Product Class: Other

HiScribe® T7 mRNA Kit with CleanCap® Reagent AG

Now includes separate tube of DTT


Catalog #E2080

Product Introduction

  • Generate up to 90 µg of Cap-1 mRNA per reaction from 1 µg of control template
  • NTPs are provided separately to enable partial or full substitution of modified NTPs
  • Template removal and RNA purification reagents included
  • Includes linearized control template for use with CleanCap® Reagent AG for verification of RNA synthesis
  • Getting ready to scale up RNA synthesis? Download our new technical note “Scaling of High-Yield In vitro Transcription Reactions for Linear Increase of RNA Production” for a generalized set of recommendations for synthesizing high yields of RNA.
 

Product Information

Description

Most eukaryotic mRNAs require a 7-methyl guanosine (m7G) cap structure at the 5´-end and a poly(A) tail at the 3′-end for efficient translation.  The HiScribe T7 mRNA Kit with CleanCap Reagent AG utilizes an optimized RNA synthesis formulation and trinucleotide cap analog technology for co-transcriptionally capping mRNAs that contain a natural Cap-1 structure in a single simplified reaction without compromising RNA yield.  By using a DNA template with a T7 promoter sequence followed by an AG initiation sequence and an encoded poly(A) tail, mRNAs can be transcribed with a 5´-m7G Cap-1 structure that is polyadenylated, translationally competent and able to evade the cellular innate immune response.  

The HiScribe T7 mRNA Kit with CleanCap Reagent AG is formatted with individual vials of NTPs and CleanCap Reagent AG to allow for partial or complete substitution of modified NTPs, with a total kit yield of 1.8 mg of mRNA.  Cap-1 mRNA synthesized from this kit is suitable for many applications, including transfections, microinjections, in vitro translation, preclinical mRNA therapeutic mRNA studies as well as RNA structure and function analysis.

This kit contains sufficient reagents for 20 reactions (20 µl each).  Each standard reaction yields ≥ 90 µg of RNA from 1 µg CLuc AG Control Template DNA.  Each kit can yield ≥ 1.8 mg RNA.

Figure: 1: CleanCap Reagent AG





FIgure 2: Schematic of CleanCap Reagent AG Promoter and Initiation Sequence





Figure 3: CleanCap Reagent AG results in higher mRNA synthesis yield than the ARCA analog

 

All reactions were performed with 5 mM CTP, 5 mM UTP and 6 mM ATP.  Standard IVT reactions included 5 mM GTP and no cap analog.  ARCA reactions contained a 4:1 ratio of ARCA:GTP (4mM:1mM).  IVT with CleanCap Reagent AG contained 5 mM GTP and 4 mM CleanCap Reagent AG and was performed according to recommended protocol (Standard mRNA Synthesis, HiScribe T7 mRNA Kit with CleanCap Reagent AG).  Reactions were incubated for 2 hours at 37°C, purified and quantified by NanoDrop®.


 
This product is related to the following categories:
RNA Capping,
RNA Synthesis In vitro Transcription (IVT),

Reagents Supplied

Reagents Supplied

The following reagents are supplied with this product:

NEB # Component Name Component # Stored at (°C) Amount Concentration
  • E2080L     -20    
      T7 RNA Polymerase Mix M0255AVIAL -20 2 x 0.1 ml Not Applicable
      LiCl Solution B2051AVIAL -20 2 x 1.4 ml Not Applicable
      CLuc AG Control Template N2078AVIAL -20 1 x 0.02 ml 0.25 mg/ml
      DNase I (RNase-free) M0303AVIAL -20 2 x 0.1 ml 2,000 units/ml
      Dithiothreitol (DTT) B1222AVIAL -20 1 x 0.5 ml 100 mM
      10X T7 CleanCap® Reagent AG Reaction Buffer B2082AAVIAL -20 1 x 0.2 ml Not Applicable
      ATP N0489AAVIAL -20 1 x 0.2 ml 60 mM
      GTP N0490AAVIAL -20 1 x 0.2 ml 50 mM
      CTP N0491AAVIAL -20 1 x 0.22 ml 50 mM
      UTP N0492AAVIAL -20 1 x 0.2 ml 50 mM
      CleanCap® Reagent AG S1413AAVIAL -20 1 x 0.2 ml 40 mM

Properties & Usage

Materials Required but not Supplied

DNA Template:    
The DNA template must be linear and contain the T7 RNA Polymerase Promoter with the correct orientation in relation to the target sequence to be transcribed, followed by an AG initiation sequence.

