Ribonucleic acid purification

Abstract

Disclosed herein are methods for purifying RNA comprising poly A. Also disclosed herein are compositions such as surfaces and oligonucleotides for purifying RNA comprising polyA. Other embodiments are also disclosed. Commercially-available resins having polythymidine oligonucleotide ligands typically contain less than 30 thymidine (2′deoxy) residues and some commercial resin suppliers utilize a distribution of dT chain lengths, not of a discreet length.

Description

BACKGROUND

Commercially-available resins having polythymidine oligonucleotide ligands typically contain less than 30 thymidine (2′deoxy) residues and some commercial resin suppliers utilize a distribution of dT chain lengths, not of a discreet length. Commercially-available oligo dT resins are predominantly kit-based and are typically utilized for small scale (<1 mg) mRNA isolations on a bench top from crude cell/tissue extracts or blood. Commercially-available matrices typically consist of cellulose, latex particles, and magnetic beads containing dT ligands. These options are not generally viable for large scale chromatographic processes for cGMP manufacture of therapeutic mRNAs. In particular, cellulose resin produces significant quantities of leached ligand, contains significant amounts of fine particulates, and has poor flow properties; making it less than ideal for column chromatography. In terms of RNA quality and purity, commercially-available, cellulose based media has been found to yield eluted PolyA containing RNA with substantial endotoxin contamination as well as considerable enzyme and DNA template carryover and contamination. RNA produced using this commercially-available cellulose resin must generally be coupled with additional separation procedures to ensure RNA is of acceptable quality for pre-clinical studies and therapeutic use. Endotoxin contamination is detrimental to patient safety and therefore a process that introduces endotoxin into a drug substance is generally not viable for use in patients.

SUMMARY

Disclosed herein is a method for purifying an RNA transcript comprising a polyA tail, the method comprising: a) obtaining a first sample comprising the RNA transcript, wherein the first sample comprises at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% RNA transcript and at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% impurities, and wherein the percentage of RNA transcript and the percentage of impurities are the inverse of each other; b) contacting the first sample with a surface linked to a plurality of thymidines or derivatives thereof and/or a plurality of uracils or derivatives thereof (polyT/U) under conditions such that the RNA transcript binds to the surface; c) eluting the RNA transcript from the surface; and d) collecting the RNA transcript in a second sample, wherein the second sample comprises at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% RNA transcript and no more than less than 1%, 1%, 2%, 3%, 4%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% impurities, and wherein the percentage of RNA transcript and the percentage of impurities are the inverse of each other.

In some aspects, the method further comprises washing the surface with a solution after step b). In some aspects, the method further comprises preheating the first sample before step b). In some aspects, one or more steps are performed using a batch process.

In some aspects, the sample comprises DNA and the sample has not been subjected to DNase treatment. In some aspects, the one or more impurities comprise an RNA that does not comprise a polyA tail, a deoxyribonucleic acid (DNA), a carbohydrate, a toxin, a polypeptide, and/or a nucleotide. In some aspects, the DNA is plasmid DNA. In some aspects, the DNA is polymerase chain reaction (PCR) product DNA. In some aspects, the DNA comprises non-amplified DNA template. In some aspects, the toxin is lipopolysaccharide (LPS). In some aspects, the toxin is an endotoxin.

In some aspects, the surface is a resin. In some aspects, the surface comprises sepharose. In some aspects, the surface comprises agarose. In some aspects, polyT/U is 5 to 200 thymidines and/or uracils in length or 10 to 50 thymidines and/or uracils in length. In some aspects, polyT/U is 20 thymidines in length. In some aspects, polyT/U is linked directly to the surface. In some aspects, polyT/U is linked to the surface via a linker.

In some aspects, the contacting step is performed at a temperature of 65° C. In some aspects, the contacting step is performed at a rate of 100 cm/h.

In some aspects, the RNA transcript and polyT/U bind one another via non-covalent bonding. In some aspects, the first sample comprises a salt solution. In some aspects, the first sample comprises a sodium chloride solution.

In some aspects, the washing step comprises applying one or more solutions comprising a salt. In some aspects, the salt is NaCl or KCl.

In some aspects, the washing step comprises applying a first salt buffer and a second salt buffer, wherein the first salt buffer has a higher salt concentration than the second salt buffer, and wherein the first salt buffer is applied before the second salt buffer. In some aspects, first salt buffer comprises 0.5M NaCl, 10 mM Tris, and 1 mM EDTA, and has a pH of 7.4. In some aspects, the second salt buffer comprises 0.1M NaCl, 10 mM Tris, and 1 mM EDTA, and has a pH of 7.4. In some aspects, the first salt buffer is applied to the surface at a temperature of 65° C. or 25° C. In some aspects, the first salt buffer is applied to the surface twice, wherein the first application is at a first temperature of 65° C., and wherein the second application is at a second temperature of 25° C. In some aspects, the second salt buffer is applied to the surface at a temperature of 25° C.

In some aspects, the elution step is performed with an elution buffer. In some aspects, the elution buffer is salt-free. In some aspects, the elution buffer comprises 10 mM Tris and 1 mM EDTA, and has a pH of 7.4. In some aspects, the elution step is performed at a temperature of 65° C.

In some aspects, the RNA transcript is the product of in vitro transcription using a non-amplified DNA template. In some aspects, the RNA transcript is 100 to 10,000 nucleotides in length.

In some aspects, the method is repeated 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, or greater than 50 times with the same surface (or any integer between each of the indicated numeric values).

Also disclosed herein is a composition comprising a surface linked to a plurality of thymidines or derivatives thereof and/or a plurality of uracils or derivatives thereof (polyT/U), wherein the surface comprises a polymer, and wherein polyT/U is linked to the surface by a linker.

In some aspects, the polymer is a crosslinked, beaded-form of a polysaccharide polymer material extracted from seaweed. In some aspects, the polymer comprises agarose. In some aspects, the polymer comprises sepharose.

In some aspects, the linker comprises 5′-hexylamine. In some aspects, the linker is coupled to polyT/U via an amide bond.

In some aspects, polyT/U is 5 to 200 thymidines and/or uracils in length or 10 to 50 thymidines and/or uracils in length. In some aspects, polyT/U is 20 thymidines in length. In some aspects, polyT/U comprises one or more modifications. In some aspects, the modification comprises a 2′-O-methyl modification, a 2′-fluoro modification, or a locked nucleic acid (LNA) modification.

In some aspects, the surface is a resin. In some aspects, the resin has a pore size of 300 to 8000 Angstroms or 1000 to 4000 Angstroms.

In some aspects, the composition can be reused 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, or greater than 50 times (or any integer between each of the indicated numeric values).

Also disclosed herein is a method for making the composition of claim [0013], the method comprising: obtaining a surface attached to a first group; and contacting the surface with a polyT/U attached to a second group, wherein the first group and the second group are reactive with one another upon contact.

In some aspects, the first group is N-hydroxysuccinimidyl (NHS) ester. In some aspects, the second group is an amino group. In some aspects, the amino group is located at the 5′ end of polyT/U.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

These and other features, aspects, and advantages of the present invention will become better understood with regard to the following description, and accompanying drawings, where:

FIG. 1a shows a schematic of poly T/U conjugation to NHS-activated Sepharose resin, where R is poly T/U. FIG. 1b shows a reaction used to synthesize a poly T/U resin conjugate with a 5′-hexylamine linker connected via a stable amide linkage (n can be any positive integer, e.g., 49 or 19).

FIG. 2 shows the general resin synthesis process overview.

FIG. 3 shows a general overview of the process used to purify polyadenylated RNA.

FIG. 4 shows gel electropherograms of binding assessment for 20mer dT Sepharose resin.

FIG. 5 shows poly dT column leaching analysis (LC-MS/MS based).

FIG. 6 shows a comparison of resin binding capacity between Applicant's poly dT resin and commercially-available dT resin upon reuse; (resin binding capacity vs. # of uses).

FIG. 7 shows endotoxin Levels in mRNA batches following purification using various poly dT resins.

FIG. 8 shows a 1.2% Agarose gel used to assess plasmid DNA removal in lot 12-04-111-I.

FIG. 9 shows Bioanalyzer electropherograms used to assess mRNA quality after dT sepharose purifications.

FIG. 10 shows a preparative UV Chromatogram from dT Sepharose Purification of 12-04-111-I.

FIG. 11 shows an RNA Quality Assessment of 12-04-1014 by Bioanalyzer chip based electrophoresis.

FIG. 12 shows a 1.2% agarose gel of 12-04-101-I Crude IVT Feedstock pre dT.

FIG. 13 shows a 1.2% agarose gel of 12-04-101-I Post dT Purification.

FIG. 14 shows yield data of 4 consecutive large scale purifications of lot 12-04-79-I.

FIG. 15 shows mRNA quality assessment data of 4 consecutive large scale purifications of lot 12-04-79-I via Bioanalyzer chip-based electrophoresis.

