CA3114892A1 - Methods and compositions for increasing capping efficiency of transcribed rna - Google Patents

Abstract

Methods and compositions for capping RNA in an in vitro transcription (IVT) mixture are provided that include a thermostable RNA polymerase variant and a cap analog such that when a DNA template is added to the mixture, and the mixture is then incubated under conditions for in vitro transcription, capped RNA is produced. The methods describe high capping efficiencies at elevated temperatures as well as at standard temperatures for IVT. The RNA polymerase used is a thermostable variant of the T7 RNA polymerase, named polymerase M20, which comprises substitutions at positions 388 and 567, in particular D388E and V567P.

Description

METHODS AND COMPOSITIONS FOR INCREASING CAPPING EFFICIENCY OF TRANSCRIBED RNA
BACKGROUND
Eukaryotic mRNAs have a cap structure at their 5'-termini. The cap consists of 7-methylguanosine (m7G) .. and a triphosphate bridge, ppp (p3), linking the 5'0H of m7G to the 5'0H of the 5'-terminal nucleotide, N, denoted m7G(5')pppN (m7G(51p3N) (Cap 0 structure). The cap structure imparts various biological functions to the capped RNA (Ramanathan et al., (2016) Nucleic Acids Research, 44,7511-7526). These include mRNA
processing and transport; imparting stability to the mRNA molecule; increasing translation efficiency; and acceleration of multiple interactions between the mRNA and the cellular machinery including the translation apparatus, immune receptors and effectors.
RNA synthesized via in vitro transcription (IVT) can be capped during the transcription reaction (in a process called "co-transcriptional capping") or afterwards (i.e., post-transcriptionally using a series of enzymatic steps) (see, e.g., Muttach et al., J. Org Chem. (2017) 13: 2819-2832). In co-transcriptional capping, a cap analog is included in the IVT reaction along with the four ribonucleotide triphosphates. Cap analogs are synthetic .. analogs of the N7-methylated guanosine triphosphate cap and can add a natural or unnatural cap to the RNA
(see Muttach, supra). Co-transcriptional capping methods are limited, however, because the cap analogue competes with GTP as initiator nucleotide in the reaction and, as such, not all mRNA obtained from such IVT is capped. This problem can be mitigated in part using an optimized ratio of cap analog to GTP (i.e., by lowering the GTP concentration) or by digesting uncapped (i.e., triphosphorylated) RNA
with a phosphatase which .. dephosphorylates the 5' end of the RNA (see Muttach, supra). However, the former solution decreases the overall efficiency of the reaction and the latter solution adds work. As such, neither method solves the problem in a practical way and consequently producing large quantities of homogenously capped RNA remains technically challenging.
Therefore, there is still a need for a way to efficiently produce homogenously capped RNA by co-.. transcriptional capping.
SUMMARY
A method is provided for capping an RNA in an in vitro transcription reaction, that includes the steps of:
(a) combining rNTPs, a DNA template, a cap analog and an RNA polymerase that comprises: (i) an amino acid sequence that is at least 80% sequence identical to SEQ ID NO:1;
and (ii) an amino acid substitution at one or more positions corresponding to positions 388 and 567 of SEQ ID
NO:1, to produce a reaction mix; and (b) incubating the reaction mix under conditions suitable for in vitro transcription of the DNA
template to produce a capped RNA copy of the template.
In examples provided herein the cap analog has the following formula:

it ti ii 00,4-0¨P -0-P-O-P -0-R4 ...µ=
0¨ 0¨ 0¨

where:
R3 is selected from guanosine, adenosine, cytidine, uridine, guanosine analog, adenosine analog, .. cytidine analog, uridine analog;
R4 is (N1p)xN2 wherein Ni and N2 are ribonucleosides, and N1 is the same or different from N2;
p is, independently for each position, a phosphate group, a phosphorothioate, phosphorodithioate, alkylphosphonate, arylphosphonate, or an N-phosphoramidate linkage; and x is 0-8 where the ribonucleosides N1 in (N1-p)x are the same or different from each other if X> 2.
R1 and R2 groups are independently selected from 0-alkyl (0-methyl), halogen, a tag, hydrogen or a hydroxyl.
The tag may be joined directly to the ribose or may be joined via a linker group. The tag may be an affinity binding group such as biotin, desthiobiotin or an oligonucleotide.
The tag may be a reactive group. The tag may be a detectable label such as a fluorescent molecule.
In addition, the sugars in Ni and N2 may be independently, for each position, selected from ribose and deoxyribose, and may comprise modifications including 2'-0-alkyl, 2'-0-methoxyethyl, 2'-0 ally!, 2'-0 alkylamine, 2'-fluororibose, and 2'-deoxyribose; and/or the bases in Ni and N2 are independently, for each position, selected from adenine, uridine, guanine, or cytidine or analogs of adenine, uridine, guanine, or cytidine, and nucleotide modifications can be selected from 1\16-methyladenine, N1-methyladenine, N6-2'-0-dimethyladenosine, pseudouridine, N1-methylpseudouridine, 5-iodouridine, 4-thiouridine, 2-thiouridine, 5-methyluridine, pseudoisocytosine, 5-methoxycytosine, 2-thiocytosine, 5-hydroxycytosine, N4-methylcytosine, 5-hydroxymethylcytosine, hypoxanthine, N1-methylguanine, 06-methylguanine, 1-methyl-guanosine, N2-methyl-guanosine, N2,N2-dimethyl-guanosine, 2-methyl-guanosine, N2-methyl-guanosine, 1-methyl-guanosine, N2,N2-dimethyl-guanosine, and isoguanine.
Other features of the cap may be its presence in the mixture as a salt or solvated form. The cap may be

2 a single stereoisomer or plurality of stereoisomers of one or more of the compounds described by Formula 1 or a salt or salts thereof.
The cap is added for in vitro transcription. It is well known in the art that an RNA polymerase is agnostic about the cap so that although a variety of caps are described herein, they represent examples and are not intended to be inclusive. The examples the describe the use of m7G-p3-A1pG2pG3p only for convenience and is not intended to be limiting.
RNA polymerase variants are provided that are preferably thermostable. More specifically, the RNA
polymerase variant may include (i) an amino acid sequence is at least 80%
sequence identity to SEQ ID NO:1;
and (ii) an amino acid substitution at one or more positions corresponding to 388, and 567 of SEQ ID NO:1.
More specifically, the RNA polymerase may additionally include an amino acid substitution of at least one position or two or all 4 positions corresponding to positions selected from the group consisting of 109, 205, 534, and 618 of SEQ ID NO:1. More specifically, the RNA polymerase variant may include a mutation or mutations corresponding to D388E and/or V567P. More specifically, the RNA polymerase variant may additionally include an amino acid substitutions at one or more positions or at least 10 positions corresponding to positions selected from the group consisting of: 75, 83, 108, 206, 227, 281, 297, 312, 323, 327, 333, 340, 354, 362, 375, 428, 446, 454, 461, 495, 510, 584, 591, 642, 711, 724, 740, 788, 832, 834, 835, 843, 847, 849, 856, 863, 866 and 877 of SEQ ID NO:1. For example, one or more or ten or more substitutions may include T75Q, A83K, E108L, K206P, V227I, I281P, V297I, Y312D, A323I, A327P, K333P, V340E, A354Q, M362P, T375K, T375N, A428P, L446F, K454P, K461R, 5495N, C510Q, A584K, D591E, K642R, K711R, A724P, K740R, G788A, M832F, D834E, T835L, A843Q, D847E, F849V, 5856T, A863P, A866K and E877R.
The RNA polymerase variants may be used in the methods and kits described herein. Examples of kits contain separately or together a cap or cap analog according to Formula 1 and an RNA polymerase variant described above plus instructions for use including for achieving at least 95%
capping, using an incubation temperature in the range of at least 30 C to about 70 C.
In one aspect, the polymerase variant may be fused to an exogenous DNA binding domain.
BRIEF DESCRIPTION OF THE DRAWINGS
The skilled artisan will understand that the drawings described below, are for illustration purposes only.
The drawings are not intended to limit the scope of the present teaching in any way.
FIG. 1 schematically illustrates how transcription is initiated from a DNA
template showing one of the two promoters recognized by T7RNA polymerase. These are duplexes having a 5' TAATACGACTCACTATA (SEQ ID
NO:2) sequence (used in FIGs. 1, 2D, 3A, 38) and the Class II promoter sequence 5' TAATACGACTCACTATT (SEQ

