{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T23:57:14Z","timestamp":1789775834490,"version":"4.0.1"},"reference-count":237,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,11,21]],"date-time":"2024-11-21T00:00:00Z","timestamp":1732147200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Mol. Biosci."],"abstract":"<jats:p>Decades of research on bacteriophage-derived RNA polymerases (RNAPs) were vital for synthesizing mRNA using the <jats:italic>in vitro<\/jats:italic> transcription (IVT) reaction for vaccines during the COVID-19 pandemic. The future success of mRNA-based products relies on the efficiency of its manufacturing process. mRNA manufacturing is a platform technology that complements the quality by design (QbD) paradigm. We applied the QbD framework in combination with key mechanistic insights on RNAP to assess the impact of IVT-associated critical process parameters (CPPs) and critical material attributes (CMAs) on the critical quality attributes (CQAs) of the mRNA drug substance and on manufacturing key performance indicators (KPIs). We also summarize the structure-function relationship of T7 RNAP and its engineered mutants aimed at enhancing the critical production of low-immunogenic mRNA therapeutics. Alternatives to the current set of standard RNAPs in large-scale IVTs are also discussed based on a phylogenetic background. Finally, the review dives into the economic implications of improving mRNA manufacturing based on the main enzyme, T7 RNAP, used to synthesize the mRNA drug substance. The review concludes by mapping the relationship between various CMAs and CPPs with different phases of the IVT reaction from a QbD perspective.<\/jats:p>","DOI":"10.3389\/fmolb.2024.1504876","type":"journal-article","created":{"date-parts":[[2024,11,21]],"date-time":"2024-11-21T05:10:39Z","timestamp":1732165839000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":21,"title":["Bacteriophage RNA polymerases: catalysts for mRNA vaccines and therapeutics"],"prefix":"10.3389","volume":"11","author":[{"given":"Adithya","family":"Nair","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zolt\u00e1n","family":"Kis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2024,11,21]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1016\/J.DRUDIS.2021.09.018","article-title":"dbDNA\u2122: an advanced platform for genetic medicines","volume":"27","author":"Adie","year":"2022","journal-title":"Drug Discov. Today"},{"key":"B2","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1016\/j.bpj.2011.12.014","article-title":"A multiphysics model of in vitro transcription coupling enzymatic reaction and precipitation formation","volume":"102","author":"Akama","year":"2012","journal-title":"Biophys. J."},{"key":"B3","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1146\/ANNUREV.BIOPHYS.35.010406.150153","article-title":"Single-molecule analysis of RNA polymerase transcription","volume":"35","author":"Bai","year":"2006","journal-title":"Annu. Rev. Biophys. Biomol. Struct."},{"key":"B4","doi-asserted-by":"publisher","first-page":"1091797","DOI":"10.3389\/fimmu.2022.1091797","article-title":"Research progress on circular RNA vaccines","volume":"13","author":"Bai","year":"2023","journal-title":"Front. Immunol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"2814","DOI":"10.1073\/PNAS.80.10.2814","article-title":"Relationship between promoter structure and template specificities exhibited by the bacteriophage T3 and T7 RNA polymerases","volume":"80","author":"Bailey","year":"1983","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B6","doi-asserted-by":"publisher","first-page":"3586","DOI":"10.1021\/BI0158472","article-title":"Kinetic and thermodynamic basis of promoter strength: multiple steps of transcription initiation by T7 RNA polymerase are modulated by the promoter sequence","volume":"41","author":"Bandwar","year":"2002","journal-title":"Biochemistry"},{"key":"B7","doi-asserted-by":"publisher","first-page":"22879","DOI":"10.1074\/JBC.M702589200","article-title":"The transition to an elongation complex by T7 RNA polymerase is a multistep process","volume":"282","author":"Bandwar","year":"2007","journal-title":"J. Biol. Chem."