FIG. 16 shows a comparison of 20mer and 50mer polythymidine Sepharose resin.

DETAILED DESCRIPTION

Terms used in the claims and specification are defined as set forth below unless otherwise specified.

Polynucleotide. The term “polynucleotide” is interchangeable with nucleic acid, and includes any compound and/or substance that comprise a polymer of nucleotides. RNA transcripts produced by the method of the invention and DNA templates used in the methods of the invention are polynucleotides. Exemplary polynucleotides include, but are not limited to, ribonucleic acids (RNAs), deoxyribonucleic acids (DNAs), threose nucleic acids (TNAs), glycol nucleic acids (GNAs), peptide nucleic acids (PNAs), locked nucleic acids (LNAs, including LNA having a β-D-ribo configuration, α-LNA having an α-L-ribo configuration (a diastereomer of LNA), 2′-amino-LNA having a 2′-amino functionalization, and 2′-amino-α-LNA having a 2′-amino functionalization) or hybrids thereof.

RNA transcript. As used herein, an “RNA transcript” refers to a ribonucleic acid produced by an in vitro transcription reaction using a DNA template and an RNA polymerase. As described in more detail below, an RNA transcript typically includes the coding sequence for a gene of interest and a poly A tail. RNA transcript includes an mRNA. The RNA transcript can include modifications, e.g., modified nucleotides. As used herein, the term RNA transcript includes and is interchangeable with mRNA, modified mRNA “mmRNA” or modified mRNA, and primary construct. Modified RNA, e.g., RNA transcripts, e.g., mRNA, are disclosed in the following which is incorporated by reference for all purposes: U.S. patent application Ser. No. 13/791,922, “MODIFIED POLYNUCLEOTIDES FOR THE PRODUCTION OF BIOLOGICS AND PROTEINS ASSOCIATED WITH HUMAN DISEASE,” filed Mar. 9, 2013.

Gene of interest. As used herein, “gene of interest” refers to a polynucleotide which encodes a polypeptide or protein of interest. Depending on the context, the gene of interest refers to a deoxyribonucleic acid, e.g., a gene of interest in a DNA template which can be transcribed to an RNA transcript, or a ribonucleic acid, e.g., a gene of interest in an RNA transcript which can be translated to produce the encoded polypeptide of interest in vitro, in vivo, in situ or ex vivo. As described in more detail below, a polypeptide of interest includes but is not limited to, biologics, antibodies, vaccines, therapeutic proteins or peptides, etc.

DNA template. As used herein, a DNA template refers to a polynucleotide template for RNA polymerase. Typically a DNA template includes the sequence for a gene of interest operably linked to a RNA polymerase promoter sequence.

Operably linked: As used herein, the phrase “operably linked” refers to a functional connection between two or more molecules, constructs, transcripts, entities, moieties or the like. For example, a gene of interest operably linked to an RNA polymerase promoter allows transcription of the gene of interest.

Poly A tail. As used herein, “poly A tail” refers to a chain of adenine nucleotides. The term can refer to poly A tail that is to be added to an RNA transcript, or can refer to the poly A tail that already exists at the 3′ end of an RNA transcript. As described in more detail below, a poly A tail is typically 5-300 nucleotides in length.

In vitro: As used herein, the term “in vitro” refers to events that occur in an artificial environment, e.g., in a test tube or reaction vessel, in cell culture, in a Petri dish, etc., rather than within an organism (e.g., animal, plant, or microbe).

It must be noted that, as used in the specification and the appended claims, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise.

Compositions

Poly T/U

Described herein are surfaces linked to poly T/U oligonucleotides. The term “poly T/U oligonucleotide” or “poly T/U” or “poly U/T” refers to a nucleic acid comprising a plurality of thymidines and/or uracils, including, but not limited to, a uracil ribonucleic acid (RNA); a thymidine deoxyribonucleic acid (DNA); or a mixed ribonucleotide-deoxyribonucleotide, i.e., the poly T/U oligonucleotide can include ribose or deoxyribose sugars or a mixture of both. Included are analogs thereof and poly T/U of various lengths. Double and single stranded forms of the poly T/U oligonucleotides are provided. In one embodiment, poly T/U is a 20-mer dT oligonucleotide.

The poly T/U oligonucleotide can include other 5-carbon or 6-carbon sugars, such as, for example, arabinose, xylose, glucose, galactose, or deoxy derivatives thereof or other mixtures of sugars.

Poly T/U Lengths

In certain embodiments, the poly T/U oligonucleotide can refer to nucleic acid molecules of 2-2000 nucleotides in length or any integer therein. In one aspect, the length of poly T/U is designed to vary with the length of the target polyA sequence, the specificity required, the reaction and the hybridization and wash conditions. In some aspects, poly T/U can range from about 5 to about 200 bases or from about 15 to about 50 bases. In some aspects, poly T/U can be 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60 or greater than 60 bases in length.

Poly T/U Chemistries

In one aspect, one or more bases of poly T/U can be modified. In some aspects, poly T/U can be modified to increase stability of poly T/U. In some aspects, poly T/U can be modified to increase chemical stability of poly T/U. In some aspects, poly T/U can be modified to increase pH stability of poly T/U. In some aspects, poly T/U can be modified to increase thermal stability of poly T/U.

In certain embodiments, the poly T/U oligonucleotide and/or an oligonucleotide sequence complementary to the poly T/U oligonucleotide can comprise a 3 ‘-oligonucleotide modification, a 5’-oligonucleotide modification, a phosphorothioate, an LNA, a PNA, a morpholino, other alternative backbones, or combinations or derivatives thereof. Suitable poly T/U oligonucleotides can be composed of naturally occurring nucleosides adenosine, guanosine, cytidine, thymidine and uridine, modified nucleosides, substituted nucleosides or unsubstituted nucleosides, or combinations thereof. The nucleosides can also be unnatural nucleosides. The nucleosides can be joined by naturally occurring phosphodiester linkages or modified linkages. The nucleosides can also be joined by phosphorothioate linkages or methylphosphonate linkages.

In some aspects, poly T/U can include or be modified with one or more modifications such as: Poly dT (DNA), Poly Uridine (RNA), 2′O-Methyl Uridine RNA (MNA), 2′Fluoro Uridine RNA (FNA), Locked Nucleic Acid (LNA), Peptide Nucleic Acid (PNA), Additional 2′ modified RNAs, Carbohydrates or derivatives thereof, or any combination of any of the above chemistries.

In some aspects, the backbone of poly T/U can include phosphate, phoshorothioate, phosphorodithioate, and/or phosphonoacetate.

In some aspects, poly T/U can include pyrimidine derivatives such as thymidine analogs, uridine analogs, and/or heterocycle modifications. In some aspects, poly T/U can include purine derivaties or analogs such as those that help maintain hydrogen bonding patterns with adenosine.

In some aspects, poly T/U can be attached to a linker. In some aspects, the linker can be at the 5′ end of poly T/U. In some aspects, the linker can be at the 3′ end of poly T/U. In some aspects, the linker can be located internally within poly T/U. Internal linkers can include spacer derivatives with or without modifications or nucleoside derivatives with or without modifications. Linkers are described in more detail herein.

In some aspects, poly T/U can be attached to a spacer. Spacers are described in more detail herein.

Surfaces

Compositions and methods of the invention can use a surface linked to poly T/U. As used herein, the term “surface” refers to a part of a support structure (e.g., a substrate) that is accessible to contact with one or more reagents, poly T/U oligonucleotides, etc. The shape, form, materials, and modifications of the surface can be selected from a range of options depending on the application. In one embodiment, the surface is sepharose. In one embodiment, the surface is agarose.

The surface can be substantially flat or planar. Alternatively, the surface can be rounded or contoured. Exemplary contours that can be included on a surface are wells, depressions, pillars, ridges, channels or the like.

Exemplary materials that can be used as a surface include, but are not limited to acrylics, carbon (e.g., graphite, carbon-fiber), cellulose (e.g., cellulose acetate), ceramics, controlled-pore glass, cross-linked polysaccharides (e.g., agarose or SEPHAROSE™), gels, glass (e.g., modified or functionalized glass), gold (e.g., atomically smooth Au(111)), graphite, inorganic glasses, inorganic polymers, latex, metal oxides (e.g., SiO2, TiO2, stainless steel), metalloids, metals (e.g., atomically smooth Au(111)), mica, molybdenum sulfides, nanomaterials (e.g., highly oriented pyrolitic graphite (HOPG) nanosheets), nitrocellulose, NYLON™. optical fiber bundles, organic polymers, paper, plastics, polacryloylmorpholide, poly(4-methylbutene), polyethylene terephthalate), poly(vinyl butyrate), polybutylene, polydimethylsiloxane (PDMS), polyethylene, polyformaldehyde, polymethacrylate, polypropylene, polysaccharides, polystyrene, polyurethanes, polyvinylidene difluoride (PVDF), quartz, rayon, resins, rubbers, semiconductor material, silica, silicon (e.g., surface-oxidized silicon), sulfide, and TEFLON™. A single material or mixture of several different materials can form a surface useful in the invention.