3

4 ID NO:4) (used in FIG. 3C).
FIG. 1 shows how conventional co-transcriptional capping methods can result in a mixture of capped products (which have a 5'- m7G -ppp) and uncapped products (which have a 5'-ppp). During the process of IVT, the RNA polymerase binds the promoter sequence in the DNA template (represented in gray) and initiates transcription from the second strand in a 5' direction at a sequence downstream of the promoter represented by the +1 nucleotide in this schematic diagram. The RNA synthesized from this template by the RNA polymerase in the presence of standard nucleotides only has a sequence of ppp-A+1G+2 (rest of the RNA). When the RNA is synthesized from this template by the RNA polymerase in the presence of the trinucleotide cap and standard nucleotides, the RNA transcript should have a 5' sequence of m7G -A+1G+2 (rest of the RNA). However, commercial T7 RNA polymerases provide inefficient 5' m7G incorporation resulting in a heterogeneous population of transcripts where some of the RNA transcripts are capped with 5' m7GAG and some are uncapped

5'-ppp-AG.
FIG. 2A-2D shows chromatograms from liquid chromatography-mass spectrometry (LC-MS) analyses of capped synthetic RNA molecules created by transcription of a 25-base pair template with promoter sequence of (SEQ ID NO:2) TAATACGACTCACTATA -A+1G+2G+3 N+25. Wild-type T7 RNA polymerase (WT-T7) was used for transcription at 37 C and a variant of WT-T7 (M20) was used for transcription at 37 C and 50 C. The transcription product was a 25-mer RNA that was capped (Cap-RNA) or if capping was incomplete, phosphorylated (ppp-RNA).
The X-axis denotes the mass of the RNA products detected and Y-axis denotes the intensity of each RNA
species. Capping efficiency was measured using the following formula:
(intensity of capped peaks)/[(intensity of capped peaks) + (intensity of the ppp peaks)].
This data shows that the thermostable polymerase M20, which is a thermostable variant of T7 RNA
polymerase that is characterized by amino acid substitutions at positions corresponding to 388 and 567 of the WT-T7 sequence among other mutations (see, e.g., US Patent Application Serial No. 15/594,090, which is incorporated by reference herein) initiates transcription using a cap analog with 100% efficiency at 37 C and 50 C, as opposed to the WT- T7 polymerase, which initiates transcription using a cap analog with only 92%
efficiency.
FIG. 2A shows the capping efficiency using WT-T7 (reaction temperature 37 C) where peaks were observed corresponding to capped RNA and also to phosphorylated uncapped RNA.
92% of the RNA was capped and 8% was phosphorylated. Several peaks are shown for capped transcripts because of the know phenomenon of addition of a single nucleotide at the 3' end. Here a 26th nucleotide may be added at the 3' end of the 25-nucleotide transcript to generate two additional peaks corresponding to an addition of C or an addition of G.
FIG. 28 shows the capping efficiency of using M20-T7 RNA polymerase (reaction temperature 37 C) where peaks were observed corresponding to capped RNA only and none to phosphorylated uncapped RNA.
100% of the RNA was capped.
FIG. 2C shows the capping efficiency of using M20-T7 RNA polymerase (reaction temperature 50 C) where peaks were observed corresponding to capped RNA only and none to phosphorylated uncapped RNA.
.. 100% of the RNA was capped.
FIG. 2D shows the 5' sequence of the promoter and first 2 nucleotides of a 25-nucleotide transcript associated with a tri-nucleotide cap and a third nucleotide and the products of transcription with (1) 5' cap m7G
pAG and (2) 5' triphosphorylated AG.
FIGs.3A-3C provide capping efficiencies using an m7G -pop-X.1 G+2 trinucleotide cap during transcription from templates that contained varying promoter sequences for initiation of transcription or varying the nucleotide at the +3 position on the sequence to be transcribed. The mutant M20-T7 RNA polymerase showed improved capping efficiency regardless of changes in the promoter sequence or in changes to the nucleotide at the +3-position compared with WT-T7. M20-T7 RNA polymerase has greater capping efficiency than the commercial T7 mutant RNA polymerase (Toyobo, Osaka, Japan).
The results shown in FIGs. 3A-3C demonstrate that the commercially available "Toyobo" variant of T7 RNA polymerase (Toyobo, Osaka, Japan) initiates transcription using a cap analog with less than 90% efficiency at 37 C and 50 C (FIG. 3A) compared with the thermostable T7 polymerase M20.
Thermostable T7 RNA
polymerase M20 initiates transcription using a cap analog with close to 100%
efficiency at 37 C and 50 C (FIG.
3B). These results are consistent for the two different promoters tested (FIG.
3B and FIG. 3C).
FIG. 3A provides in tabular form, the capping efficiency comparing T7-WT RNA
polymerase (37 C) and Toyobo mutant T7 RNA polymerase (37 C and 50 C) for the same DNA template as FIG. 2A-2C namely a promoter sequence of TAATACGACTCACTATA (SEQ ID NO:2) with an adjacent 25 nucleotides. The transcript sequence starts at the AGG adjacent to the promoter sequence.
FIG. 3B provides the capping efficiencies observed using the same promoter sequence as in FIG. 3A but .. where the transcription start site for the 25 nucleotides adjacent to the promoter on the DNA template is AGA
instead of AGG. The results for WT-T7 (37 C) and M20-T7 RNA polymerase (37 C
and 50 C) show that M20-T7 RNA polymerase transcribes this template as efficiently as the template in FIG. 3A.
FIG. 3C provides the capping efficiencies observed using a different promoter sequence from FIG. 3A
and FIG. 3B namely with a promoter sequence of TAATACGACTCACTATT (SEQ ID NO:4) and where the adjacent 25 nucleotides of DNA template for transcription start with AGG. The results for WT-T7 (37 C) and M20-T7 RNA
polymerase (37 C and 50 C) show that M20-T7 RNA polymerase transcribes this template as efficiently as the template in FIG. 3A and 3B.
FIG. 4A-4C shows that capping efficiency of a 1.7kb functional mRNA is increased when transcription is done with the RNA polymerase variant M20. This data shows that the M20 polymerase initiates transcription of a 1.7Kb mRNA using a cap analog with almost 100% efficiency at 37 C and 50 C.
FIG. 4A is a schematic representation of the process involved in measuring the capping efficiency of a 1.7kb long mRNA. The capped RNA is subjected to gel electrophoresis, RNaseH-mediated fragmentation to resolve the 5' end into capped and uncapped products and then subjected to MS
analyses for evaluating the capping efficiency.
FIG. 4B Gel electrophoresis analyses of the RNase-H treated mRNA showing the presence and separation of the capped and the uncapped (ppp) 5' RNA fragments.
FIG. 4C Increased capping efficiency was observed with M20 RNA polymerase variant at 37 C and 50 C
as compared to WT-T7 when m7G-ppp-A-p-G polynucleotide cap was used in the reaction. Capping efficiency is measured using the following formula: (intensity of capped peaks)/[(intensity of capped peaks) + (intensity of the ppp peaks)].
DESCRIPTION OF EMBODIMENTS
Methods and compositions for increasing co-transcriptional capping efficiency of in vitro transcribed RNA is provided using an engineered RNA polymerase variant. Present embodiments utilize any of multiple types of polynucleotide caps as substrates for the polymerase variant for IVT
of DNA templates to form capped RNA molecules.
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as .. commonly understood by one of ordinary skill in the art to which this invention belongs. Singleton, et al., DICTIONARY OF MICROBIOLOGY AND MOLECULAR BIOLOGY, 2D ED., John Wiley and Sons, New York (1994), and Hale & Markham, THE HARPER COLLINS DICTIONARY OF BIOLOGY, Harper Perennial, N.Y. (1991) provide one of skill with the general meaning of many of the terms used herein. Still, certain terms are defined below for the sake of clarity and ease of reference. Preferably, any further interpretations of terms should be consistent with US 10,034,951.
As used herein, the term "in vitro transcription" (IVT) refers to a cell-free reaction in which a double-stranded DNA (dsDNA) template is copied by a DNA-directed RNA polymerase to produce a product that contains RNA molecules that have been copied from the template.
As used herein, the term "DNA template" refers to a dsDNA molecule that is transcribed in an IVT
reaction. DNA templates have a promoter (e.g., a T7, T3 or 5P6 promoter) recognized by the RNA polymerase upstream of the region that is transcribed.
As used herein, the term "RNA product" refers to the product of an IVT
reaction. The RNA product of IVT
contains a mixture of RNA molecules and, depending on how the transcription is done, may contain double-