},{"key":"B8","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1016\/S0022-2836(02)01034-3","article-title":"The energetics of consensus promoter opening by T7 RNA polymerase","volume":"324","author":"Bandwar","year":"2002","journal-title":"J. Mol. Biol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1038\/s41434-022-00343-4","article-title":"Enzymatically amplified linear dbDNATM as a rapid and scalable solution to industrial lentiviral vector manufacturing","volume":"30","author":"Barreira","year":"2022","journal-title":"Gene Ther."},{"key":"B10","unstructured":"T7 RNA Polymerase Interacts with its Promoter from One Side of the DNA the interactions of T7 RNA polymerase with its promoter DNA have been previously probed in footprinting experiments with either DNase I or (methidiumpropyl-EDTA)-Fe(II) to cleave unprotected DNA\n          \n          \n            \n              Basu\n              S.\n            \n            \n              Maitra\n              U.\n            \n            \n              Ikeda\n              R. A.\n            \n            \n              Richardson\n              C. C.\n            \n          \n          \n          1989"},{"key":"B11","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1007\/978-1-4684-3246-6_2","article-title":"Initiation of transcription by RNA polymerases of E. coli and phage T3","volume":"44","author":"Bautz","year":"1974","journal-title":"Adv. Exp. Med. Biol."},{"key":"B12","doi-asserted-by":"publisher","first-page":"6929","DOI":"10.1021\/bi00527a028","article-title":"Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory","volume":"20","author":"Berg","year":"1981","journal-title":"Biochemistry"},{"key":"B13","doi-asserted-by":"publisher","first-page":"626","DOI":"10.1016\/0006-291X(76)91191-8","article-title":"Specificity of RNA chain initiation by bacteriophage T7-induced RNA polymerase","volume":"68","author":"Bishayee","year":"1976","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"B14","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1038\/s41434-020-00204-y","article-title":"Self-amplifying RNA vaccines for infectious diseases","volume":"28","author":"Bloom","year":"2020","journal-title":"Gene Ther."},{"key":"B15","doi-asserted-by":"publisher","first-page":"3415","DOI":"10.1002\/BIT.28806","article-title":"Quality by design approach to improve quality and decrease cost of in vitro transcription of mRNA using design of experiments","volume":"121","author":"Boman","year":"2024","journal-title":"Biotechnol. Bioeng."},{"key":"B16","article-title":"T7 RNA polymerase variants and methods of using the same","author":"Brakmann","year":"2015"},{"key":"B17","doi-asserted-by":"publisher","first-page":"5144","DOI":"10.1021\/BI016057V","article-title":"Role of T7 RNA polymerase His784 in start site selection and initial transcription","volume":"41","author":"Brieba","year":"2002","journal-title":"Biochemistry"},{"key":"B18","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1021\/bi992324+","article-title":"Roles of histidine 784 and tyrosine 639 in ribose discrimination by T7 RNA polymerase","volume":"39","author":"Brieba","year":"2000","journal-title":"Biochemistry"},{"key":"B19","doi-asserted-by":"publisher","first-page":"3882","DOI":"10.1021\/BI002716C","article-title":"The T7 RNA polymerase intercalating hairpin is important for promoter opening during initiation but not for RNA displacement or transcription bubble stability during elongation","volume":"40","author":"Brieba","year":"2001","journal-title":"Biochemistry"},{"key":"B20","doi-asserted-by":"publisher","first-page":"5772","DOI":"10.1016\/s0021-9258(19)83846-2","article-title":"Bacteriophage SP6-specific RNA polymerase. I. Isolation and characterization of the enzyme","volume":"257","author":"Butler","year":"1982","journal-title":"J. Biol. Chem."},{"key":"B21","doi-asserted-by":"publisher","first-page":"jkac070","DOI":"10.1093\/G3JOURNAL\/JKAC070","article-title":"Engineering efficient termination of bacteriophage T7 RNA polymerase transcription","author":"Calvopina-Chavez","year":"2022","journal-title":"Genes.|Genomes|Genetics"},{"key":"B22","article-title":"4basebio: unlocking the potential of synthetic DNA","author":"Cameron","year":"2024","journal-title":"Glob. Pharma, NA-NA"},{"key":"B23","doi-asserted-by":"publisher","first-page":"825","DOI":"10.1016\/0022-2836(81)90421-6","article-title":"Sequences of three class II promoters for the bacteriophage T7 RNA polymerase","volume":"153","author":"Carter","year":"1981","journal-title":"J. Mol. Biol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"100999","DOI":"10.1016\/J.JBC.2021.100999","article-title":"High-salt transcription of DNA cotethered with T7 RNA polymerase to beads generates increased yields of highly pure RNA","volume":"297","author":"Cavac","year":"2021","journal-title":"J. Biol. Chem."