In some aspects, a surface comprises a polymer.

In some aspects, a surface comprises Sepharose™. An example is shown below, where n is any positive integer:

In some aspects, a surface comprises agarose. An example is shown below, where n is a positive integer:

Structure of agarose: D-galactose and 3,6-anhydro-α-L-galactopyranose repeating Unit.

In some aspects, a surface comprises a Polystyrene based polymer. A Polystyrene divinyl benzene copolymer synthesis schematic is shown below:

In some aspects, a surface comprises an Acrylic based polymer. Poly (methylmethacrylate) is an example shown below, wherein n is any positive integer:

In some aspects, a surface comprises a Dextran based polymer. A Dextran example is shown below:

In some aspects, a surface comprises silica. An example is shown below:

In some aspects, a surface comprises a polyacrylamide. An example cross-linked to N—N-methylenebisacrylamide is shown below:

In some aspects, a surface comprises tentacle based phases, e.g., methacrylate based.

A number of surfaces known in the art are suitable for use with the methods of the invention. Suitable surfaces comprise materials including but not limited to borosilicate glass, agarose, sepharose, magnetic beads, polystyrene, polyacrylamide, membranes, silica, semiconductor materials, silicon, organic polymers, ceramic, glass, metal, plastic polycarbonate, polycarbonate, polyethylene, polyethyleneglycol terephthalate, polymethylmethacrylate, polypropylene, polyvinylacetate, polyvinylchloride, polyvinylpyrrolidinone, and soda-lime glass.

In one embodiment, the surface is modified to contain channels, patterns, layers, or other configurations (e.g., a patterned surface). The surface can be in the form of a bead, box, column, cylinder, disc, dish (e.g., glass dish, PETRI dish), fiber, film, filter, microtiter plate (e.g., 96-well microtiter plate), multi-bladed stick, net, pellet, plate, ring, rod, roll, sheet, slide, stick, tray, tube, or vial. The surface can be a singular discrete body (e.g., a single tube, a single bead), any number of a plurality of surface bodies (e.g., a rack of 10 tubes, several beads), or combinations thereof (e.g., a tray comprises a plurality of microtiter plates, a column filled with beads, a microtiter plate filed with beads).

In some aspects, a surface can include a membrane based resin matrix. In some aspects, a surface can include a resin such as a porous resin or a non-porous resin. Examples of porous resins can include: Additional Agarose based resins (e.g., Cyanogen bromide activated sepharose (GE); WorkBeads™ 40 ACT and WorkBeads 40/10000 ACT (Bioworks)), Methacrylate: (Tosoh 650M derivatives etc.), Polystyrene Divinylbenzene (Life Tech Poros media/GE Source media), Fractogel, Polyacrylamide, Silica, Controlled pore glass, Dextran derivatives, Acrylamide derivatives, and/or Additional polymers; or any combination thereof.

In some aspects, a surface can include one or more pores. In some aspects, pore sizes can be from 300 to 8,000 Angstroms, e.g., 500 to 4,000 Angstroms in size.

In some aspects, a surface can include one or more particles. Examples of particle sizes are 5 um-500 um, 20 um-300 um, and 50 um-200 um. In some aspects, particle size can be 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200 um.

Poly T/U can be immobilized, coated on, bound to, stuck, adhered, or attached to any of the forms of surfaces described herein (e.g., bead, box, column, cylinder, disc, dish (e.g., glass dish, PETR1 dish), fiber, film, filter, microtiter plate (e.g., 96-well microtiter plate), multi-bladed stick, net, pellet, plate, ring, rod, roll, sheet, slide, stick, tray, tube, or vial).

In one embodiment, the surface is modified to contain chemically modified sites that can be used to attach, either covalently or non-covalently, poly T/U to discrete sites or locations on the surface. “Chemically modified sites” in this context includes, but is not limited to, the addition of a pattern of chemical functional groups including amino groups, carboxy groups, oxo groups and thiol groups, that can be used to covalently attach poly T/U, which generally also contain corresponding reactive functional groups. Examples of surface functionalizations are: Amino derivatives, Thiol derivatives, Aldehyde derivatives, Formyl derivatives, Azide Derivatives (click chemistry), Biotin derivatives, Alkyne derivatives, Hydroxyl derivatives, Activated hydroxyls or derivatives, Carboxylate derivatives, activated carboxylate derivates, Activated carbonates, Activated esters, NHS Ester (succinimidyl), NHS Carbonate (succinimidyl), Imidoester or derivated, Cyanogen Bromide derivatives, Maleimide derivatives, Haloacteyl derivatives, Iodoacetamide/iodoacetyl derivatives, Epoxide derivatives, Streptavidin derivatives, Tresyl derivatives, Diene/conjugated diene derivatives (diels alder type reaction), Alkene derivatives, Substituted phosphate derivatives, Bromohydrin/halohydrin, Substituted disulfides, Pyridyl-disulfide Derivatives, Aryl azides, Acyl azides, Azlactone, Hydrazide derivatives, Halobenzene derivatives, Nucleoside derivatives, Branching/multi functional linkers, Dendrimeric funcationalities, and/or Nucleoside derivatives; or any combination thereof.

In some aspects, a surface is linked to poly T/U. In some aspects, the binding capacity of the linked surface can be, e.g., >1 mg/mL, >5 mg/mL, >10 mg/mL, >20 mg/mL, >30 mg/mL, or >40 mg/mL.

Linkers

In some aspects, a surface and/or poly T/U can be attached to a linker. The term “linker” can refer to a connection between two molecules or entities, for example, the connection between poly T/U and a spacer or the connection between poly T/U and a surface (e.g., a 5′ hexylamine linker). The linker can be formed by the formation of a covalent bond or a non-covalent bond. Suitable covalent linkers can include, but are not limited to the formation of an amide bond, an oxime bond, a hydrazone bond, a triazole bond, a sulfide bond, an ether bond, an enol ether bond, an ester bond, or a disulfide bond.

A “linker” can refer to either the two or more groups present prior to contact between the groups (e.g. linker precursor groups); or the new group(s) or bond(s) formed after contact between the two or more groups (e.g., linker group(s)). See “Surface synthesis” section for examples of linkers (e.g., first group, second group, bond) and various reaction schemes.

In some aspects, the linker is a 5′-hexylamine linker. In some aspects, the 5′-hexylamine linker can be formed as shown below, where n is any positive integer, e.g., 5 to 500. For example, n is 19 for a 20-mer; and n is 49 for a 50-mer.

In some embodiments, linkers can optionally be included at a variety of positions within or on poly T/U and/or a surface. Suitable linkers include alkyl and aryl groups, including heteroalkyl and heteroaryl, and substituted derivatives of these. In some instances, linkers can be amino acid based and/or contain amide linkages. Examples of linkers are: Amino derivatives, Thiol derivatives, Aldehyde derivatives, Formyl derivatives, Azide Derivatives (click chemistry), Biotin derivatives, Alkyne derivatives, Hydroxyl derivatives, Activated hydroxyls or derivatives, Carboxylate derivatives, activated carboxylate derivates, Activated carbonates, Activated esters, NHS Ester (succinimidyl), NHS Carbonate (succinimidyl), Imidoester or derivated, Cyanogen Bromide derivatives, Maleimide derivatives, Haloacteyl derivatives, Iodoacetamide/iodoacetyl derivatives, Epoxide derivatives, Streptavidin derivatives, Tresyl derivatives, Diene/conjugated diene derivatives (diels alder type reaction), Alkene derivatives, Substituted phosphate derivatives, Bromohydrin/halohydrin, Substituted disulfides, Pyridyl-disulfide Derivatives, Aryl azides, Acyl azides, Azlactone, Hydrazide derivatives, Halobenzene derivatives, Nucleoside derivatives, Branching/multi functional linkers, Dendrimeric funcationalities, and/or Nucleoside derivatives; or any combination thereof.

Spacers

A surface can include a spacer in addition to or instead of a linker. Spacers can include atoms such as carbon or molecules, e.g., carbohydrates, nucleic acids such as DNA or RNA, and/or amino acids; or combinations or analogs thereof. In some aspects, spacers can range from about 5 to about 200 atoms or from about 15 to about 50 atoms. In some aspects, spacers can be 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 atoms in length.

Methods

RNA Purification

Also disclosed herein are methods for purifying RNA comprising polyA. In some aspects, a method for purifying an RNA transcript comprising a polyA tail includes obtaining a first sample comprising the RNA transcript, wherein the first sample comprises at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% RNA transcript and at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% impurities; contacting the first sample with a surface linked to a plurality of thymidines or derivatives thereof and/or a plurality of uracils or derivatives thereof (polyT/U) under conditions such that the RNA transcript binds to the surface; eluting the RNA transcript from the surface; and collecting the RNA transcript in a second sample, wherein the second sample comprises at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% RNA transcript and no more than less than 1%, 2%, 3%, 4%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% impurities.