6 stranded RNA (dsRNA) molecules. The molecular events that generate dsRNA
molecules in IVT reactions is unknown, but they can be detected using an antibody that is specific for dsRNA
or liquid chromatography (e.g., HPLC), for example.
As used herein, the term "variant" protein refers to a protein that has an amino acid sequence that is different from a naturally occurring amino acid sequence (i.e., having less than 100% sequence identity to the amino acid sequence of a naturally occurring protein) but that is at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 98% or at least 99% identical to the naturally occurring amino acid sequence. Thus the variant may have one or more amino acid substitutions relative to a wild-type protein. A variant protein may include a "fusion" protein. The term "fusion protein" refers to a protein composed of a plurality of polypeptide components that are unjoined in their native state. Fusion proteins may be a combination of two, three or even four or more different proteins. The term polypeptide includes fusion proteins, including, but not limited to, a fusion of two or more heterologous amino acid sequences, a fusion of a polypeptide with: a heterologous targeting sequence, a linker, an epitope tag, a detectable fusion partner, such as a fluorescent protein, 13-galactosidase, luciferase, etc., and the like. A fusion protein may have one or more heterologous domains added to the N-terminus, C-terminus, and or the middle portion of the protein.
If two parts of a fusion protein are "heterologous", they are not part of the same protein in its natural state.
As used herein, the term "buffering agent", refers to an agent that allows a solution to resist changes in pH when acid or alkali is added to the solution. Examples of suitable non-naturally occurring buffering agents that may be used in the compositions, kits, and methods of the invention include, for example, Tris, HEPES, TAPS, MOPS, tricine, or M ES.
The term "pharmaceutical acceptable excipient" is any solvent that is compatible with administration to a living mammalian organism via transdermal, oral, intravenous, or other administration means used in the art.
Examples of pharmaceutical acceptable excipients include those described for example in US 2017/0119740.
The term "non-naturally occurring" refers to a composition that does not exist in nature.
Any protein described herein may be non-naturally occurring, where the term "non-naturally occurring"
refers to a protein that has an amino acid sequence and/or a post-translational modification pattern that is different from the protein in its natural state. For example, a non-naturally occurring protein may have one or more amino acid substitutions, deletions or insertions at the N-terminus, the C-terminus and/or between the N-and C-termini of the protein. A "non-naturally occurring" protein may have an amino acid sequence that is different from a naturally occurring amino acid sequence (i.e., having less than 100% sequence identity to the amino acid sequence of a naturally occurring protein) but that is at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 98% or at least 99% identical to the naturally occurring amino acid sequence. In certain cases, a non-naturally occurring protein may contain an N-terminal methionine or may lack one or more

7 post-translational modifications (e.g., glycosylation, phosphorylation, etc.) if it is produced by a different (e.g., bacterial) cell.
In the context of a nucleic acid, the term "non-naturally occurring" refers to a nucleic acid that contains:
a) a sequence of nucleotides that is different from a nucleic acid in its natural state (i.e., having less than 100%
sequence identity to a naturally occurring nucleic acid sequence), b) one or more non-naturally occurring nucleotide monomers (which may result in a non-natural backbone or sugar that is not G, A, T or C) and/or c) may contain one or more other modifications (e.g., an added label or other moiety) to the 5'- end, the 3' end, and/or between the 5'- and 3'-ends of the nucleic acid.
In the context of a preparation, the term "non-naturally occurring" refers to:
a) a combination of components that are not combined by nature, e.g., because they are at different locations, in different cells or different cell compartments; b) a combination of components that have relative concentrations that are not found in nature; c) a combination that lacks something that is usually associated with one of the components in nature; d) a combination that is in a form that is not found in nature, e.g., dried, freeze dried, crystalline, aqueous; and/or e) a combination that contains a component that is not found in nature. For example, a preparation may contain a "non-naturally occurring" buffering agent (e.g., Tris, HEPES, TAPS, MOPS, tricine or M ES), a detergent, a dye, a reaction enhancer or inhibitor, an oxidizing agent, a reducing agent, a solvent or a preservative that is not found in nature.
The term "cap analog" includes natural caps such as 7mG and any compound of the general formula R3 0 a a 11 11 li N
________________________ 0¨P¨O ¨ ¨P¨OP¨O¨R4 i 0¨ 0¨ 0 Wherein R3 is selected from guanosine, adenosine, cytidine, uridine, guanosine analog, adenosine analog, cytidine analog, uridine analog;
R4 is (N1p)xN2wherein Ni and N2 are ribonucleosides, and N1 is the same or different from N2;
p is, independently for each position, a phosphate group, a phosphorothioate, phosphorodithioate, alkylphosphonate, arylphosphonate, or an N-phosphoramidate linkage; and x is 0-8 where the ribonucleosides N1 in (N1-p)x are the same or different from each other if X> 2.
R1 and R2 groups are independently selected from 0-alkyl (0-methyl), halogen, a tag, hydrogen or a hydroxyl.
Cap analogs are added at the 5' end of an RNA transcript in a process called co-transcriptional capping to yield a 5' capped RNA (see, e.g., Muttach, supra).