Modified NTPs:    
Biotin-, Fluorescein-, Digoxigenin-, Aminoallyl-, Pseudouridine-5—Triphosphate, etc.

General:    
Thermocycler, microcentrifuge, nuclease-free water, nuclease-free tubes and tips

Purification:    
Phenol, chloroform, ethanol, 3 M Sodium Acetate, pH 5.2 or Ammonium Acetate, Monarch® RNA Cleanup Kit (500 µg; T2050), equipment and reagents for RNA quantitation

Gel Analysis:    
Gels, running buffers, loading dye, nucleic acid ladders, gel apparatus, power supply
 

Features

  • Streamlined workflow with single-step co-transcriptional capping
  • CleanCap® Reagent AG trinucleotide cap technology results in a natural Cap-1 structure, maximizing translatability and minimizing immune response from synthetic mRNA
  • High capping efficiency (> 95% capped material1)
  • Optimized for high yields
  • Suitable for full- or partial- modified nucleotide substitution

1Final capping is dependent upon the CleanCap Reagent, DNA template and final mRNA sequence. Secondary structure due to RNA length and base composition can affect final capping efficiency. 

 

Protocols, Manuals & Usage

Protocols

  1. Standard RNA Synthesis Protocol using the HiScribe T7 mRNA Kit with CleanCap Reagent AG (NEB #E2080)
  2. mRNA Synthesis Protocol with Modified Nucleotides using the HiScribe T7 mRNA Kit with CleanCap Reagent AG (NEB #E2080)

Manuals

The Product Manual includes details for how to use the product, as well as details of its formulation and quality controls.

Application Notes

Tools & Resources

Selection Charts

FAQs & Troubleshooting

FAQs

  1. Do I need to change my promoter sequence to use CleanCap® Reagent AG?
  2. How can I change the initiating sequence of my dsDNA template?
  3. Will the 5′ base of my RNA be an “A”?
  4. Can an uncut plasmid be used as a template for the HiScribe®; T7 mRNA Kit with CleanCap® Reagent AG?
  5. Can modified nucleotides be used with the HiScribe®; T7 mRNA Kit with CleanCap® Reagent AG?
  6. How can I improve the yield of RNA when using the HiScribe®; T7 mRNA Kit with CleanCap® Reagent AG?
  7. How can I purify the RNA synthesized using this kit?
  8. Can components from other HiScribe®; kits, T7 RNA Polymerase (NEB #M0251) or RNAPol Reaction Buffer (NEB #B9012) be substituted in this kit?
  9. Do you recommend template-encoding the poly(A) tail or using E. coli Poly(A) Polymerase?
  10. Can I use a different CleanCap® Reagent analog with this kit? 
  11. Are modified nucleotides included in the kit?
  12. Do I need to add DTT to the reaction?

Troubleshooting

 

Verify that the sequence following the T7 promoter contains the AG initiating sequence.

Control Reaction

The CLuc AG control template is a linearized plasmid containing the Cypridina luciferase gene under the transcriptional control of the T7 promoter. The initiating sequence has been changed to an AG by site-directed mutagenesis to be compatible with CleanCap Reagent AG. The size of the run-off transcript is ~1.76 kb. The control reaction, following the standard reaction protocol, should yield > 90 µg of RNA in 2 hours at 37°C. If the control reaction is not working, there may be technical issues with the reaction set up. Repeat the reaction following the protocol exactly (thawing specified reagents to room temperature, setting the reaction up at room temperature, and adding the components in the exact order listed in the manual. Take every precaution to avoid RNase contamination. The control plasmid sequence can be found within the DNA Sequences and Maps Tool under the name “pCMV-CLuc2 AG Control Plasmid”. The CLuc AG control template is generated by linearizing the plasmid with the restriction enzyme XbaI.