In some aspects, the method can further includes washing the surface with a solution after the contacting step. In some aspects, the method can further include preheating the first sample before the contacting step. In some aspects, preheating can be at a temperature of 25, 35, 45, 55, 65, 70, 75, 80, 85, or 90° C.

In some aspects, one or more steps of the method are performed using a batch process. In some aspects, one or more steps of the method are performed using a column. In some aspects, the column can be heated and/or jacketed.

In some aspects, the first sample comprises DNA and the sample has not been subjected to DNase treatment. In some aspects, the one or more impurities comprise an RNA that does not comprise a polyA tail, a deoxyribonucleic acid (DNA), a carbohydrate, a toxin, a polypeptide, and/or a nucleotide. In some aspects, the DNA is plasmid DNA. In some aspects, the DNA is polymerase chain reaction (PCR) product DNA. In some aspects, the DNA comprises non-amplified DNA template. In some aspects, the toxin is lipopolysaccharide (LPS). In some aspects, the toxin is an endotoxin.

In some aspects, the surface is a resin. In some aspects, the surface comprises sepharose and/or agarose. In some aspects, polyT/U is 5 to 200 thymidines and/or uracils in length or 10 to 50 thymidines and/or uracils in length. In some aspects, polyT/U is 20 thymidines in length. In some aspects, polyT/U is linked directly to the surface. In some aspects, polyT/U is linked to the surface via a linker. Examples of linkers that can be used for linking are: Amino derivatives, Thiol derivatives, Aldehyde derivatives, Formyl derivatives, Azide Derivatives (click chemistry), Biotin derivatives, Alkyne derivatives, Hydroxyl derivatives, Activated hydroxyls or derivatives, Carboxylate derivatives, activated carboxylate derivates, Activated carbonates, Activated esters, NHS Ester (succinimidyl), NHS Carbonate (succinimidyl), Imidoester or derivated, Cyanogen Bromide derivatives, Maleimide derivatives, Haloacteyl derivatives, Iodoacetamide/iodoacetyl derivatives, Epoxide derivatives, Streptavidin derivatives, Tresyl derivatives, Diene/conjugated diene derivatives (diels alder type reaction), Alkene derivatives, Substituted phosphate derivatives, Bromohydrin/halohydrin, Substituted disulfides, Pyridyl-disulfide Derivatives, Aryl azides, Acyl azides, Azlactone, Hydrazide derivatives, Halobenzene derivatives, Nucleoside derivatives, Branching/multi functional linkers, Dendrimeric funcationalities, and/or Nucleoside derivatives; or any combination thereof.

In some aspects, the contacting step is performed at a temperature of 65° C. In some aspects, the contacting step is performed at 4 to 90C. In some aspects, the contacting step is performed at 20 to 70C. In some aspects, the contacting step is performed at 4, 25, 35, 45, 55, 65, 70, 75, 80, 85, or 90C.

In some aspects, the contacting step is performed at a rate of 100 cm/h. In some aspects, the contacting step is performed at a rate of 5 to 7000 cm/h, e.g., 50 to 500 cm/h. In some aspects, the contacting step can be performed in a recirculation mode.

In some aspects, the contacting step is performed using a batch process.

In some aspects, the RNA transcript and polyT/U bind one another via non-covalent bonding. In some aspects, the solution comprising the RNA transcript comprises salt during the contacting step with the surface. Salts are described herein.

In some aspects, the first sample comprises a salt solution. In some aspects, the salt concentration is 0.1-5M, 0.3-2.5M, or 0.5-1M. In some aspects, the salt is a sodium salt, e.g., NaCl. In some aspects, the salt is potassium salt, lithium salt, magnesium salt, calcium salt, and/or ammonium salt. In some aspects, the first sample comprises a sodium chloride solution.

In some aspects, the method can further includes washing the surface with a solution after the contacting step.

In some aspects, the washing step comprises applying one or more solutions comprising a salt. In some aspects, the salt is NaCl or KCl. In some aspects, the salt is NaCl. In some aspects, the salt can be sodium salts, potassium salts, magnesium salts, lithium salts, calcium salts, manganese salts, cesium salts, ammonium salts, and/or alkylammonium salts. In some aspects, the salt can be NaCl, KCl, MgCl2, Ca2+, MnCl2, and/or LiCl.

In some aspects, the washing step comprises applying a first salt buffer and a second salt buffer, wherein the first salt buffer has a higher salt concentration than the second salt buffer, and wherein the first salt buffer is applied before the second salt buffer. In some aspects, the first salt buffer comprises 0.5M NaCl, 10 mM Tris, and 1 mM EDTA, and has a pH of 7.4. In some aspects, the pH can be 4 to 9, e.g., 6 to 8. In some aspects, the second salt buffer comprises 0.1M NaCl, 10 mM Tris, and 1 mM EDTA, and has a pH of 7.4. In some aspects, the pH can be 4 to 9, e.g., 6 to 8. In some aspects, the first salt buffer is applied to the surface at a temperature of 65° C. or 25° C. In some aspects, the temperature can be 4 to 85C. In some aspects, the first salt buffer is applied to the surface twice, wherein the first application is at a first temperature of 65° C., and wherein the second application is at a second temperature of 25° C. In some aspects, the second salt buffer is applied to the surface at a temperature of 25° C. In some aspects, the temperature can be 4 to 85C.

In some aspects, the elution step is performed with an elution buffer. In some aspects, the elution buffer is salt-free. In some aspects, the elution buffer comprises 10 mM Tris and 1 mM EDTA, and has a pH of 7.4. In some aspects, the elution buffer comprises water. In some aspects, the elution buffer comprises a low ionic strength un-buffered salt solution. In some aspects, the elution buffer comprises a low ionic strength buffered salt solution.

Examples of buffers that can be used are shown below in Table A. For example the buffers shown in Table A can be used in one or more elution buffers, first salt buffers, second salt buffers, and solutions used during the contacting step.

TABLE A
Buffer	pKa 25° C.	pH range
ACES	6.78	6.1-7.5
acetate	4.76	3.6-5.6
ADA	6.59	6.0-7.2
AMP (2-amino-2-methyl-1-propanol)	9.69	8.7-10.4
AMPD (2-amino-2-methyl-1,3-	8.80	7.8-9.7
propanediol)
AMPSO	9.00	8.3-9.7
BES	7.09	6.4-7.8
BICINE	8.26	7.6-9.0
bis-tris	6.46	5.8-7.2
BIS-TRIS propane	6.80, 9.00	6.3-9.5
borate	9.23, 12.74, 13.80	8.5-10.2
cacodylate	6.27	5.0-7.4
carbonate (pK1)	6.35	6.0-8.0
carbonate (pK2)	10.33	9.5-11.1
CHES	9.50	8.6-10.0
citrate (pK1)	3.13	2.2-6.5
citrate (pK2)	4.76	3.0-6.2
citrate (pK3)	6.40	5.5-7.2
DIPSO	7.52	7.0-8.2
EPPS, HEPPS	8.00	7.6-8.6
ethanolamine	9.50	6.0-12.0
formate	3.75	3.0-4.5
glycine (pK1)	2.35	2.2-3.6
glycine (pK2)	9.78	8.8-10.6
glycylglycine (pK1)	3.14	2.5-3.8
glycylglycine (pK2)	8.25	7.5-8.9
HEPBS	8.30	7.6-9.0
HEPES	7.48	6.8-8.2
HEPPSO	7.85	7.1-8.5
histidine	1.70, 6.04, 9.09	5.5-7.4
hydrazine	8.10	7.5-10.0
imidazole	6.95	6.2-7.8
malate (pK1)	3.40	2.7-4.2
malate (pK2)	5.13	4.0-6.0
maleate (pK1)	1.97	1.2-2.6
maleate (pK2)	6.24	5.5-7.2
MES	6.10	5.5-6.7
MOBS	7.60	6.9-8.3
MOPS	7.14	6.5-7.9
MOPSO	6.87	6.2-7.6
phosphate (pK1)	2.15	1.7-2.9
phosphate (pK2)	7.20	5.8-8.0
phosphate (pK3)	12.33
piperazine (pK1)	5.33	5.0-6.0
piperazine (pK2)	9.73	9.5-9.8
piperidine	11.12	10.5-12.0
PIPES	6.76	6.1-7.5
POPSO	7.78	7.2-8.5
propionate	4.87	3.8-5.6
pyridine	5.23	4.9-5.9
pyrophosphate	0.91, 2.10, 6.70, 9.32	7.0-9.0
succinate (pK1)	4.21	3.2-5.2
succinate (pK2)	5.64	5.5-6.5
TABS	8.90	8.2-9.6
TAPS	8.40	7.7-9.1
TAPSO	7.61	7.0-8.2
taurine (AES)	9.06	8.4-9.6
TES	7.40	6.8-8.2
Tricine	8.05	7.4-8.8
triethanolamine (TEA)	7.76	7.0-8.3
Trizma (tris)	8.06	7.5-9.0

In some aspects, the elution step is performed at a temperature of 65° C. In some aspects, the elution step is performed at a temperature of 4 to 95C. In some aspects, the elution step is performed at a temperature of 25 to 80C. In some aspects, the elution step is performed at a temperature of 45 to 70C.