8 Cap analogs include dinucleotide cap analogs, e.g., of formula m2G(51p3(5')G, in which a guanine nucleotide (G) is linked via its 5'0H to the triphosphate bridge. In some dinucleotide cap analogs the 3'-OH group is replaced with hydrogen or OCH3 (U.S. 7,074,596; Kore, Nucleotides, Nucleotides, and Nucleic Acids, 2006, 25:
307-14; and Kore, Nucleotides, Nucleotides, and Nucleic Acids, 2006, 25: 337-40). Dinucleotide cap analogs .. include m2G(51p3G, 3'-0Me-m2G(51p3G (ARCA). The term "cap analog" also includes trinucleotide cap analogs (defined below) as well as other, longer, molecules (e.g., cap analog that have four, five or six or more nucleotides joined to the triphosphate bridge).
In a cap analog, the sugars in Ni and N2 may be independently, for each position, selected from ribose and deoxyribose, and may comprise modifications including 2'-0-alkyl, 2'-0-methoxyethyl, 2'-0 ally!, 2'-0 alkylamine, 2'-fluororibose, and 2'-deoxyribose; and/or the bases in Ni and N2 may be independently, for each position, selected from adenine, uridine, guanine, or cytidine or analogs of adenine, uridine, guanine, or cytidine, and nucleotide modifications can be selected from N6-methyladenine, N1-methyladenine, N6-2'-0-dimethyladenosine, pseudouridine, N1-methylpseudouridine, 5-iodouridine, 4-thiouridine, 2-thiouridine, 5-methyluridine, pseudoisocytosine, 5-methoxycytosine, 2-thiocytosine, 5-hydroxycytosine, N4-methylcytosine, 5-hydroxymethylcytosine, hypoxanthine, N1-methylguanine, 06-methylguanine, 1-methyl-guanosine, N2-methyl-guanosine, N2,N2-dimethyl-guanosine, 2-methyl-guanosine, N2-methyl-guanosine, 1-methyl-guanosine, N2,N2-dimethyl-guanosine, and isoguanine.
The term "trinucleotide cap analog" refers to a cap analog wherein x=1.
Several trinucleotide cap analogs, e.g., m2G(51p3ApG, m2G(51p3AmpG (Am is adenine with a 2'0Me-ribose), m2G(51p3m6AmpG (m6A is N6-methyladenine), and m2G(51p3m6ApG are disclosed by Ishikawa, et al., Nucleic Acid Symp. Ser., 2009 53:129-30, and many others are described in US 2018/0105551, which publications are incorporated by reference herein.
Provided herein, among other things, is a method for capping an RNA in an IVT
reaction, co-transcriptionally, i.e., using a cap analog and achieving at least 95% capping efficiency.
In some embodiments, the method may comprise (a) combining rNTPs, or modified rNTPs, a DNA
template, a cap analog and a RNA polymerase that comprises: (i) an amino acid sequence is at least 80%
sequence identity to SEQ ID NO:1; and (ii) an amino acid substitution at one or more positions corresponding to positions 388 and 567 of SEQ ID NO:1, to produce a reaction mix; and (b) incubating the reaction mix under conditions suitable for IVT of the DNA template to produce a capped RNA copy of the template. This method, in which the capping is done co-transcriptionally, results in a product that is almost completely capped (e.g., at least 90%, at least 98% or at least 99% capped) and, as such, the RNA product can potentially be used without any post-transcriptional enzymatic steps. In some embodiments the polymerase may be thermostable and, as

9 such, the reaction can be done at a temperature that is in the range of 30 C
to 70 C, e.g., a temperature of 37 C, a temperature of 50 C or a temperature in the range of 50 C to 65 C.
In some embodiments, the RNA polymerase (M20) used in the method: (i) may have an amino acid sequence with at least 80% sequence identity (e.g., at least 90%, at least 90%, at least 95%, at least 97%, at least 98% or at least 99% identity) to SEQ ID NO:1; and (ii) may comprise one or more (e.g., at least two, at least three, at least five, or at least ten) amino acid substitutions at one or more positions corresponding to positions 75, 83, 108, 109, 205, 206, 227, 281, 297, 312, 323, 327, 333, 340, 354, 362, 375, 388, 428, 446, 454, 461, 495, 510, 534, 567, 584, 591, 618, 642, 711, 724, 740, 788, 832, 834, 835, 843, 847, 849, 856, 863, 866, and 877 of SEQ ID NO:1 (WT-T7), shown below:
SEQ ID NO:1:
MNTINIAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPL
ITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEA
RFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEML
IESTGMVSLHRQNAGVVGQDSETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGR
RPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELPMKP
EDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFN
PQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAE
QDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAM LRDEVGGRAVNLLPSETVQDIYGIVAKK
VNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQ
VLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRK
RCAVHWVTPDGFPVWQEYKKPIQTRLNLM FLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLR
KTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPAL
PAKGNLNLRDILESDFAFA
Examples of variants include RNA polymerases with an amino acid substitution at one or more (e.g., at least two, three, four, five or six) positions corresponding to positions selected from 109, 205, 388, 534, 567 and 618 of SEQ ID NO:1. In some embodiments, the polymerase may comprise an amino acid substitution at one or both positions corresponding to positions 388 and 567.
For example, the RNA polymerase: having an amino acid sequence with at least 80% sequence identity (e.g., at least 90%, at least 95%, at least 97%, at least 98% or at least 99%
identity) to SEQ ID NO:1; and may include one or more (e.g., at least two, at least three, at least five, or at least ten) of the following amino acid substitutions: T75Q, A83K, E108L, K206P, V227I, I281P, V297I, Y312D, A323I, A327P, K333P, V340E, A354Q, M362P, T375K, T375N, A428P , L446F, K454P, K461R, 5495N, C510Q, A584K, D591E, K642R, K711R, A724P, K740R, G788A, M832F, D834E, T835L, A843Q, D847E, F849V, 5856T, A863P, A866K, and E877R, wherein the amino acid substitutions are at positions that correspond to positions in SEQ
ID NO:1.
The variant RNA polymerase may include one or more (e.g., one, two, three, four, five or all six) of the following amino acid substitutions: 1109L, H2055, D388E, L534V, V567P and G618Q, wherein the amino acid substitutions are at positions that correspond to positions in SEQ ID NO:1, as well as well as optionally one or more (e.g., at least two, at least three, at least five, or at least ten) of the following amino acid substitutions:
T75Q, A83K, E108L, K206P, V227I, I281P, V297I, Y312D, A323I, A327P, K333P, V340E, A354Q, M362P, T375K, T375N, A428P , L446F, K454P, K461R, S495N, C510Q, A584K, D591E, K642R, K711R, A724P, K740R, G788A, M832F, D834E, T835L, A843Q, D847E, F849V, S856T, A863P, A866K, and E877R, wherein the amino acid .. substitutions are at positions that correspond to positions in SEQ ID NO:1 The variant RNA polymerase may contain any or all of the features described in US 2017/0247670.
The variant RNA polymerase may also be a variant SP6 RNA polymerase or variant T3 RNA polymerase all of which are closely related in sequence function and properties.
In one embodiment, the method for optimizing the efficiency of capping of an RNA with a cap analog .. includes forming a mixture of reagents with a DNA template, wherein the reagent mixture includes a mixture of rNTPs, and/or modified nucleotides, a cap analog and an RNA polymerase variant of the type described in US
Patent Application Serial No. 15/594,090 and exemplified herein with a variant identified as M20 where M20 has at least 80% sequence identity (e.g., at least 90%, at least 95%, or 100%
sequence identity) with SEQ ID NO:1, one or both mutations corresponding to position 388 and 567 in SEQ ID NO:1, and potentially other mutations .. up to and including any, some or all of the mutations described above. At least 95% of the transcript formed in the reaction mixture containing the variant RNA polymerase was capped. The efficiency of capping of a newly formed transcript using the reaction mixture was shown to be significantly greater when the RNA polymerase is mutant T7 compared with WT-T7. Confirmation of improved efficiency of co-transcriptional capping to provide at least 95% capping was also demonstrated using Mass spectrometry (Mass Spec) where the capped to .. uncapped RNA having 5'ppp was compared.
RNA polynucleotide caps can be in a salt or solvated form. RNA polynucleotide caps can be single stereoisomers or a plurality of stereoisomers of one or more of the compounds described by Formula 1 or a salt or salts thereof.
The modified cap may include a tag optional attached on the R1 and/or R2 groups by a linker, Examples .. of tags include detectable labels for example those detected by fluorescence or by color facilitating the detection and quantitation of RNA after transcription. The modified cap may include a binding moiety (such as biotin, desthiobiotin, digoxigenin; groups that form an irreversible bond with a protein tag (benzylguanine or benzylchoropyrimidine (SNAP-tag); benzylcytosine (CLIP-tag); haloalkane (HaloTag)) or the like to facilitate enrichment leading to for example, identification by size or mass. One or more components of the transcription .. reaction (initiating capped oligonucleotide primer and/or NTPs) may be labeled with a detectable label (such as anthraniloyl group, Alexa Fluor dyes; coumarin dyes, BODIPY dyes, Quantum Dots, ATTO dyes) or marker so that the RNA after can be identified, for example, by size, mass, affinity capture or color. The detectable label is a fluorescent dye; and the affinity capture label is biotin or others.

