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TRANSCRIPTION FOR ENZYME-
BASED CAPPING (POST-
TRANSCRIPTIONAL CAPPING)
Standard RNA synthesis reactions produce
the highest yield of RNA transcript (typically
≥100 μg per 20 μl in a 1 hr reaction using the
HiScribe
™
Quick T7 High Yield RNA Synthesis
Kit, NEB #E2050S). Transcription reactions are
highly scalable, and can be performed using an
all-inclusive kit (e.g., HiScribe kits), or individual
reagents. More information on the HiScribe kits
can be found later in the article.
Following transcription, the RNA is treated with
DNase I (NEB #M0303) to remove the DNA
template, and purified using an appropriate
column, kit or magnetic beads, prior to capping.
This method produces high yields of RNA with
5´-triphosphate termini that must be converted
to cap structures. In the absence of template-
encoded poly(A) tails, transcripts produced using
this method bear 3´ termini that also must be
polyadenylated in a separate enzymatic step, as
described below in “Post-transcriptional capping
and Cap-1 methylation”.
TRANSCRIPTION
WITH DINUCLEOTIDE
CO-TRANSCRIPTIONAL CAPPING
In co-transcriptional capping, a cap analog is
introduced into the transcription reaction, along
with the four standard nucleotide triphosphates,
in an optimized ratio of cap analog to GTP 4:1.
This allows initiation of the transcript with the cap
structure in a large proportion of the synthesized
RNA molecules. This approach produces a mixture
of transcripts, of which ~80% are capped, and the
remainder have 5´-triphosphate ends. Decreased
overall yield of RNA products results from the
lower concentration of GTP in the reaction
(Figure4).
There are several cap analogs used in co-
transcriptional RNA capping (3,4). The most
common are the standard 7-methyl guanosine
(m7G) cap analog and anti-reverse cap analog
(ARCA), also known as 3´ O-me 7-meGpppG cap
analog. ARCA is methylated at the 3´ position
of the m7G, preventing RNA elongation by
phosphodiester bond formation at this position.
Thus, transcripts synthesized using ARCA contain
5´-m7G cap structures in the correct orientation,
with the 7-methylated G as the terminal
residue. In contrast, the m7G cap analog can be
incorporated in either the correct or the reverse
orientation.
HiScribe T7 ARCA mRNA Synthesis kits
(NEB #E2060 and #E2065) contain reagents,
including an optimized mix of ARCA and NTPs,
for streamlined reaction setup for synthesis of co-
transcriptionally capped RNAs.
TRANSCRIPTION WITH
CLEANCAP
®
REAGENT AG
CO-TRANSCRIPTIONAL CAPPING
The use of CleanCap reagent AG results
in significant advantages over traditional
dinucleotide co-transcriptional capping. CleanCap
Reagent AG is a trinucleotide with a 5´-m7G
joined by a 5´-5´ triphosphate linkage to an AG
sequence . The adenine has a methyl group on the
2´-O position (Figure 4). The incorporation of
this trinucleotide in the beginning of a transcript
results in a Cap-1 structure.
In order to use CleanCap Reagent AG in an in
vitro transcription reaction the template must
contain an AG in place of a GG following the T7
promoter in the initiation sequence.
Unlike traditional co-transcriptional capping,
reduction of GTP concentration is not required
and therefore yield is higher and high capping
eencies, >95%, are achieved (Figure 5).
TRANSCRIPTION WITH COMPLETE
SUBSTITUTION WITH MODIFIED
NUCLEOTIDES
RNA synthesis can be carried out with a
mixture of modified nucleotides in place of the
regular mixture of A, G, C and U triphosphates.
For expression applications, the modified
nucleotides of choice are the naturally occurring
5´-methylcytidine and/or pseudouridine in the
place of C and U, respectively. These have been
demonstrated to confer desirable properties to
the mRNA, such as increased mRNA stability,
increased translation, and reduced immune
response in the key applications of protein
replacement and stem-cell dierentiation (1). It
is important to note that nucleotide choice can
influence the overall yield of mRNA synthesis
reactions.
Fully substituted RNA synthesis can be achieved
using the HiScribe T7 mRNA Kit with CleanCap
Reagent AG (NEB #E2080), HiScribe T7 High-
Yield RNA Synthesis Kit (NEB #E2040) or
HiScribe SP6 RNA Synthesis Kit (NEB #E2070)
in conjunction with NTPs with the desired
modification. Transcripts made with complete
replacement of one or more nucleotides may be
post-transcriptionally capped (see next section), or
may be co-transcriptionally capped by including
CleanCap Reagent AG, ARCA or another cap
analog, as described previously.
If partial replacement of nucleotides is desired, the
HiScribe T7 ARCA mRNA Synthesis Kits (NEB
#E2060 and #E2065), may be used with added
modified NTPs, to produce co-transcriptionally
capped mRNAs, as described above. Alternatively,
the HiScribe T7 Quick RNA Synthesis Kit (NEB
#E2050) may be used to prepare transcripts for
post-transcriptional capping.
POST-TRANSCRIPTIONAL CAPPING
AND CAP-1 METHYLATION
Post-transcriptional capping is often
performed using the mRNA capping system
from Vaccinia virus. This enzyme complex
converts the 5´-triphosphate ends of in vitro
transcripts to m7G-cap (Cap-0) required for
ecient protein translation in eukaryotes. The
Vaccinia Capping System (NEB #M2080)
comprises three enzymatic activities (RNA
triphosphatase, guanylyltransferase, guanine
N7-methyltransferase) that are necessary for
the formation of the complete Cap-0 structure,
m7Gppp5´N, using GTP and the methyl
donor S-adenosylmethionine. As an added
option, the inclusion of the mRNA Cap 2´
O-Methyltransferase (NEB #M0366) in the
same reaction results in formation of the Cap-1
structure (m7Gppp5´Nm), a natural modification
in many eukaryotic mRNAs responsible for
evading cellular innate immune response against
foreign RNA. This enzyme-based capping
approach results in a high proportion of capped
message, and it is easily scalable. The resulting
capped RNA can be further modified by poly(A)
addition before final purification.
FIGURE 4:
Structure of CleanCap
Reagent AG
OPP
O
OO
O
O
O
H
2
N
HN
N
+
CH
3
CH
3
N
N
O
O
HO OH
OP
P
O
O
O
NH
2
N
N
N
N
OO
O
OO
3Na
+
O
OHHO
O
NH
2
N
N
N
NH
FIGURE 5:
Comparison of RNA yields
from in vitro transcription
reactions
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 (4 mM:1 mM). IVT
with CleanCap Reagent AG contained 5 mM GTP and 4 mM CleanCap
Reagent AG and was performed as described below (Standard mRNA
Synthesis). Reactions were incubated for 2 hours at 37°C, purified and
quantified by NanoDrop
®
.
0
20
40
60
80
100
120
Standard
IVT
IVT with
ARCA
IVT with
CleanCap
®
Reagent AG
RNA Yield (µg)