In some aspects, the RNA transcript is the product of in vitro transcription using a non-amplified DNA template. In some aspects, the RNA transcript is 100 to 10,000 nucleotides in length. In some aspects, the RNA transcript is 500 to 4000 nucleotides in length. In some aspects, the RNA transcript is 800 to 3000 nucleotides in length.

Surface Synthesis

Also disclosed herein are methods of surface synthesis and attachment of poly T/U. In some aspects, a method for making a surface includes obtaining a surface attached to a first group; and contacting the surface with a polyT/U attached to a second group, wherein the first group and the second group are reactive with one another upon contact.

In some aspects, the first group is N-hydroxysuccinimidyl (NHS) ester. In some aspects, the first group is NHS carbonate. In some aspects, the second group is an amino group. In some aspects, the amino group is located at the 5′ end of polyT/U.

In some aspects, examples of the first group are: Amino derivatives, Thiol derivatives, Aldehyde derivatives, Formyl derivatives, Azide Derivatives (click chemistry), Biotin derivatives, Alkyne derivatives, Hydroxyl derivatives, Activated hydroxyls or derivatives, Carboxylate derivatives, activated carboxylate derivates, Activated carbonates, Activated esters, NHS Ester (succinimidyl), NHS Carbonate (succinimidyl), Imidoester or derivated, Cyanogen Bromide derivatives, Maleimide derivatives, Haloacteyl derivatives, Iodoacetamide/iodoacetyl derivatives, Epoxide derivatives, Streptavidin derivatives, Tresyl derivatives, Diene/conjugated diene derivatives (diels alder type reaction), Alkene derivatives, Substituted phosphate derivatives, Bromohydrin/halohydrin, Substituted disulfides, Pyridyl-disulfide Derivatives, Aryl azides, Acyl azides, Azlactone, Hydrazide derivatives, Halobenzene derivatives, Nucleoside derivatives, Branching/multi functional linkers, Dendrimeric funcationalities, and/or Nucleoside derivatives; or any combination thereof.

In some aspects, examples of the second group are: Amino derivatives, Thiol derivatives, Aldehyde derivatives, Formyl derivatives, Azide Derivatives (click chemistry), Biotin derivatives, Alkyne derivatives, Hydroxyl derivatives, Activated hydroxyls or derivatives, Carboxylate derivatives, activated carboxylate derivates, Activated carbonates, Activated esters, NHS Ester (succinimidyl), NHS Carbonate (succinimidyl), Imidoester or derivated, Cyanogen Bromide derivatives, Maleimide derivatives, Haloacteyl derivatives, Iodoacetamide/iodoacetyl derivatives, Epoxide derivatives, Streptavidin derivatives, Tresyl derivatives, Diene/conjugated diene derivatives (diels alder type reaction), Alkene derivatives, Substituted phosphate derivatives, Bromohydrin/halohydrin, Substituted disulfides, Pyridyl-disulfide Derivatives, Aryl azides, Acyl azides, Azlactone, Hydrazide derivatives, Halobenzene derivatives, Nucleoside derivatives, Branching/multi functional linkers, Dendrimeric funcationalities, and/or Nucleoside derivatives; or any combination thereof.

In some aspects, the first group and the second group react to form a bond. In some aspects the bond is an amide bond.

In some aspects, the first group and the second group can be either of the groups (or the group) shown on the left-hand side of the arrow in the reaction schemes shown/detailed below; and the bond can be the group shown on the right-hand side of the arrow(s) in the reaction schemes shown/detailed below.

Amide (substituted amine+substituted succinimidyl ester yields an amide bond) or (azlactone+amine) or (amine+acyl azide) or (amine+succinic anhydride) or (carboxyl+amine with carbodiimide derivatives). For example:

Thioether bond (thiol+maleimide) or (Thiol+haloacetyl) or (thiol+epoxide) or (Halohydrin (ie bromohydrin)+thiol) or (tresyl+thiol) or (thiol+acryloyl derivative) or (sulfhydryl+fluorobenzene derivatives). For example:

Carbamate (Succinimidyl Carbonate+Amine) or (Carbonyldiimizaole Derivative+Amine). For Example:

Triazole (alkyne+azide (click chemistry)). For example:

Triazoline (alkene+azide). For example:

Secondary amine (Aldehyde+amine [reductive amination], or (epoxide+amine) or (Halohydrin (ie bromohydrin)+amine) or (tresyl+amine). For example:

iii. Halohydrin (ie bromohydrin)+amine

• • iv. Amine+tresyl

Substituted cylclohexene (conjugated diene+substituted alkene[diels alder reaction). For example:

Hydrazone linkage (hydrazide+aldehyde). For example:

Thiourea linkage (isothiocyanate+amine). For example:

Ester (hydroxyl+carboxyl (w/1,1-carbonyldiimidazole[CDI])

Substituted disulfide (substituted thiol+pyridal disulfide (aryldisulfide). For example:

Isourea derivative (cyanogen bromide+amine). For example:

(Strept)avidin/Biotin

Substituted Ether (Halohydrin (ie bromohydrin)+hydroxyl)

Arylamine bond (Amine+fluorobenzene derivative). For example:

Amidine linkage (amine+imidoester derivative). For example:

Phosphoramidate bond (alkyl phosphate derivative+amine). For example:

Any use of bifunctional crosslinkers, e.g., Homobifunctional/heterobifunctional, PEG linkers, Peptide linkers, and/or EDC Linkers.

Any use of photochemistry/photoconjugation, e.g., Arylazides and/or Benzophenones.

Examples

Below are examples of specific embodiments for carrying out the present invention. The examples are offered for illustrative purposes only, and are not intended to limit the scope of the present invention in any way. Efforts have been made to ensure accuracy with respect to numbers used (e.g., amounts, temperatures, etc.), but some experimental error and deviation should, of course, be allowed for.

The practice of the present invention will employ, unless otherwise indicated, conventional methods of protein chemistry, biochemistry, recombinant DNA techniques and pharmacology, within the skill of the art. Such techniques are explained fully in the literature. See, e.g., T. E. Creighton, Proteins: Structures and Molecular Properties (W.H. Freeman and Company, 1993); A. L. Lehninger, Biochemistry (Worth Publishers, Inc., current addition); Sambrook, et al., Molecular Cloning: A Laboratory Manual (2nd Edition, 1989); Methods In Enzymology (S. Colowick and N. Kaplan eds., Academic Press, Inc.); Remington's Pharmaceutical Sciences, 18th Edition (Easton, Pennsylvania: Mack Publishing Company, 1990); Carey and Sundberg Advanced Organic Chemistry 3rd Ed. (Plenum Press) Vols A and B (1992).

General Materials and Methods

Resin Synthesis

The purpose of this protocol was to synthesize Oligo dT sepharose resin for use as a medium for affinity based chromatographic purification of polyadenylated mRNA. Bulk NHS activated Sepharose 4 FF was functionalized with a 20mer polythymidine oligonucleotide containing a 5′-hexylamine linker via a stable amide linkage.

FIG. 1a shows a schematic of poly T/U conjugation to NHS-activated Sepharose resin. FIG. 1b shows a reaction used to synthesize a poly T/U resin conjugate with a 5′-hexylamine linker via a stable amide linkage (n can be any positive integer, e.g., 49 or 19). FIG. 2 shows the general resin synthesis process overview.

Materials:

	Material	Vendor	Part #
	NHS-Activated Sepharose 4 FF	GE Healthcare
	Resin
	20mer Polythymidine	OligoFactory
	oligonucleotide with 5'
	hexylamine linker (HPLC
	Purified/desalted/lyophilized)
	Seq: 5'NH2-(C6)-dT-dT- dT- dT- dT- dT-
	dT- dT- dT- dT- dT- dT- dT- dT- dT- dT-
	dT- dT- dT- dT- 3'
Stock
Solutions
	Dimethylsulfoxide (DMSO)	Sigma Aldrich	D8418-
	Molecular Biology Grade		500 ML
	Sodium Bicarbonate (NaHCO3),	Sigma Aldrich	S5761-
	powder, Molecular Biology		500G
	Grade
	0.1 M Hydrochloric Acid	Sigma Aldrich	84434-
			500 ML
	1 M Tris HCl pH 8.0	Invitrogen	15568025
	3 M Sodium Actetate (NaOAc)	Ambion	AM9740
	pH 5.5
	Ethanol, Molecular Biology	Fisher
	Grade
	DNase/RNase free water	MilliQ or
		Equivalent
Prepared
Solutions
	1mM Hydrochloric Acid
	100 mM Tris HCl pH 8
	100 mM Sodium Acetate pH 5.5
	20% v/v Ethanol
	100 mM NaHCO3
	2:1 v/v DMSO: 100 mM
	NaHCO3

Preparation of Conjugation Reaction Mixture:

The dry weight to UV weight of dT ligand was obtained. Poly thymidine lyophilized powder was weighed out and dissolved in water (0.5 mg/mL); and then mixed by vortexing. The UV concentration of solution was then obtained on plate reader assuming 1 AU=800 ug/mL (RNA). The dry weight to UV weight conversion was then calculated.