The methods and compositions provided here can be used for the in vitro synthesis by enzyme-dependent transcription of any desired DNA template and sequence to make a 5 '-capped RNA. For example, the DNA template may have a sequence consistent with naturally occurring or synthetic mRNA, tRNA, guide RNA, small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), small cajal body-specific RNA (scaRNA). The transcribed RNA may include one or more modified nucleoside monophosphates, one or more modified sugars in addition to the cap polynucleotide structure (Formula 1).
The cap polynucleotide can have a structure that resembles either a Cap 0 structure (no methylation of 2'0H of +1 ribose), a Cap 1 structure (methylation of 2'0H of +1 ribose), or a Cap 2 structure (methylation of 2'0H of +2 ribose) similar to natural cap structures.
While the methods described herein describe a thermostable T7 RNA polymerase variant mediated transcription reaction, other enzymes, including natural or mutated variants that may be utilized include, for example, SP6 and T3 RNA polymerases and RNA polymerases from other sources including thermostable RNA
polymerases.
Kits including, the cap analog and the polymerase variant for performing transcription are also contemplated with one or more of the following reagents: modified or unmodified cap analog, one or more unmodified NTPs, one or more modified NTPs, an RNA polymerase or variant, other enzymes, a reaction buffer, magnesium and a DNA template. The kit may also include instructions for incubating the reaction at a temperature in the range of 30 C to 70 C, e.g., a temperature of 37 C, a temperature of 50 C or a temperature in the range of 37 C-50 C or 50 C to 65 C.
In some embodiments, the RNA product may encode a protein, e.g., a therapeutic protein or a protein expected to alter the cells into which it is introduced and, as such, the RNA
molecules in the RNA product may have a 5' untranslated region (5' UTR), one or more coding sequences, and a 3' translated region (3' UTR), where the 3' and 5' UTRs facilitate translation of the one or more coding sequence to produce a protein within the cells. In other embodiments, the RNA product may be a therapeutic RNA. In some embodiments the RNA
product may be a guide RNA, a short hairpin RNA, a siRNA, a microRNA, a long noncoding RNA, or a protein-coding RNA (which may encode a recombinant protein or a protein that is native to the cells). In some embodiments, the RNA product may contain modified nucleotides (triphosphates for which can be added to the IVT reaction).
In these embodiments, modified nucleotides may be incorporated into the IVT
RNA. Incorporation of modified nucleotides can increase in translation efficiency of the RNA and increased stability of the RNA.
Modifications can be present either in the sugars (e.g., 2'-fluororibose, ribose, 2'-deoxyribose, arabinose, and hexose); and/or in the phosphate groups (e.g., phosphorothioates and 5'-N-phosphoramidite linkages); and/or in the nucleotide base (for example, see: US 8,383,340; WO 2013/151666; US
9,428,535132; US 2016/0032316).

In some embodiments, the RNA product may be altered during or after the transcription reaction, e.g., to decrease the rate at which the RNA products are degraded in the cells. In some embodiment, the RNA product may contain capped RNAs (see, for example: WO 2016/090262; WO 2014/152673; WO
2009/149253;
Strenkowska, et al., (2016), Nucleic Acids Research, 44(20):9578-90). RNAs with poly A tails of varying length and labeled RNAs can also be produced.
In some embodiments, the method may further comprise testing or using the RNA
product (e.g., administering the RNA to a mammalian cell that in vitro (i.e., grown in culture), ex vivo or in vivo, without performing post-transcriptional enzymatic step that removes ppp-G and adds a m7G-ppp to the 5' end of the RNA product.
In any embodiment, the IVT may be done using natural NTPs, i.e., GTP, CTP, UTP
and ATP to produce a product that does not contain modified nucleosides.
In any embodiment, the IVT may be done using NTPs corresponding to G, C, U and A in the absence of pseudo-uridine triphosphate to produce a product that does not contain pseudo-uridine. The cells into which the RNA product is introduced may be in vitro (i.e., cells that have been cultured in vitro on a synthetic medium).
In these embodiments, the RNA product may be transfected into the cells. In other embodiments, the cells into which the RNA product is introduced may be in vivo (cells that are part of a mammal). In these embodiments, the introducing may be done by administering the RNA product to a subject in vivo. In some embodiments, the cells into which the RNA product is introduced may present ex vivo (cells that are part of a tissue, e.g., a soft tissue that has been removed from a mammal or isolated from the blood of a mammal).
Methods for making a formulation are also provided. In some embodiments, the method may comprise combining an RNA product made by transcribing a template DNA as described above with a pharmaceutically acceptable excipient to produce a formulation.
In some embodiments, the method comprises (a) transcribing a template DNA with the RNA polymerase using the method described above to produce a capped RNA product with or without modifications; and (b) combining the RNA product with a pharmaceutically acceptable excipient;
wherein the method is done in the absence of a post-transcriptional capping step.
In some embodiments, the method may include administering the formulation to a mammalian subject in an effective therapeutic dose, where the subject may be a human or any non-human animal (e.g., mouse, rat, rabbit, dog, cat, cattle, swine, sheep, horse or primate). Alternatively, the capped RNA may be administered to non-mammalian subject or eukaryotic or prokaryotic cells in vivo or in vivo.
The capped RNA can either be naked or formulated with a suitable excipient for administration to a subject, e.g., a human. Formulations can include liquid formulations (solutions, suspensions, dispersions), topical formulations (gels, ointments, drops, creams), liposomal formulations (such as those described in: US 9,629,804 82; US 2012/0251618 Al; WO 2014/152211; US 2016/0038432 Al). The formulations may include encapsulating the RNA in virus particles.
In some embodiments, capped RNA product can be delivered into the cells by packaging them into nanoparticles such as cationic lipids and polymers, non-viral carriers like protamine. Direct introduction of the RNA into the cell using transfection, microinjection, electroporation, sonoporation can also be implemented.
The delivery (localized or systemic) and the packaging of the RNA (with or without modifications) can be performed at temperatures optimal for the delivery approach or the formulation used (such as those described in: US 9,629,804 82; US 2012/0251618 Al; WO 2014/152211; US 2016/0038432 Al;
US 2016/0032316 Al; US
9,597,413 82; US 2012/0258176).
The methods and compositions provided here can be used for the in vitro synthesis of capped RNA
products encoding proteins such as antigens for vaccines, for cancer immunotherapies (such as those described in: US 8,217,016 82; US 2012/0009221 Al; US 2013/0202645 Al; US 9,587,003 82;
Sahin et. al., (2014): Nature Reviews Drug Discovery 13, 759-80), or allergy tolerance (such as those described in Sahin (2014), supra), or for producing recombinant or naturally occurring protein for protein replacement therapeutics (such as those described in: US 2016/0032316 Al; US 8,680,069; PCT/U52013/031821;
PCT/U52014/028330; US 9,181,321; US
9,220,792 82; US 9,233,141132; Sahin (2014), supra), supplementation therapeutics (such as those described in Sahin (2014), supra), cell reprogramming (such as those described in: US
2011/0143436 Al; US 8,802,438; US
9,371,544; WO 2009/077134 A2; Sahin (2014), supra), genome editing/engineering (such as those described in Sahin (2014), supra). Introduction of capped RNA into target cells can change the cell phenotype by production of proteins or by affecting expression of targets in the cell.
All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference. This includes provisional application serial no.
62/741,111 filed October 4, 2018.
EMBODIMENTS
Embodiment 1. A method for capping an RNA in an IVT reaction, comprising:
(a) combining rNTPs, a DNA template, a cap analog and a RNA polymerase that comprises: (i) an amino acid sequence that is at least 80% sequence identical to SEQ ID NO:1; and (ii) an amino acid substitution at one or more positions corresponding to positions 388 and 567 of SEQ ID NO:1, to produce a reaction mix; and (b) incubating the reaction mix under conditions suitable for IVT of the DNA
template to produce a capped RNA copy of the template.
Embodiment 2. The method of embodiment 1, wherein the cap analog is a dinucleotide cap analog.