},{"key":"B25","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1007\/PL00006271","article-title":"On the evolution of the single-subunit RNA polymerases","volume":"45","author":"Cermakian","year":"1997","journal-title":"J. Mol. Evol."},{"key":"B26","doi-asserted-by":"publisher","first-page":"6637","DOI":"10.1016\/S0021-9258(19)43401-7","article-title":"Studies on T3-induced ribonucleic acid polymerase: III. Purification and characterization of the T3-INDUCED ribonucleic acid polymerase from bacteriophage T3-INFECTED ESCHERICHIA coli cells","volume":"248","author":"Chakraborty","year":"1973","journal-title":"J. Biol. Chem."},{"key":"B27","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1038\/228227A0","article-title":"New RNA polymerase from Escherichia coli infected with bacteriophage T7","volume":"228","author":"Chamberlin","year":"1970","journal-title":"Nature"},{"key":"B28","doi-asserted-by":"publisher","first-page":"2235","DOI":"10.1016\/S0021-9258(19)44211-7","article-title":"Characterization of T7-specific ribonucleic acid polymerase: I. General properties of the enzymatic reaction and the template specificity of the enzyme","volume":"248","author":"Chamberlin","year":"","journal-title":"J. Biol. Chem."},{"key":"B29","doi-asserted-by":"publisher","first-page":"2245","DOI":"10.1016\/S0021-9258(19)44212-9","article-title":"Characterization of T7-specific ribonucleic acid polymerase: II. Inhibitors of the enzyme and their application to the study of the enzymatic reaction","volume":"248","author":"Chamberlin","year":"","journal-title":"J. Biol. Chem."},{"key":"B30","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1016\/S1874-6047(08)60276-0","article-title":"4 bacteriophage DNA-dependent RNA polymerases","volume":"15","author":"Chamberlin","year":"1982","journal-title":"Enzym. Ess."},{"key":"B31","doi-asserted-by":"publisher","first-page":"721","DOI":"10.1146\/annurev.bi.43.070174.003445","article-title":"The selectivity of transcription","volume":"43","author":"Chamberlin","year":"1974","journal-title":"Annu. Rev. Biochem."},{"key":"B32","doi-asserted-by":"publisher","first-page":"1129","DOI":"10.1016\/0006-291X(72)90330-0","article-title":"Characterization of T7 specific RNA polymerase. 3. Inhibition by derivatives of rifamycin SV","volume":"49","author":"Chamberlin","year":"1972","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.1101\/2023.10.28.564488","article-title":"Co-transcriptional capping using an RNA capping enzyme-T7 RNA polymerase fusion protein","volume":"2023","author":"Chan","year":"2023","journal-title":"bioRxiv"},{"key":"B34","doi-asserted-by":"publisher","first-page":"5413","DOI":"10.1093\/NAR\/15.13.5413","article-title":"Construction of bacteriophage T7 late promoters with point mutations and characterization by in vitro transcription properties","volume":"15","author":"Chapman","year":"1987","journal-title":"Nucleic Acids Res."},{"key":"B35","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1038\/19999","article-title":"Structural basis for initiation of transcription from an RNA polymerase-promoter complex","volume":"399","author":"Cheetham","year":"1999","journal-title":"Nature"},{"key":"B36","doi-asserted-by":"publisher","first-page":"2305","DOI":"10.1126\/SCIENCE.286.5448.2305","article-title":"Structure of a transcribing T7 RNA polymerase initiation complex","volume":"286","author":"Cheetham","year":"1999","journal-title":"Science"},{"key":"B37","doi-asserted-by":"publisher","first-page":"1155","DOI":"10.1038\/NBT1001","article-title":"Evolution of a T7 RNA polymerase variant that transcribes 2\u2019-O-methyl RNA","volume":"22","author":"Chelliserrykattil","year":"2004","journal-title":"Nat. Biotechnol."},{"key":"B38","doi-asserted-by":"publisher","first-page":"13017","DOI":"10.1038\/S41598-022-17249-1","article-title":"N1-methyl-pseudouridine is incorporated with higher fidelity than pseudouridine in synthetic RNAs","volume":"12","author":"Chen","year":"2022","journal-title":"Sci. Rep."},{"key":"B39","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.tibtech.2023.05.007","article-title":"Rise of the RNA machines \u2013 self-amplification in mRNA vaccine design","volume":"41","author":"Comes","year":"2023","journal-title":"Trends Biotechnol."