The amount of resin to be made was then determined and the amount of ligand (UV weight) needed to conjugate to resin was calculated. A 100 mM sodium bicarbonate (NaHCO₃) solution was prepared with a pH of 8-8.5.

The total amount of dT ligand needed was dissolved (calculated as above and using conversion factor dry weight: UV weight conversion obtained as above) in 100 mM NaHCO₃ at a concentration of 15 mg/mL.

Volume of DMSO equivalent to 2×volume of poly dT in 100 mM NaHCO₃ solution was added to the 15 mg/mL polydT in 100 mM NaHCO₃ (e.g., Add 30 mL DMSO to 15 mL of 15 mg/mL poly dT in 100 mM NaHCO₃). Final effective coupling solution was 5 mg/mL polythymidine ligand in 2:1 v/v DMSO:100 mM NaHCO₃. UV quantitation on dT solution was then performed.

Resin Conjugation:

The slurry concentration of NHS Sepharose 4FF Resin in isopropanol (IPA) was the determined: Slurry %: Volume of Resin (mL)/Total solution (mL). The resin/IPA mix was then shaken until the slurry was completely homogenous and no resin was deposited at the bottom of the container. In a tube, the homogenous slurry was added and centrifuged at 4000 RPM for 5 min.

The volume of settled resin was recorded after centrifugation and the % slurry calculated. Resin was measured out into appropriate centrifuge compatible, DMSO resistant RXN vessels. A volume of DMSO was added to resin/IPA slurry equivalent to achieve 50% total slurry. Note that in lieu of DMSO, 1 mM HCl can also be substituted to wash resin prior to conjugation.

The resin was centrifuged at 4000 RPM for 5 min and all IPA/DMSO solution was removed. All bulk solution was the poured off and then the remaining residual was poured out.

A volume of DMSO equivalent to the resin volume was added to the settled resin and re-slurried. Resin was centrifuged at 4000 RPM for 5 min and poured off all IPA/DMSO solution as above. This step was then repeated.

The polythymidine conjugation reaction: 5 mg/mL polythymidine in 2:1 DMSO: 100 mM NaHCO₃ prepared above was added to resin at a load of 2 mg dT/mL of resin as described above. The reaction mixture was re-slurried until completely homogeneous. The mixture was allowed to react at ambient temperature (20-25° C.) for 2 hours while continuously mixing on an orbital shaker/wave system rocking tray or equivalent. The mixture was centrifuged at 4000 RPM for 10 min and then the reaction mixture was poured off. UV quantitation was then performed on the post conjugation reaction mixture and a mass balance was performed to calculate % dT remaining and effectively % dT coupled to the resin.

Blocking of Unconjugated Sites on Resin:

A volume of 100 mM Tris HCl pH 8 equivalent to the resin volume was added to each tube. Re-slurried the entire mixture until completely homogeneous. The mixture was allowed to react at ambient temperature (20-25° C.) for 2 hours while continuously mixing on an orbital shaker/wave system rocking tray or equivalent. The mixture was then centrifuged at 4000 RPM for 10 min. All bulk solution then poured off.

Acid/Base Treatment:

A volume of 100 mM sodium acetate pH 5.5 equivalent to the resin volume was added to each tube. Re-slurried the entire mixture until completely homogeneous. The homogeneous mixture was then allowed to stand for 2 minutes, then centrifuged at 4000 RPM for 5 min and poured off all bulk solution.

A volume of 100 mM Tris HCl pH8 equivalent to the resin volume was then added to each tube. Re-slurried the entire mixture until completely homogeneous. The homogeneous mixture was allowed to stand for 2 minutes, then centrifuged at 4000 RPM for 5 min and poured off all bulk solution.

Resin Storage:

Where applicable, a volume of 20% ethanol solution equivalent to 0.75×the resin volume was added to each tube. Re-slurried the entire mixture until completely homogeneous. All resin was pooled and mixed for 2 minutes by vigorously shaking. Resin is stored in 20% ethanol at 4° C., as needed.

Quality Control:

Quality control can be performed to ensure that the functionalization of the resin was successful and to determine the binding capacity for the prepared resin lot. The procedure is generally outlined below.

RNA Purification

The purpose of this protocol was to selectively purify polyadenylated mRNA using oligo dT (polythymidine) affinity chromatography resin at small scale using a solid phase extraction vacuum manifold. Short mRNA transcripts, abort sequences, and protein were typically removed as mRNA containing poly A tail is captured on the resin and the aforementioned impurities flow through and do not bind to the resin.

FIG. 3 shows a general overview of the process used to purify polyadenylated RNA.

Materials:

	Vendor (where
Material	applicable)	Part #
5 M Sodium chloride (Bioultra)	Sigma
DNase/RNase free water	Teknova or
	equivalent
10X Tris EDTA (TE) Buffer (100 mM Tris
HCl 10 mM EDTA pH 7.4)
High Salt Equilibration/Wash Buffer (0.5 M
NaCl, 10 mM Tris HCl, 1 mM EDTA pH 7.4)
5X Sample Buffer (2.5 M NaCl, 50 mM Tris
HCl 5 mM EDTA, pH 7.4)
Low Salt Wash Buffer (0.1 M NaCl, 10 mM
Tris HCl, 1 mM EDTA pH 7.4)
Elution Buffer (10 mM Tris HCl, 1 mM EDTA
pH 7.4)
Oligo dT Cellulose	Sigma
20mer Oligo dT Sepharose
Solid phase extraction columns/ Spin columns	Biotage/Invitrogen
DNase/RNase-free water	Teknova or	W3350 or
	equivalent	equivalent
DNase/RNase/pyrogen free certified 200 μL
PCR tubes/PCR plates/2.0 mL microfuge
tube/15 mL conical tube/50 mL conical tube
Ethanol (molecular biology grade)	Fisher or equivalent
0.2 um filter	Millipore or
	equivalent

Procedure:

The amount of oligo dT resin to use for purification was determined and the column was packed. The elution buffer was placed at 65° C. until immediately prior to product elution. mRNA was then prepared to be loaded on dT resin by adding 5×sample buffer to mRNA sample(s) and preheating the mRNA containing solution to 65° C. and heating at 65° C. for 15 min in an oven or for 10 min in a water bath.

The resin was then equilibrated with high salt buffer in one or more columns. If using Sigma resin slurry solid resin in high salt buffer: Add 2-3 column volumes of high salt buffer to the columns and drain liquid in column. Repeat 2×. If using Applicant's dT Sepharose resin slurried in 20% EtOH: Add 2-3 column volumes of high salt buffer to the columns and drain liquid in column. Repeat 2×.

65° C. preheated mRNA solution was added to the resin column, reslurried in mRNA/sample buffer solution and placed at 65° C. for 15 min in an oven or for 10 min in a water bath with periodic shaking. The mRNA/resin solution was placed at ambient temperature (20-25° C.) for 30 minutes while shaking continuously and keeping the resin as a slurry. The liquid in column was drained into a clean centrifuge tube. A volume of high salt buffer equal to 2-3 resin volumes was added to wash the unbound material off of the resin and repeated once. A volume of low salt buffer equal to 2-3 resin volumes was added to wash the unbound material off of the resin and repeated twice. The mRNA full length product (FLP) was eluted using 2-3 resin volumes of 65° C. elution buffer; ensuring a slow flow rate to maximize contact time of 65° C. elution buffer with resin and repeated with 1-2 resin volumes of elution buffer.

UV quantitation was performed on mRNA in the elution fraction and flowthrough/wash fraction to calculate recovery/yield. Bioanalyzer gel analysis was performed on elution fraction (mRNA FLP containing fraction) to ensure electropherogram contains a single discreet peak at the appropriate size with no lower molecular weight impurities.

The mRNA can be diafiltered into water using a UF/TFF step. The mRNA can be diafiltered into water via UF spin filters or TFF prior to lyophilization. All salts are generally removed prior to formulating mRNA into a desired buffer/matrix.

Example 1: Sepharose Resin Preparation and Quality Control

Activated Resin: NHS activated Sepharose FF.