Low Yield of Full-length RNA

If the transcription reaction generates full-length RNA but yields are significantly lower than expected, it is possible that contaminants in the DNA template are inhibiting the RNA Polymerase or the DNA template concentration may be incorrect or too low. Additional purification of the DNA template may be required. Phenol:chloroform extraction is recommended (see template DNA preparation section).

Low yield of Short Transcript

High yields of short transcripts (< 300 nts) are achieved by extending incubation time and increasing the amount of template. Incubation of reactions up to 16 hours (overnight) or using up to 2 μg of template DNA can help achieve maximum yield.

RNA Transcript Smearing on Denaturing Gel

If the RNA appears degraded (smeared) on a denaturing agarose or polyacrylamide gel, the DNA template may be contaminated with RNase. DNA templates contaminated with RNase can affect the length and yield of RNA synthesized (smear below the expected RNA length). If the DNA template is contaminated with RNase, we recommend performing phenol:chloroform extraction followed by ethanol precipitation (see template DNA preparation section) and dissolving the DNA in nuclease-free water.

RNA Transcript of Larger Size than Expected

If the RNA transcript appears larger than the expected size on a denaturing gel when compared to a single-stranded RNA ladder, the plasmid DNA that is used for the template may not be completely digested. Even if small amounts of undigested circular plasmid DNA is present, T7 RNA Polymerase can produce large amounts of long transcripts. Check the digestion of the plasmid for complete digestion compared to a sample of undigested plasmid. If undigested plasmid is present repeat the restriction digest. Alternatively, larger sized bands may be observed when the RNA is not completely denatured due to the presence of strong secondary structure.

RNA Transcript of Smaller Size than Expected

If denaturing gel analysis indicates the presence of smaller bands than expected it is most likely due to premature termination by T7 RNA Polymerase. Sequences that resemble T7 RNA Polymerase termination signals will cause premature termination. For GC-rich templates, or templates with known strong secondary structure, incubation at 42°C may improve the yield of full-length transcript.

 

Quality, Safety & Legal

Quality Assurance Statement

Quality Control tests are performed on each new lot of NEB product to meet the specifications designated for it. Specifications and individual lot data from the tests that are performed for this particular product can be found and downloaded on the Product Specification Sheet, Certificate of Analysis, data card or product manual. Further information regarding NEB product quality can be found here.

Specifications

The Specification sheet is a document that includes the storage temperature, shelf life and the specifications designated for the product. The following file naming structure is used to name these document files: [Product Number]_[Size]_[Version]

Certificate Of Analysis

The Certificate of Analysis (COA) is a signed document that includes the storage temperature, expiration date and quality controls for an individual lot. The following file naming structure is used to name these document files: [Product Number]_[Size]_[Version]_[Lot Number]

Safety DataSheets

The following is a list of Safety Data Sheet (SDS) that apply to this product to help you use it safely.

Legal and Disclaimers

Products and content are covered by one or more patents, trademarks and/or copyrights owned or controlled by New England Biolabs, Inc (NEB). The use of trademark symbols does not necessarily indicate that the name is trademarked in the country where it is being read; it indicates where the content was originally developed. The use of this product may require the buyer to obtain additional third-party intellectual property rights for certain applications. For more information, please email [email protected].

This product is intended for research purposes only. This product is not intended to be used for therapeutic or diagnostic purposes in humans or animals.

New England Biolabs (NEB) is committed to practicing ethical science – we believe it is our job as researchers to ask the important questions that when answered will help preserve our quality of life and the world that we live in. However, this research should always be done in safe and ethical manner. Learn more.

Licenses

CleanCap® and products incorporating it are sold under license from TriLink BioTechnologies, LLC and may be used for research use only, not for use in diagnostics, therapeutics procedures or for use in humans. For additional information, please see the product’s Limited Use License at https://www.trilinkbiotech.com/cleancap-research-license

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