},{"key":"B40","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1038\/s42003-020-01167-x","article-title":"Maximizing transcription of nucleic acids with efficient T7 promoters","volume":"3","author":"Conrad","year":"2020","journal-title":"Commun. Biol."},{"key":"B41","doi-asserted-by":"publisher","first-page":"2400012","DOI":"10.1002\/BIOT.202400012","article-title":"Expanding the RNA polymerase biocatalyst solution space for mRNA manufacture","volume":"19","author":"Curry","year":"2024","journal-title":"Biotechnol. J."},{"key":"B42","unstructured":"Starting guidelines for the use of SP6 RNA Polymerase for mRNA synthesis\n          \n          \n          2023"},{"key":"B43","doi-asserted-by":"publisher","first-page":"7909","DOI":"10.1093\/NAR\/GKX495","article-title":"T7 RNA polymerase translocation is facilitated by a helix opening on the fingers domain that may also prevent backtracking","volume":"45","author":"Da","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"B44","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1016\/J.TIBTECH.2022.03.012","article-title":"Quality by Design for enabling RNA platform production processes","volume":"40","author":"Daniel","year":"2022","journal-title":"Trends Biotechnol."},{"key":"B45","doi-asserted-by":"publisher","first-page":"2035","DOI":"10.1073\/PNAS.81.7.2035","article-title":"Cloning and expression of the gene for bacteriophage T7 RNA polymerase","volume":"81","author":"Davanloo","year":"1984","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B46","doi-asserted-by":"publisher","first-page":"S133","DOI":"10.1016\/J.JCYT.2024.03.255","article-title":"Synthetic, enzymatically produced dna for gene therapy and vaccine applications","volume":"26","author":"Dhir","year":"2024","journal-title":"Cytotherapy"},{"key":"B47","article-title":"inventors; Translate Bio, Inc, assignee; Large scale synthesis of messenger RNA. United States patent application US 2018\/0258423 A1","author":"Dias","year":"2018"},{"key":"B48","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1007\/BF00261733","article-title":"The gene for Klebsiella bacteriophage K11 RNA polymerase: sequence and comparison with the homologous genes of phages T7, T3, and SP6","volume":"221","author":"Dietz","year":"1990","journal-title":"Mol. Gen. Genet."},{"key":"B49","doi-asserted-by":"publisher","first-page":"560","DOI":"10.1038\/s41587-022-01525-6","article-title":"An engineered T7 RNA polymerase that produces mRNA free of immunostimulatory byproducts","volume":"41","author":"Dousis","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"B50","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1016\/S0079-6603(08)60924-1","article-title":"Bacteriophages T7 and T3 as model systems for RNA synthesis and processing","volume":"19","author":"Dunn","year":"1977","journal-title":"Prog. Nucleic Acid. Res. Mol. Biol."},{"key":"B51","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1038\/newbio230094a0","article-title":"Different template specificities of phage T3 and T7 RNA polymerases","volume":"230","author":"Dunn","year":"1971","journal-title":"Nat. New Biol."},{"key":"B52","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1126\/science.1163433","article-title":"The structure of a transcribing T7 RNA polymerase in transition from initiation to elongation","volume":"322","author":"Durniak","year":"2008","journal-title":"Science"},{"key":"B53","article-title":"inventors; ModernaTX, Inc, assignee; Fed-batch in vitro transcription process","author":"Elich","year":"2020","journal-title":"WO 2020\/185811 A1"},{"key":"B54","first-page":"9988612","article-title":"inventors; the Board of Regents of the University of Texas System, assignee; T7 RNA polymerase variants with expanded substrate range and enhanced transcriptional yield","author":"Ellington","year":"2018","journal-title":"U. S. Pat."