Ligand: The ligand utilized was a 20-mer polythymidine (2′deoxy) oligonucleotide containing a 5′ hexylamine linker. The ligand was synthesized using standard solid phase synthesis methods, was chromatographically purified, and lyophilized prior to use.

The 20mer polythymidine ligand (890 mg) was dissolved in a 100 mM sodium bicarbonate solution (pH-8.5) at −15 mg/mL. Dimethylsulfoxide (DMSO) was added to the ligand containing solution to achieve a final concentration of 5 mg/mL in 67/33 (v/v %) DMSO/100 mM NaHCO₃.

Activated resin (425 mL) was centrifuged at 500×g to remove the Isopropanol, re-slurried, washed twice, each time with 1 resin volume equivalent 1 mM HCl for 5 minutes, the resin was centrifuged and HCl was poured off.

Upon complete removal of HCl, all polythymidine oligo solution (5 mg/mL in 67/33 (v/v %) DMSO/100 mM NaHCO₃ was added to the resin and re-slurried; the coupling reaction was performed at 25° C. for 4 hours under constant shaking using an orbital shaker to maintain consistent slurry and to prevent resin settling.

The reaction was centrifuged at 500×g and the coupling solution was poured off and quantified by UV absorbance at 260 nm to assess coupling efficiency. It was determined that 99% of starting material had bound to the resin.

To block any remaining unconjugated sites on the resin, the resin was treated with 425 mL of 100 mM Tris HCl pH 8; the mixture was re-slurried and was allowed to react at 25° C. for 4 hours under constant shaking using an orbital shaker to maintain consistent slurry and to prevent resin settling. The reaction was centrifuged at 500×g and the solution was poured off.

The resin was re-slurried and washed with 425 mL of 100 mM sodium acetate solution pH 5 for 5 minutes. The mixture was centrifuged at 500×g and the solution was poured off.

The resin was re-slurried and washed with 425 mL of 100 mM Tris HCl solution pH 8 for 5 minutes. The mixture was centrifuged at 500×g and the solution was poured off.

A 20%/80% water/ethanol (v/v %) solution was added to the resin to achieve a 55% slurry; The resin was re-slurried a final time and was stored at 4° C. This resin is typically referred to as Applicant's dT resin or similar terminology.

For additional quality control (QC), the binding capacity of the resin and the resin's ability to capture poly A containing RNA was tested with an excess of GCSF encoded mRNA lot: “GCSF PD 29” loaded onto a 2.5 mL column packed with the synthesized lot of resin. Binding capacity was determined to be 1.4 mg RNA/mL resin by UV absorbance measurement at 260 nm. RNA of acceptable quality was observed via chip based electrophoresis using a Biorad Experion Bioanalyzer system. The gel electropherogram can be seen in FIG. 4.

Example 2: dT Column Leaching Analysis

Quantitation of total residual thymidine was performed using LC-MS/MS analysis. Purified and capped mRNA was subjected to a nuclease P1 digestion followed by treatment with bovine alkaline phosphatase (BAP). RNA and DNA were digested to individual nucleotides and abundances of each individual nucleotide (from DNA and RNA) were assayed and quantified using tandem mass spectrometry.

FIG. 5 denotes comparative leaching data of polythymidine ligand from mRNA lots purified using commercially available poly dT resin (GE cellulose) with mRNA lots purified using Applicant's dT resin. Lot 12-04-90-C-B represents GCSF encoded chemically modified mRNA purified using commercially available poly dT resin; this lot generated 6881 ppm leachate. Lot 12-04-114-C represents GCSF encoded chemically modified mRNA purified using Applicant's 20mer dT sepharose; this lot generated 895 ppm leachate Lot 12-04-122-C represents GCSF encoded chemically modified mRNA purified using Applicant's 20mer dT sepharose.; this lot generated 115 ppm leachate.

This demonstrates that dT ligand leaching generated per mg RNA from Applicant's dT resin was significantly less than commercially-available dT resin.

Example 3: Resin Re-Use Analysis

The resins (Sigma cellulose or Applicant's dT resin) were packed into SPE columns and the purifications were performed on a solid phase extraction vacuum manifold (Biotage). 1 gram of “Sigma dT Cellulose 1” (Sigma part #03131-1G) was packed in a 5 mL column. 150 mg of “Sigma dT Cellulose 2” (Part #75349-5G) was packed in a 5 mL column. 1 mL of 20mer Applicant's dT Sepharose was packed in a 5 mL column. Binding capacity experiments utilized GCSF PD 29 mRNA (encoding for GCSF and containing a 140A tail) as a feedstock and was loaded in excess onto each resin. The elutions were quantified by UV absorbance at 260 nm.

FIG. 6 shows a comparison of resin binding capacity between Applicant's poly dT resin and commercially available dT resin upon re-use (4 iterations/resin); (resin binding capacity vs. # of uses). Left to right in each experimental group: Iteration 1 is the first bar; iteration 2 is the second bar; iteration 3 is the third bar; and iteration 4 is the fourth bar (note that iteration 4 was not performed using the Sigma resin). The iterations were performed sequentially.

Diminishing binding capacity was seen as # of runs increase for Sigma's commercially available resin; in contrast Applicant's dT sephaorse resin does not exhibit a substantially reduced capacity.

Example 4: Endotoxin Analysis

Endotoxin Levels in mRNA batches following purification using various poly dT resins was analyzed. Endotoxin measurements were performed using a LAL-based assay Endosafe®-PTS™ instrument (Charles River Labs).

As seen in FIG. 7, a large abundance of endotoxin was present post dT purification using commercially available GE resin (samples 1-5). Applicant's dT resin actively clears endotoxin (samples 9-12).

Sample 5 (highly contaminated with endotoxin >46 EU/mg) was further purified using a column packed with Applicant's dT resin; After one round of purification (Sample 6) endotoxin was cleared significantly to 2.19 EU/mg; After a second round of purification with Applicant's oligo dT resin, endotoxin levels were reduced below the limit of quantitaion, <0.12 EU/mg (Sample 7).

From this data set it is apparent that eluted material using commercially available dT resin contains RNA highly contaminated with endotoxin. Applicant's dT resin was able to actively remove endotoxin from samples highly contaminated with endotoxin.

Example 5: DNA Removal Analysis

A 65 mg batch of chemically modified GCSF encoded mRNA, Lot 12-04-111-1 (922 bases), was transcribed with T7 RNA polymerase (12,740 units) using 1.46 mg of a 3781 base pair linearized plasmid template containing a T7 promoter and a 141 base poly A:T tract for 4 hours at 37° C. The transcription reaction was diafiltered into water using 100 kDa MWCO Amicon filters (EMD Millipore). The mRNA was subsequently purified on an AKTA Avant 150 (GE Healthcare) chromatography system using 100 mL of Applicant's 20mer dT Sepharose resin packed in a 5 cm id×5.1 cm glass column. The column was equilibrated using 0.5M NaCl 10 mM Tris HCl 1 mM EDTA pH 7.4. The RNA was preheated to 65° C. prior to loading using an inline mobile phase heater (Timberline Instruments), was loaded at 100 cm/h, in the aforementioned buffer. After loading, 2CV of high salt buffer was charged over the column, followed by 2CV of 0.1M NaCl 10 mM Tris HCl pH 7.4 to wash off weakly bound species. The polyadenylated RNA was eluted at 65° C. into 10 mM Tris HCl 1 mM EDTA pH 7.4. The flowthrough fraction and elution fraction were dia-filtered into water and concentrated using 100 kDa MWCO Amicon spin filters (EMD Millipore). The eluted material was quantified and the RNA quality was assessed via chip based electrophoresis using a Biorad Experion Bioanalyzer system.

By UV quantitation at 260 nm, 92% of total OD260 loaded was recovered. DNA removal was assessed using a 1.2% agarose precast SybrSafe gel (Life Technologies). As seen in FIG. 8, removal of plasmid DNA template was observed in the flowthrough fraction. The elution fraction containing purified mRNA shows no detectable plasmid DNA band. The published limit of detection on this gel is 0.5 ng/band. No DNA was detected upon loading 6 ug of RNA (elution), which denotes levels of DNA present in the RNA sample are less than 83 PPM. mRNA quality pre and post dT purification can be seen referring to the gel electropherogram in FIG. 9. The preparative UV chromatogram from the dT purification of 12-04-111-I can be seen in FIG. 10.

From this experiment, it is evident that Applicants 20 mer dT Sepharose resin facilitated the removal of plasmid DNA template from the RNA transcript.