Embodiment 3. The method of embodiment 1, wherein the cap analog is a trinucleotide cap analog.
Embodiment 4. The method of any prior embodiment, wherein the cap analog is of the formula R3 0 a a II fl 11 rwon wherein:
R3 is selected from guanosine, adenosine, cytidine, uridine, guanosine analog, adenosine analog, cytidine analog, uridine analog;
R4 is (N1p),(N2 wherein Ni and N2 are ribonucleosides, and N1 is the same or different from N2;
p is, independently for each position, a phosphate group, a phosphorothioate, phosphorodithioate, alkylphosphonate, arylphosphonate, or an N-phosphoramidate linkage; and x is 0-8 where the ribonucleosides N1 in (N1-p)x are the same or different from each other if X> 2.
R1 and R2 groups are independently selected from 0-alkyl (0-methyl), halogen, a tag, hydrogen or a hydroxyl.
Embodiment 5. The method of embodiment 4, wherein the sugars in Ni and N2 are independently, for each position, selected from ribose and deoxyribose, and may comprise modifications including 2'-0-alkyl, 2'-0-methoxyethyl, 2'-0 ally!, 2'-0 alkylamine, 2'-fluororibose, and 2'-deoxyribose; and/or the bases in Ni and N2 are independently, for each position, selected from adenine, uridine, guanine, or cytidine or analogs of adenine, uridine, guanine, or cytidine, and nucleotide modifications can be selected from N6-methyladenine, N1-methyladenine, N6-2'-0-dimethyladenosine, pseudouridine, N1-methylpseudouridine, 5-iodouridine, 4-thiouridine, 2-thiouridine, 5-methyluridine, pseudoisocytosine, 5-methoxycytosine, 2-thiocytosine, 5-hydroxycytosine, N4-methylcytosine, 5-hydroxymethylcytosine, hypoxanthine, N1-methylguanine, 06-methylguanine, 1-methyl-guanosine, N2-methyl-guanosine, N2,N2-dimethyl-guanosine, 2-methyl-guanosine, N2-methyl-guanosine, 1-methyl-guanosine, N2,N2-dimethyl-guanosine, and isoguanine.
Embodiment 6. The method of any prior embodiment, wherein the RNA polymerase comprises an amino acid substitution at positions corresponding to positions 388 and 567 of SEQ ID NO:1.
Embodiment 7. The method of any prior embodiment, wherein the RNA polymerase further comprises an amino acid substitution of at least one position corresponding to positions selected from 109, 205, 534, and 618 of SEQ ID NO:1.

Embodiment 8. The method of any prior embodiment, wherein the RNA polymerase further comprises an amino acid substitution of at least three two positions corresponding to positions selected from 109, 205, 534 and 618 of SEQ ID NO:1.
Embodiment 9. The method of any prior embodiment, wherein the RNA polymerase further comprises .. an amino acid substitution at positions corresponding to positions 109, 205, 534 and 618 of SEQ ID NO:1.
Embodiment 10. The method of any prior embodiment, wherein the RNA polymerase comprises an amino acid sequence that is at least 95% sequence identical to SEQ ID NO:1.
Embodiment 11. The method according to any of the previous embodiments, wherein the capping efficiency is greater than 95%.
Embodiment 12. The method according to embodiment 9, wherein incubating in step (b) further comprises: performing in vitro transcription at a temperature of at least 30 C
to about 70 C.
Embodiment 13. A composition comprising:
rNTPs, a cap analog, and an RNA polymerase that comprises: (i) an amino acid sequence that is at least 80% sequence identical to SEQ ID NO:1; and (ii) an amino acid substitution at one or more positions corresponding to positions 388 and 567 of SEQ ID NO:1.
Embodiment 14. The composition of embodiment 13, wherein the cap analog is of the formula ii il II

41"0"7 wherein:
R3 is selected from guanosine, adenosine, cytidine, uridine, guanosine analog, adenosine analog, cytidine analog, uridine analog;
R4 is (N1p)xN2wherein N1 and N2 are ribonucleosides, and N1 is the same or different from N2;
p is, independently for each position, a phosphate group, a phosphorothioate, phosphorodithioate, alkylphosphonate, arylphosphonate, or an N-phosphoramidate linkage; and x is 0-8 where the ribonucleosides N1 in (N1-p)x are the same or different from each other if X> 2.
R1 and R2 groups are independently selected from 0-alkyl (0-methyl), halogen, a tag, hydrogen or a hydroxyl;

Embodiment 15. The composition of embodiment 12 or 13, wherein the sugars in Ni and N2 are independently, for each position, selected from ribose and deoxyribose, and may comprise modifications including 2'-0-alkyl, 2'-0-methoxyethyl, 2'-0 ally!, 2'-0 alkylamine, 2'-fluororibose, and 2'-deoxyribose; and/or the bases in Ni and N2 are independently, for each position, selected from adenine, uridine, guanine, or cytidine or analogs of adenine, uridine, guanine, or cytidine, and nucleotide modifications can be selected from N6-methyladenine, N1-methyladenine, N6-2'-0-dimethyladenosine, pseudouridine, N1-methylpseudouridine, 5-iodouridine, 4-thiouridine, 2-thiouridine, 5-methyluridine, pseudoisocytosine, 5-methoxycytosine, 2-thiocytosine, 5-hydroxycytosine, N4-methylcytosine, 5-hydroxymethylcytosine, hypoxanthine, N1-methylguanine, 06-methylguanine, 1-methyl-guanosine, N2-methyl-guanosine, N2,N2-dimethyl-guanosine, 2-methyl-guanosine, N2-methyl-guanosine, 1-methyl-guanosine, N2,N2-dimethyl-guanosine, and isoguanine.
Embodiment 16. The composition of any of embodiments 12 or 14, wherein the cap analog is a dinucleotide cap analog or trinucleotide cap analog.
Embodiment 17. The composition of any of embodiments 12-15, wherein the RNA
polymerase comprises an amino acid substitution at positions corresponding to positions 388 and 567 of SEQ ID NO:1.
Embodiment 18. The composition of any of embodiments 12-16, wherein the RNA
polymerase further comprises an amino acid substitution of at least one position corresponding to positions selected from 109, 205, 534, and 618 of SEQ ID NO:1.
Embodiment 19. The composition of any of embodiments 11-17, wherein the RNA
polymerase comprises an amino acid substitution of at least two or three positions corresponding to positions selected from 109, 205, 534 and 618 of SEQ ID NO:1.
Embodiment 20. The composition of any of embodiments 12-18, wherein the RNA
polymerase further comprises an amino acid substitution at positions corresponding to positions 109, 205, 534 and 618 of SEQ ID
NO:1.
Embodiment 21. The composition of any of embodiments 12-18, further comprising a nucleic acid template.
Embodiment 22. A kit comprising:
(a) a cap analog;
(b) an RNA polymerase that comprises: (i) an amino acid sequence is at least 80% sequence identity to SEQ ID NO:1; and (ii) an amino acid substitution at one or more positions corresponding to positions 388 and 567 of SEQ ID NO:1; and (iii) instructions for use including for achieving at least 95% capping, using an incubation temperature in the range of at least 30 C to about 70 C.
Embodiment 23. The kit of embodiment 22, wherein the cap analog is of the formula:

7on wherein:
R3 is selected from guanosine, adenosine, cytidine, uridine, guanosine analog, adenosine analog, cytidine analog, uridine analog;
R4 is (N1p),(N2 wherein Ni and N2 are ribonucleosides, and N1 is the same or different from N2;
p is, independently for each position, a phosphate group, a phosphorothioate, phosphorodithioate, alkylphosphonate, arylphosphonate, or an N-phosphoramidate linkage; and x is 0-8 where the ribonucleosides Ni in (Ni-p)x are the same or different from each other if X> 2.
R1 and R2 groups are independently selected from 0-alkyl (0-methyl), halogen, a tag, hydrogen or a hydroxyl.
Embodiment 24. The kit according to embodiment 22 or 23, wherein the sugars in Ni and N2 are independently, for each position, selected from ribose and deoxyribose, and may comprise modifications including 2'-0-alkyl, 2'-0-methoxyethyl, 2'-0 ally!, 2'-0 alkylamine, 2'-fluororibose, and 2'-deoxyribose; and/or the bases in Ni and N2 are independently, for each position, selected from adenine, uridine, guanine, or cytidine or analogs of adenine, uridine, guanine, or cytidine, and nucleotide modifications can be selected from N6-methyladenine, N1-methyladenine, N6-2'-0-dimethyladenosine, pseudouridine, N1-methylpseudouridine, 5-iodouridine, 4-thiouridine, 2-thiouridine, 5-methyluridine, pseudoisocytosine, 5-methoxycytosine, 2-thiocytosine, 5-hydroxycytosine, N4-methylcytosine, 5-hydroxymethylcytosine, hypoxanthine, N1-methylguanine, 06-methylguanine, 1-methyl-guanosine, N2-methyl-guanosine, N2,N2-dimethyl-guanosine, 2-methyl-guanosine, N2-methyl-guanosine, 1-methyl-guanosine, N2,N2-dimethyl-guanosine, and isoguanine.
Embodiment 24. The kit of any of embodiment 22 -23, wherein the cap analog is a dinucleotide cap analog or trinucleotide cap analog.
Embodiment 25. The kit of any of embodiment 22-24, wherein the RNA polymerase comprises an amino acid substitution at positions corresponding to positions 388 and 567 of SEQ
ID NO:1.
Embodiment 26. The kit of any of embodiment 22-25, wherein the RNA polymerase further comprises an amino acid substitution of at least one position corresponding to positions selected from 109, 205, 534, and 618 of SEQ ID NO:1.

Embodiment 27. The kit of any of embodiment 22-26, wherein the RNA polymerase further comprises an amino acid substitution of at least three two positions corresponding to positions selected from 109, 205, 534 and 618 of SEQ ID NO:1.
Embodiment 28. The kit of any of embodiment 22-27, wherein the RNA polymerase further comprises an amino acid substitution at positions corresponding to positions 109, 205, 534 and 618 of SEQ ID NO:1.
EXAMPLES
Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it is readily apparent to those of ordinary skill in the art in light of the .. teachings of this invention that certain changes and modifications may be made thereto without departing from the spirit or scope of the appended claims. To exemplify the claimed invention, figures have been provided and described in some detail above. The results they demonstrate may be achieved using the methods described below.
Example 1: Method for capping RNA transcripts IVT and synthesis of IVT RNA controls (absent caps) IVT reactions were performed according to the description provided by New England Biolabs, Ipswich, MA, catalog 2017/2018 with WT-T7 and with T7 RNA polymerase from Toyobo using the optimized protocol from Toyobo and T7 RNA variants (M20) using the protocol described for WT-T7 RNA polymerase (New England Biolabs Inc, Ipswich, MA). The double stranded DNA templates for FIG. 1, 2A-2D
and 3A-3C were generated by annealing two single-stranded DNA oligonucleotides. The DNA template for FIG.
4A-C was double stranded plasmid DNA linearized using restriction endonuclease Notl at a site downstream of the T7 promoter (New England Biolabs Inc, Ipswich, MA,). Reactions were performed at 37 C or 50 C
for 1 hour. The RNA products of IVT RNAs were processed through a spin column (Norgen Biotek Corp., Ontario, or MEGACLEARTM, Thermo .. Fisher Scientific, Waltham, Mass.) to remove unincorporated nucleotides before mass-spectrometry analyses.
IVT and synthesis of IVT RNA controls (with caps by co-transcriptional capping) Using the same method as above, 4mM of the trinucleotide cap (m7G -ppp-A-p-G) was used for each reaction according to methods described by Trilink Biotechnologies, CA.
Assay for measuring capping efficiency using LC-Mass spectrometry The spin column processed RNA was subjected to liquid chromatography mass spectroscopy (LC-MS) analyses (Novatia LLC, PA). The capping efficiency was determined using the following formula (intensity of capped peaks)/[ (intensity of capped peak) + (intensity of the ppp peak)].
Assay for measuring capping efficiency of long mRNAs In vitro transcribed mRNAs were generated with RNA polym erase variants in presence of trinucleotide caps (Trilink BioTechnologies, San Diego, CA) were processed through a spin column (MEGACLEARTm, Thermo Fisher Scientific, Waltham, Mass.) to remove unincorporated nucleotides. A
25mer oligonucleotide whose sequence is complementary to the 5' end of the transcribed capped RNA was annealed to the RNA and the annealed oligonucleotide-RNA hybrid was then subjected to RNaseH (New England Biolabs Inc, Ipswich, MA) digestion. The reaction products were then separated by gel electrophoresis so that the 25mer double stranded capped RNA was detected in one band on the gel and the uncapped products were observed in a second band as shown in FIG. 4B. The nucleic acid in both bands were separately extracted and subjected to liquid chromatography mass spectroscopy (LC-MS) analyses. Capping efficiency was determined using the following formula (intensity of capped peaks)/[(intensity of capped peak) + (intensity of the ppp peak)].

Claims (28)

In the claims:

1. A method for capping an RNA in an in vitro transcription reaction, comprising:
(a) combining rNTPs, a DNA template, a cap analog and an RNA polymerase that comprises: (i) an amino acid sequence that is at least 80% sequence identical to SEQ ID NO:1;
and (ii) an amino acid substitution at one or more positions corresponding to positions 388 and 567 of SEQ ID NO:1, to produce a reaction mix; and (b) incubating the reaction mix under conditions suitable for in vitro transcription of the DNA
template to produce a capped RNA copy of the template.

2. The method of claim 1, wherein the cap analog is of the formula:
wherein:
R3 is selected from guanosine, adenosine, cytidine, uridine, guanosine analog, adenosine analog, cytidine analog, uridine analog;
R4 is (N1p)xN2wherein Ni and N2 are ribonucleosides, and Ni is the same or different from N2;
p is, independently for each position, a phosphate group, a phosphorothioate, phosphorodithioate, alkylphosphonate, arylphosphonate, or an N-phosphoramidate linkage; and x is 0-8 where the ribonucleosides Ni in (Ni-p)x are the same or different from each other if X> 2.
R1 and R2 groups are independently selected from 0-alkyl (0-methyl), halogen, a tag, hydrogen or a hydroxyl.

3. The method accordingly claim 1, wherein the sugars in Ni and N2 are independently, for each position, selected from ribose and deoxyribose, and may comprise modifications including 2'-0-alkyl, 2'-0-methoxyethyl, 2'-0 allyl, 2'-0 alkylamine, 2'-fluororibose, and 2'-deoxyribose; and/or the bases in Ni and N2 are independently, for each position, selected from adenine, uridine, guanine, or cytidine or analogs of adenine, uridine, guanine, or cytidine, and nucleotide modifications can be selected from N6-methyladenine, N1-methyladenine, N6-2'-0-dimethyladenosine, pseudouridine, N1-methylpseudouridine, 5-iodouridine, 4-thiouridine, 2-thiouridine, 5-methyluridine, pseudoisocytosine, 5-methoxycytosine, 2-thiocytosine, 5-hydroxycytosine, N4-methylcytosine, 5-hydroxymethylcytosine, hypoxanthine, N1-methylguanine, 06-methylguanine, 1-methyl-guanosine, N2-methyl-guanosine, N2,N2-dimethyl-guanosine, 2-methyl-guanosine, N2-methyl-guanosine, 1-methyl-guanosine, N2,N2-dimethyl-guanosine, and isoguanine.