},{"key":"B55","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1016\/B978-012243740-3\/50010-7","article-title":"RNA polymerases","author":"Eun","year":"1996","journal-title":"Biochemistry"},{"key":"B56","doi-asserted-by":"publisher","first-page":"2908","DOI":"10.1021\/BI962397I","article-title":"Initiation, elongation, and processivity of carboxyl-terminal mutants of T7 RNA polymerase","volume":"36","author":"Gardner","year":"1997","journal-title":"Biochemistry"},{"key":"B57","doi-asserted-by":"publisher","first-page":"1162","DOI":"10.1038\/2281162a0","article-title":"In vitro synthesis of a DNA dependent RNA polymerase coded on coliphage T7 genome","volume":"228","author":"Gelfand","year":"1970","journal-title":"Nature"},{"key":"B58","doi-asserted-by":"publisher","first-page":"e118","DOI":"10.1093\/NAR\/GKZ700","article-title":"Efficient inhibition of RNA self-primed extension by addition of competing 3\u2032-capture DNA-improved RNA synthesis by T7 RNA polymerase","volume":"47","author":"Gholamalipour","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"B59","doi-asserted-by":"publisher","first-page":"9253","DOI":"10.1093\/NAR\/GKY796","article-title":"3\u2032 end additions by T7 RNA polymerase are RNA self-templated, distributive and diverse in character\u2014RNA-Seq analyses","volume":"46","author":"Gholamalipour","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"B60","doi-asserted-by":"publisher","first-page":"2858","DOI":"10.1016\/S0021-9258(19)42709-9","article-title":"Characterization of T7-specific ribonucleic acid polymerase: IV. Resolution of the major in vitro transcripts by gel electrophoresis","volume":"249","author":"Golomb","year":"1974","journal-title":"J. Biol. Chem."},{"key":"B61","doi-asserted-by":"publisher","first-page":"44277","DOI":"10.1074\/JBC.M409118200","article-title":"Initial bubble collapse plays a key role in the transition to elongation in T7 RNA polymerase","volume":"279","author":"Gong","year":"2004","journal-title":"J. Biol. Chem."},{"key":"B62","doi-asserted-by":"publisher","first-page":"23533","DOI":"10.1074\/JBC.M604023200","article-title":"Mechanism of instability in abortive cycling by T7 RNA polymerase","volume":"281","author":"Gong","year":"2006","journal-title":"J. Biol. Chem."},{"key":"B63","doi-asserted-by":"publisher","first-page":"38","DOI":"10.3389\/fmolb.2017.00038","article-title":"Circular RNAs: biogenesis, function and role in human diseases","volume":"4","author":"Greene","year":"2017","journal-title":"Front. Mol. Biosci."},{"key":"B64","volume-title":"T7 RNA polymerase variants with cysteine-serine substitutions","author":"Greif","year":"2017"},{"key":"B65","doi-asserted-by":"publisher","first-page":"5958","DOI":"10.1073\/PNAS.0407141102","article-title":"A mutation in T7 RNA polymerase that facilitates promoter clearance","volume":"102","author":"Guilleres","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B66","article-title":"inventors; Centre National de la Recherche Scientifique, assignee; Polypeptides derived from RNA polymerases and use thereof","author":"Guillerez","year":"2004","journal-title":"U. S. Pat. Appl. U. S. 2004\/0091854A1"},{"key":"B67","doi-asserted-by":"publisher","first-page":"109412","DOI":"10.1016\/J.BEJ.2024.109412","article-title":"Maximizing the mRNA productivity for in vitro transcription by optimization of fed-batch strategy","volume":"210","author":"Guo","year":"2024","journal-title":"Biochem. Eng. J."},{"key":"B68","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1016\/J.JMB.2006.02.001","article-title":"Translocation by T7 RNA polymerase: a sensitively poised Brownian ratchet","volume":"358","author":"Guo","year":"2006","journal-title":"J. Mol. Biol."},{"key":"B69","doi-asserted-by":"publisher","first-page":"2284","DOI":"10.1016\/S0006-3495(99)77067-0","article-title":"Direct observation of one-dimensional diffusion and transcription by Escherichia coli RNA polymerase","volume":"77","author":"Guthold","year":"1999","journal-title":"Biophys. J."},{"key":"B70","doi-asserted-by":"publisher","first-page":"709","DOI":"10.1016\/S0006-3495(99)77237-1","article-title":"Single-molecule imaging of RNA polymerase-DNA interactions in real time","volume":"76","author":"Harada","year":"1999","journal-title":"Biophys. J."},{"key":"B71","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1038\/35051126","article-title":"Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase","volume":"409","author":"Harada","year":"2001","journal-title":"Nature"},{"key":"B72","doi-asserted-by":"publisher","first-page":"18802","DOI":"10.1074\/jbc.273.30.18802","article-title":"Characterization of an unusual, sequence-specific termination signal for T7 RNA polymerase","volume":"273","author":"He","year":"1998","journal-title":"J. Biol. Chem."