Example 6: DNA Removal Analysis (2)

A 5 mg batch of chemically modified GCSF encoded mRNA, Lot 12-04-101-1 (922 bases), was transcribed with T7 RNA polymerase (7,000 units) using 250 ug of a 3781 base pair linearized plasmid template containing a T7 promoter and a 141 base poly A:T tract for 4 hours at 37° C. This was a relatively high load of DNA in the transcription reaction. The transcription reaction was diafiltered into water using 100 kDa MWCO Amicon filters (EMD Millipore). 2 mg of mRNA was subsequently purified on a solid phase extraction vacuum manifold (Biotage) using 3 mL of Applicant's 20mer dT Sepharose resin packed in a 10 mL SPE column. The column was equilibrated using 0.5M NaCl 10 mM Tris HCl 1 mM EDTA pH 7.4. The RNA was preheated to 65° C. prior to loading using a water bath and was loaded in the aforementioned buffer. After loading, 2CV of high salt buffer was charged over the column, followed by 2CV of 0.1M NaCl 10 mM Tris HCl pH 7.4 to wash off weakly bound species. The polyadenylated RNA was eluted at 65° C. into 10 mM Tris HCl 1 mM EDTA pH 7.4 using pre-heated buffer. The flowthrough fraction and elution fraction were diafiltered into water and concentrated using 100 kDa MWCO Amicon spin filters (EMD Millipore). The eluted material was quantified and the RNA quality was assessed via chip based electrophoresis using a Biorad Experion Bioanalyzer system (FIG. 11).

By UV quantitation at 260 nm, 91% of total OD260 loaded was recovered. DNA removal was assessed using a 1.2% agarose precast SybrSafe gel (Life Technologies). As seen in FIG. 12 and FIG. 13, removal of plasmid DNA template was observed in the flowthrough fraction. The elution fraction containing purified mRNA showed no detectable plasmid DNA band. The published limit of detection on this gel is 0.5 ng/band. No DNA was detected upon loading 1.5 ug of RNA (elution), which denotes levels of DNA present in the RNA sample are less than 333 PPM.

From this experiment, it is evident that Applicants 20 mer dT Sepharose resin facilitated the removal of plasmid DNA template from the RNA transcript.

Example 7: Resin Robustness Analysis

Lot 12-04-79-I mRNA post in vitro transcription was purified at large scale. The lot was broken into 4 purification runs. All four runs were performed sequentially. The RNA was purified using a 100 mL column (3.5 cm id×10.4 cm) packed with 20mer dT sepharose on a Biorad Duoflow FPLC system. The column was equilibrated using 0.5M NaCl 10 mM Tris HCl 1 mM EDTA pH 7.4. The RNA was preheated to 65° C. prior to loading using an inline mobile phase heater (Timberline Instruments), was loaded at 100 cm/h, in the aforementioned buffer. After loading, 2CV of high salt buffer was charged over the column, followed by 2CV of 0.1M NaCl 10 mM Tris HCl pH 7.4 to wash off weakly bound species. The polyadenylated RNA was eluted at 65° C. into 10 mM Tris HCl 1 mM EDTA pH 7.4. The eluted material was quantified and the RNA quality was assessed via chip-based electrophoresis using a Biorad Experion Bioanalyzer system.

By UV quantitation at 260 nm, yield can be seen in FIG. 14. RNA quality can be seen in the Bioanalyzer gel electropherograms of FIG. 15. Yield and purity were both consistent across four consecutive runs demonstrating resin robustness.

Example 8: 20-Mer Vs. 50-Mer Polythymidine Ligand Length Comparison Analysis

To compare polythymidine ligand lengths, 4 lots of resin were synthesized. Two were synthesized using a 20mer polythymidine (2′ deoxy) oligonucleotide containing a 5′ hexylamine linker and was conjugated to NHS activated Sepharose 4 FF resin. The other two were synthesized using a 50mer polythymidine (2′ deoxy) oligonucleotide containing a 5′ hexylamine linker and was conjugated to NHS activated Sepharose 4 FF resin. Two different ligand loadings were used for each ligand length, 7 mg ligand/mL resin and 15 mg ligand/mL resin. Both ligands were synthesized using solid phase synthetic methods, HPLC purified, and lyophilized. All dT sepharose resin preps (4) were synthesized in parallel using the same methodology at 5 mL scale (resin). To assess maximum binding capacity, the resins were saturated with the ligand. 35 mg of each ligand (for each 7 mg ligand/mL resin prep) was dissolved in in a 100 mM sodium bicarbonate solution (pH-8.5) at −15 mg/mL. 75 mg of each ligand (for each 15 mg ligand/mL resin prep) was dissolved in in a 100 mM sodium bicarbonate solution (pH-8.5) at −15 mg/mL. Dimethylsulfoxide (DMSO) was added to the ligand containing solution to achieve final concentration of 5 mg/mL in 67/33 (v/v %) DMSO/100 mM NaHCO₃.

Activated resin (5 mL) was centrifuged at 4000 rpm to remove the Isopropanol, re-slurried, washed twice, each time with 1 resin volume equivalent 1 mM HCl for 5 minutes, the resin was centrifuged and HCl was poured off.

Upon complete removal of HCl, all polythymidine oligo solution (5 mg/mL in 67/33 (v/v %) DMSO/100 mM NaHCO₃ was added to each respective resin prep and re-slurried; the coupling reactions were performed at 25° C. for 4 hours under constant shaking using an orbital shaker to maintain consistent slurry and to prevent resin settling.

The reactions were centrifuged at 4000 rpm and the coupling solution was poured off and quantified by UV absorbance at 260 nm to assess coupling efficiency. All four preparations, the two loads for the 20mer and the two loads for the 50mer resin conjugates were confirmed to be saturated. See FIG. 16.

To block any remaining unconjugated sites on the resins, the resins were treated with 5 mL of 100 mM Tris HCl pH 8; the mixture was re-slurried and was allowed to react at 25° C. for 4 hours under constant shaking using an orbital shaker to maintain consistent slurry and to prevent resin settling. The reaction was centrifuged at 4000 rpm and the solution was poured off.

The resin was re-slurried and washed with 5 mL of 100 mM sodium acetate solution pH 5 for 5 minutes. The mixture was centrifuged at 4000 rpm and the solution was poured off.

The resin was re-slurried and washed with 425 mL of 100 mM Tris HCl solution pH 8 for 5 minutes. The mixture was centrifuged at 4000 rpm and the solution was poured off.

A 20%/80% water/ethanol (v/v %) solution was added to the resin; The resin was re-slurried a final time and was stored at 4° C.

Binding capacities were determined for the four preps and can be seen in FIG. 16. An excess of poly A (140) containing RNA, GCSF PD 29 was loaded onto 2 mL of each resin; The resins were packed into 5 mL SPE columns and the purifications were performed in parallel on a solid phase extraction vacuum manifold (Biotage). Both 20mer and 50mer polythymidine Sepharose preps could bind poly A containing RNA. 20mer dT produced higher binding capacities.

While the invention has been particularly shown and described with reference to a preferred embodiment and various alternate embodiments, it will be understood by persons skilled in the relevant art that various changes in form and details can be made therein without departing from the spirit and scope of the invention.

All references, issued patents and patent applications cited within the body of the instant specification are hereby incorporated by reference in their entirety, for all purposes.

Claims

1. A method for purifying a ribonucleic acid (RNA) transcript comprising a polyA tail, the method comprising: a) obtaining a first sample comprising the RNA transcript, wherein the first sample comprises at least 5% impurities, and wherein the percentage of RNA transcript and the percentage of impurities are the inverse of each other;b) contacting the first sample with a surface linked to twenty thymidines via a linker under conditions such that the RNA transcript binds to the surface;c) eluting the RNA transcript from the surface; andd) collecting the RNA transcript in a second sample, wherein the level of impurities is lower in the second sample than the level of impurities in the first sample.

2. The method of claim 1, further comprising washing the surface with a solution after step b).

3. The method of claim 1, further comprising preheating the first sample before step b).

4. The method of claim 1, wherein one or more steps are performed using a batch process.

5. The method of claim 1, wherein the sample comprises deoxyribonucleic acid (DNA) and the sample has not been subjected to DNase treatment.

6. The method of claim 1, wherein the one or more impurities comprise an RNA that does not comprise a polyA tail, DNA, a carbohydrate, a toxin, a polypeptide, and/or a nucleotide.

7. The method of claim 1, wherein the contacting step is performed at a temperature of 65° C.

8. The method of claim 1, wherein the contacting step is performed at a rate of 100 cm/h.

9. The method of claim 1, wherein the RNA transcript and the twenty thymidines bind one another via non-covalent bonding.

10. The method of claim 1, wherein the first sample comprising the RNA transcript is a salt solution.

11. The method of claim 1, wherein the first sample comprising the RNA transcript is a sodium chloride solution.

12. The method of claim 1, wherein the elution step is performed with an elution buffer.

13. The method of claim 1, wherein the elution step is performed at a temperature of 65° C.

14. The method of claim 1, wherein the RNA transcript is the product of in vitro transcription using a non-amplified DNA template.

15. The method of claim 1, wherein the RNA transcript is 100 to 10,000 nucleotides in length.

16. The method of claim 1, wherein the method is repeated at least 2-times with the same surface.