4. The method of any of claims 1-3, wherein the cap analog is a dinucleotide cap analog or trinucleotide cap analog.

5. The method of any of claims 1-4, wherein the RNA polymerase comprises amino acid substitutions at positions corresponding to positions 388 and 567 of SEQ ID NO:1.

6. The method of any of claims 1-5, wherein the RNA polymerase further comprises an amino acid substitution of at least one position corresponding to positions selected from 109, 205, 534, and 618 of SEQ
ID NO:1.

7. The method of any of claims 1-6, wherein the RNA polymerase further comprises an amino acid substitution of at least two or three positions corresponding to positions selected from 109, 205, 534 and 618 of SEQ ID NO:1.

8. The method of any of claims 1-7, wherein the RNA polymerase comprises an amino acid substitution at positions corresponding to positions 109, 205, 534 and 618 of SEQ ID NO:1.

9. The method of any of claims 1-8, wherein the RNA polymerase comprises an amino acid sequence that is at least 95% sequence identical to SEQ ID NO:1.

10. The method according to any of the previous claims, wherein the capping efficiency is greater than 95%.

11. The method according to any of the previous claims, wherein incubating in step (b) further comprises:
performing in vitro transcription at a temperature of at least 30 C to about 70 C.

12. A composition comprising:
rNTPs, a cap analog, and an RNA polymerase that comprises: (i) an amino acid sequence that is at least 80% sequence identical to SEQ ID NO:1; and (ii) an amino acid substitution at one or more positions corresponding to positions 388 and 567 of SEQ ID NO:1.

13. The composition of claim 12, wherein the cap analog is of the formula wherein:
R3 is selected from guanosine, adenosine, cytidine, uridine, guanosine analog, adenosine analog, cytidine analog, uridine analog;
R4 is (N1p)xN2 wherein Ni and N2 are ribonucleosides, and Ni is the same or different from N2;
p is, independently for each position, a phosphate group, a phosphorothioate, phosphorodithioate, alkylphosphonate, arylphosphonate, or an N-phosphoramidate linkage; and x is 0-8 where the ribonucleosides Ni in (Ni-p)x are the same or different from each other if X> 2.
R1 and R2 groups are independently selected from 0-alkyl (0-methyl), halogen, a tag, hydrogen or a hydroxyl;

14. The composition of claims 12 or 13, wherein the sugars in Ni and N2 are independently, for each position, selected from ribose and deoxyribose, and may comprise modifications including 2'-0-alkyl, 2'-0-methoxyethyl, 2'-0 allyl, 2'-0 alkylamine, 2'-fluororibose, and 2'-deoxyribose; and/or the bases in Ni and N2 are independently, for each position, selected from adenine, uridine, guanine, or cytidine or analogs of adenine, uridine, guanine, or cytidine, and nucleotide modifications can be selected from N6-methyladenine, N1-methyladenine, N6-2'-0-dimethyladenosine, pseudouridine, N1-methylpseudouridine, 5-iodouridine, 4-thiouridine, 2-thiouridine, 5-methyluridine, pseudoisocytosine, 5-methoxycytosine, 2-thiocytosine, 5-hydroxycytosine, N4-methylcytosine, 5-hydroxymethylcytosine, hypoxanthine, N1-methylguanine, 06-methylguanine, 1-methyl-guanosine, N2-methyl-guanosine, N2,N2-dimethyl-guanosine, 2-methyl-guanosine, N2-methyl-guanosine, 1-methyl-guanosine, N2,N2-dimethyl-guanosine, and isoguanine.

15. The composition of claims 12 or 14, wherein the cap analog is a dinucleotide cap analog or trinucleotide cap analog.

16. The composition of any of claims 12-15, wherein the RNA polymerase comprises an amino acid substitution at positions corresponding to positions 388 and 567 of SEQ ID NO:1.

17. The composition of any of claims 12-16, wherein the RNA polymerase further comprises an amino acid substitution of at least one position corresponding to positions selected from 109, 205, 534, and 618 of SEQ
ID NO:1.

18. The composition of any of claims 11-17, wherein the RNA polymerase comprises an amino acid substitution of at least two or three positions corresponding to positions selected from 109, 205, 534 and 618 of SEQ ID
NO:1.

19. The composition of any of claims 12-18, wherein the RNA polymerase further comprises an amino acid substitution at positions corresponding to positions 109, 205, 534 and 618 of SEQ ID NO:1.

20. The composition of any of claims 12-18, further comprising a nucleic acid template.

21. A kit comprising:
(a) a cap analog;
(b) an RNA polymerase that comprises: (i) an amino acid sequence is at least 80% sequence identity to SEQ ID NO:1; and (ii) an amino acid substitution at one or more positions corresponding to positions 388 and 567 of SEQ ID NO:1; and (iii) instructions for use including for achieving at least 95%
capping, using an incubation temperature in the range of at least 30 C to about 70 C.

22. The kit of claim 21, wherein the cap analog is of the formula wherein:
R3 is selected from guanosine, adenosine, cytidine, uridine, guanosine analog, adenosine analog, cytidine analog, uridine analog;
R4 is (N1p)x1\12 wherein Ni and N2 are ribonucleosides, and Ni is the same or different from N2;
p is, independently for each position, a phosphate group, a phosphorothioate, phosphorodithioate, alkylphosphonate, arylphosphonate, or an N-phosphoramidate linkage; and x is 0-8 where the ribonucleosides Ni in (Ni-p)x are the same or different from each other if X> 2.
R1 and R2 groups are independently selected from 0-alkyl (0-methyl), halogen, a tag, hydrogen or a hydroxyl.

23. The kit according to claim 21 or 22, wherein the sugars in Ni and N2 are independently, for each position, selected from ribose and deoxyribose, and may comprise modifications including 2'-0-alkyl, 2'-0-methoxyethyl, 2'-0 allyl, 2'-0 alkylamine, 2'-fluororibose, and 2'-deoxyribose; and/or the bases in Ni and N2 are independently, for each position, selected from adenine, uridine, guanine, or cytidine or analogs of adenine, uridine, guanine, or cytidine, and nucleotide modifications can be selected from N6-methyladenine, N1-methyladenine, N6-2'-0-dimethyladenosine, pseudouridine, N1-methylpseudouridine, 5-iodouridine, 4-thiouridine, 2-thiouridine, 5-methyluridine, pseudoisocytosine, 5-methoxycytosine, 2-thiocytosine, 5-hydroxycytosine, N4-methylcytosine, 5-hydroxymethylcytosine, hypoxanthine, N1-methylguanine, 06-methylguanine, 1-methyl-guanosine, N2-methyl-guanosine, N2,N2-dimethyl-guanosine, 2-methyl-guanosine, N2-methyl-guanosine, 1-methyl-guanosine, N2,N2-dimethyl-guanosine, and isoguanine.

24. The kit of any of claims 21-23, wherein the cap analog is a dinucleotide cap analog or trinucleotide cap analog.

25. The kit of any of claims 21-24, wherein the RNA polymerase comprises an amino acid substitution at positions corresponding to positions 388 and 567 of SEQ ID NO:1.

26. The kit of any of claims 21-25, wherein the RNA polymerase further comprises an amino acid substitution of at least one position corresponding to positions selected from 109, 205, 534, and 618 of SEQ ID NO:1.

27. The kit of any of claims 21-26, wherein the RNA polymerase further comprises an amino acid substitution of at least three two positions corresponding to positions selected from 109, 205, 534 and 618 of SEQ ID NO:1.

28. The kit of any of claims 21-27, wherein the RNA polymerase further comprises an amino acid substitution at positions corresponding to positions 109, 205, 534 and 618 of SEQ ID NO:1.