},{"key":"B73","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1146\/annurev.bi.57.070188.004203","article-title":"Structure and function of bacterial sigma factors","volume":"57","author":"Helmann","year":"1988","journal-title":"Annu. Rev. Biochem."},{"key":"B74","doi-asserted-by":"publisher","first-page":"8204","DOI":"10.1021\/acsomega.3c08732","article-title":"Digital twin fundamentals of mRNA in vitro transcription in variable scale toward autonomous operation","volume":"9","author":"Hengelbrock","year":"2023","journal-title":"ACS Omega"},{"key":"B75","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1016\/J.SBI.2021.11.002","article-title":"Adaptive machine learning for protein engineering","volume":"72","author":"Hie","year":"2022","journal-title":"Curr. Opin. Struct. Biol."},{"key":"B76","article-title":"Compositions and methods for synthesizing 5\u2032- capped RNAs","author":"Hogrefe","year":"2017"},{"key":"B77","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1016\/S0079-6603(08)60710-2","article-title":"Structure\u2014function relationships in Escherichia coli promoter DNA","volume":"38","author":"Horwitz","year":"1990","journal-title":"Prog. Nucleic Acid. Res. Mol. Biol."},{"key":"B78","doi-asserted-by":"publisher","first-page":"42477","DOI":"10.1074\/jbc.X500006200","article-title":"The discovery of RNA polymerase","volume":"280","author":"Hurwitz","year":"2005","journal-title":"J. Biol. Chem."},{"key":"B79","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1016\/0006-291X(60)90094-2","article-title":"The enzymic incorporation of ribonucleotides into polyribonucleotides and the effect of DNA","volume":"3","author":"Hurwitz","year":"1960","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"B80","volume-title":"Mutant T7 RNA polymerase GP1(lys22) exhibiting altered promoter recognition","author":"Ikeda","year":"1995"},{"key":"B81","doi-asserted-by":"publisher","first-page":"3614","DOI":"10.1073\/PNAS.83.11.3614","article-title":"Interactions of the RNA polymerase of bacteriophage T7 with its promoter during binding and initiation of transcription","volume":"83","author":"Ikeda","year":"","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B82","doi-asserted-by":"publisher","first-page":"10419","DOI":"10.1021\/BI000365W","article-title":"Studies of promoter recognition and start site selection by T7 RNA polymerase using a comprehensive collection of promoter variants","volume":"39","author":"Imburgio","year":"2000","journal-title":"Biochemistry"},{"key":"B83","doi-asserted-by":"publisher","first-page":"1662","DOI":"10.1039\/D4DD00127C","article-title":"Bioprocessing 4.0: a pragmatic review and future perspectives","volume":"3","author":"Isoko","year":"2024","journal-title":"Digit. Discov."},{"key":"B84","article-title":"inventors; GreenLight Biosciences, Inc, assignee; T7 RNA polymerase variants. United States patent application US 2021\/0180034 A1","author":"Jain","year":"2021"},{"key":"B85","doi-asserted-by":"publisher","first-page":"30451","DOI":"10.1074\/JBC.271.48.30451","article-title":"Equilibrium and stopped-flow kinetic studies of interaction between T7 RNA polymerase and its promoters measured by protein and 2-aminopurine fluorescence changes","volume":"271","author":"Jia","year":"1996","journal-title":"J. Biol. Chem."},{"key":"B86","doi-asserted-by":"publisher","first-page":"4223","DOI":"10.1021\/BI9630467","article-title":"Kinetic mechanism of transcription initiation by bacteriophage T7 RNA polymerase","volume":"36","author":"Jia","year":"1997","journal-title":"Biochemistry"},{"key":"B87","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1016\/S0022-2836(05)80092-0","article-title":"Identification of a region of the bacteriophage T3 and T7 RNA polymerases that determines promoter specificity","volume":"215","author":"Joho","year":"1990","journal-title":"J. Mol. Biol."},{"key":"B88","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1038\/S41525-023-00387-4","article-title":"Breaking the mold with RNA\u2014a \u201cRNAissance\u201d of life science","volume":"9","author":"Jones","year":"2024","journal-title":"NPJ Genom Med."},{"key":"B89","doi-asserted-by":"publisher","first-page":"645","DOI":"10.1016\/s0021-9258(18)52483-2","article-title":"Specific contacts between the bacteriophage T3, T7, and SP6 RNA polymerases and their promoters","volume":"266","author":"Jorgensen","year":"1991","journal-title":"J. Biol. Chem."