analogs containing fluorophosphate moieties serve as attractive molecular tools for studies on RNA metabolism and modification of natural RNA properties.

Structural diagram of fluorophosphate (oligo)nucleotide analogs.

Fig.1 Synthesis of fluorophosphate (oligo)nucleotide analogs.1

  • Fluorophosphate-containing Cap Applications
    Through capping reactions with fluorophosphate moieties, we can get various nucleoside fluorophosphates that are chemically stable and synthetically available fluorophosphate nucleotide analogs. These modified mRNAs have shown multiple applications:
    • Monitor the activity of enzymes with various specificities and metal-ion requirements, including human mRNA decapping scavenger (DcpS) enzyme—a therapeutic target for spinal muscular atrophy.
    • Serve as reporter ligands for protein binding studies, as exemplified by studying the interaction of fluorophosphate mRNA cap analogs with eukaryotic translation initiation factor (eIF4E).

Fluorophosphate-containing Cap Services

With years of experience, Creative Biolabs provides a one-stop mRNA service, expanding from mRNA synthesis, modification, delivery, stability test to other downstream applications services. Our custom mRNA mapping services cover a wide range of capping moieties, including but not limited to ARCAs, fluorescent, fluorophosphate, to meet different applications. We have developed efficient synthetic methods for RNA containing the fluorophosphate moiety. To incorporate cap structures to the RNA, Creative Biolabs offers a variety of capping options, commonly cotranscriptional enzymatic labeling (a single-step workflow and permits non-canonical cap structures) or posttranscriptional enzymatic labeling (nearly 100% capping on a large quantity of in vitro transcription RNA) approaches. Usually, we choose P-imidazolides to react readily with fluorides to yield fluorophosphates for capping.

mRNA cap mediates essential biological functions during the process of gene expression and regulation. Creative Biolabs takes pride in providing one-stop mRNA manufacturing for your scientific needs, and our suite of analytical services allows you to thoroughly characterize your mRNA. If you are interested in our services or need more scientific support, please feel free to contact us.

Inquire About Our Services


  • Advanced Capping Methods: Offers both co-transcriptional and post-transcriptional enzymatic capping.
  • High Efficiency: Achieves nearly 100% capping efficiency with large quantities of in vitro transcribed RNA.
  • Custom Solutions: Tailored capping options to meet specific research needs.
  • Experienced Provider: Leverages extensive expertise in mRNA modification and synthesis.
  • Versatile Applications: Ideal for enzyme activity monitoring, protein binding studies, and RNA metabolism research.


Q: What is a Fluorophosphate-containing cap?

A: It is a synthetic cap analog used to modify mRNA, incorporating fluorophosphate moieties to enhance stability and functionality.

Q: Why use Fluorophosphate-containing caps for mRNA?

A: They increase mRNA stability, provide resistance to decapping enzymes, and facilitate tracking and studying mRNA dynamics.

Q: What are the applications of Fluorophosphate-containing caps?

A: Applications include enzyme activity monitoring, protein binding studies, and RNA metabolism research.

Q: How are Fluorophosphate-containing caps added to mRNA?

A: They can be incorporated co-transcriptionally or post-transcriptionally using enzymatic labeling techniques.

Q: What are the benefits of using Fluorophosphate-containing caps?

A: They offer enhanced chemical stability, nearly 100% capping efficiency, and improved analytical capabilities.

Q: Can Creative Biolabs customize Fluorophosphate-containing caps?

A: Yes, we offer tailored solutions, including specific fluorophosphate modifications to meet unique research requirements.

Published Data

The article details the development and analysis of fluorophosphate-containing cap analogues designed to enhance the study of mRNA. These analogues are modified to include fluorescent labels such as anthraniloyl (Ant) and N-methylanthraniloyl (Mant), which enable the tracking and imaging of mRNA in biological systems without significantly altering their biological properties. The study demonstrates that these analogues possess high quantum yields, stability, and are suitable for use in various fluorescence-based assays. Additionally, the modifications in the cap structure improve resistance to enzymatic degradation, making them valuable tools for investigating cap-related processes in mRNA translation, turnover, and interactions with cap-binding proteins.

Fluorescence experiment results of different fluorophosphate mRNA cap analogs.

Fig.2 Time-synchronized fluorescence quenching titration curves for titration of eIF4E with fluorophosphate mRNA cap analogs.2

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  1. Baranowski, M. R.; et al. Synthesis of fluorophosphate nucleotide analogues and their characterization as tools for 19F NMR studies. The Journal of organic chemistry. 2015, 80(8): 3982-3997.
  2. Baranowski, Marek R., et al. "Synthesis of fluorophosphate nucleotide analogues and their characterization as tools for 19F NMR studies." The Journal of organic chemistry 80.8 (2015): 3982-3997.
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