},{"key":"B90","doi-asserted-by":"publisher","first-page":"5779","DOI":"10.1016\/S0021-9258(19)83847-4","article-title":"Bacteriophage SP6-specific RNA polymerase. II. Mapping of SP6 DNA and selective in vitro transcription","volume":"257","author":"Kassavetis","year":"1982","journal-title":"J. Biol. Chem."},{"key":"B91","doi-asserted-by":"publisher","first-page":"3848","DOI":"10.1093\/NAR\/GKM332","article-title":"Single-molecule analysis of 1D diffusion and transcription elongation of T7 RNA polymerase along individual stretched DNA molecules","volume":"35","author":"Kim","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"B92","doi-asserted-by":"publisher","first-page":"1226","DOI":"10.1039\/D1NP00067E","article-title":"Beyond the approved: target sites and inhibitors of bacterial RNA polymerase from bacteria and fungi","volume":"39","author":"Kirsch","year":"2022","journal-title":"Nat. Prod. Rep."},{"key":"B93","doi-asserted-by":"publisher","first-page":"e10060","DOI":"10.1002\/AMP2.10060","article-title":"Rapid development and deployment of high-volume vaccines for pandemic response","volume":"2","author":"Kis","year":"","journal-title":"J. Adv. Manuf. Process"},{"key":"B94","doi-asserted-by":"publisher","first-page":"3","DOI":"10.3390\/VACCINES9010003","article-title":"Resources, production scales and time required for producing RNA vaccines for the global pandemic demand","volume":"9","author":"Kis","year":"","journal-title":"Vaccines"},{"key":"B95","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1016\/S0022-2836(05)80091-9","article-title":"Discrimination between bacteriophage T3 and T7 promoters by the T3 and T7 RNA polymerases depends primarily upon a three base-pair region located 10 to 12 base-pairs upstream from the start site","volume":"215","author":"Klement","year":"1990","journal-title":"J. Mol. Biol."},{"key":"B96","doi-asserted-by":"publisher","first-page":"695","DOI":"10.1016\/J.MOLCEL.2018.04.018","article-title":"Correlating transcription initiation and conformational changes by a single-subunit RNA polymerase with near base-pair resolution","volume":"70","author":"Koh","year":"2018","journal-title":"Mol. Cell."},{"key":"B97","doi-asserted-by":"publisher","first-page":"2653","DOI":"10.1093\/nar\/15.6.2653","article-title":"Nucleotide sequence and expression of the cloned gene of bacteriophage SP6 RNA polymerase","volume":"15","author":"Kotani","year":"1987","journal-title":"Nucleic Acids Res."},{"key":"B98","doi-asserted-by":"publisher","first-page":"7057","DOI":"10.1093\/NAR\/12.18.7057","article-title":"Functional messenger RNAs are produced by SP6 in vitro transcription of cloned cDNAs","volume":"12","author":"Krieg","year":"1984","journal-title":"Nucleic Acids Res."},{"key":"B99","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1016\/0378-1119(88)90129-1","article-title":"RNA synthesis: strategies for the use of bacteriophage RNA polymerases","volume":"72","author":"Krupp","year":"1988","journal-title":"Gene"},{"key":"B100","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1038\/D41573-022-00035-Z","article-title":"The mRNA vaccine development landscape for infectious diseases","volume":"21","author":"Kumar","year":"2022","journal-title":"Nat. Rev. Drug Discov."},{"key":"B101","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1111\/J.1432-1033.1973.TB03093.X","article-title":"Comparison of Escherichia coli and T3 RNA polymerases. Differential inhibition of transcription by various drugs","volume":"38","author":"K\u00fcpper","year":"1973","journal-title":"Eur. J. Biochem."},{"key":"B102","doi-asserted-by":"publisher","first-page":"2819","DOI":"10.1074\/JBC.M208405200","article-title":"Binding of the priming nucleotide in the initiation of transcription by T7 RNA polymerase","volume":"278","author":"Kuzmine","year":"2003","journal-title":"J. Biol. Chem."},{"key":"B103","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1006\/JMBI.2000.4316","article-title":"Pre-steady-state kinetics of initiation of transcription by T7 RNA polymerase: a new kinetic model","volume":"305","author":"Kuzmine","year":"2001","journal-title":"J. Mol. Biol."},{"key":"B104","doi-asserted-by":"publisher","first-page":"101086","DOI":"10.1016\/j.jbc.2021.101086","article-title":"Probing steps in DNA transcription using single-molecule methods","volume":"297","author":"Lee","year":"2021","journal-title":"J. Biol. Chem."},{"key":"B105","doi-asserted-by":"publisher","first-page":"1426129","DOI":"10.3389\/fmolb.2024.1426129","article-title":"Understanding the impact of in vitro transcription byproducts and contaminants","volume":"11","author":"Lenk","year":"2024","journal-title":"Front. Mol. Biosci."},{"key":"B106","doi-asserted-by":"publisher","first-page":"3722","DOI":"10.1021\/BI9524373","article-title":"Major groove recognition elements in the middle of the T7 RNA polymerase promoter","volume":"35","author":"Li","year":"1996","journal-title":"Biochemistry"},{"key":"B107","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1016\/0014-5793(73)80224-8","article-title":"In vivo and in vitro transcription of T7 early genes by T7 RNA polymerase","volume":"33","author":"Lillehaug","year":"1973","journal-title":"FEBS Lett."},{"key":"B108","doi-asserted-by":"publisher","first-page":"465","DOI":"10.1006\/JMBI.2001.4601","article-title":"Fluorescence characterization of the transcription bubble in elongation complexes of T7 RNA polymerase","volume":"308","author":"Liu","year":"2001","journal-title":"J. Mol. Biol."},{"key":"B109","doi-asserted-by":"publisher","first-page":"2725","DOI":"10.1074\/jbc.M108856200","article-title":"Promoter clearance by T7 RNA polymerase. Initial bubble collapse and transcript dissociation monitored by base analog fluorescence","volume":"277","author":"Liu","year":"2002","journal-title":"J. Biol. Chem."},{"key":"B110","doi-asserted-by":"publisher","first-page":"36262","DOI":"10.1074\/JBC.M109.056820","article-title":"Transcription elongation complex stability: the topological lock","volume":"284","author":"Liu","year":"2009","journal-title":"J. Biol. Chem."},{"key":"B111","doi-asserted-by":"publisher","first-page":"2487","DOI":"10.3389\/fmicb.2019.02487","article-title":"Klebsiella phage KP34 RNA polymerase and its use in RNA synthesis","volume":"10","author":"Lu","year":"2019","journal-title":"Front. Microbiol."},{"key":"B112","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1006\/JMBI.1998.1854","article-title":"Pausing and termination by bacteriophage T7 RNA polymerase","volume":"280","author":"Lyakhov","year":"1998","journal-title":"J. Mol. Biol."},{"key":"B113","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1128\/MMBR.00055-15","article-title":"Bacterial transcription as a target for antibacterial drug development","volume":"80","author":"Ma","year":"2016","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"B114","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1006\/JMBI.1994.1277","article-title":"Characterization of two types of termination signal for bacteriophage T7 RNA polymerase","volume":"238","author":"Macdonald","year":"1994","journal-title":"J. Mol. Biol."},{"key":"B115","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1021\/sb5000115","article-title":"Preventing T7 RNA polymerase read-through transcription-A synthetic termination signal capable of improving bioprocess stability","volume":"4","author":"Mairhofer","year":"2015","journal-title":"ACS Synth. Biol."},{"key":"B116","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/NAR\/GKAE599","article-title":"A new approach to RNA synthesis: immobilization of stably and functionally co-tethered promoter DNA and T7 RNA polymerase","volume":"2024","author":"Malag","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"B117","doi-asserted-by":"publisher","first-page":"e36","DOI":"10.1093\/NAR\/GKAD027","article-title":"High-salt transcription from enzymatically gapped promoters nets higher yields and purity of transcribed RNAs","volume":"51","author":"MalagodaPathiranage","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"B118","doi-asserted-by":"publisher","first-page":"2690","DOI":"10.1021\/bi00384a006","article-title":"Kinetic analysis of T7 RNA polymerase-promoter interactions with small synthetic promoters","volume":"26","author":"Martin","year":"1987","journal-title":"Biochemistry"},{"key":"B119","doi-asserted-by":"publisher","first-page":"2760","DOI":"10.1021\/BI00433A002","article-title":"T7 RNA polymerase does not interact with the 5\u2019-phosphate of the initiating nucleotide","volume":"28","author":"Martin","year":"1989","journal-title":"Biochemistry"},{"key":"B120","doi-asserted-by":"publisher","first-page":"3966","DOI":"10.1021\/BI00411A012","article-title":"Processivity in early stages of transcription by T7 RNA polymerase","volume":"27","author":"Martin","year":"1988","journal-title":"Biochemistry"},{"key":"B121","article-title":"inventors; University of Massachusetts, assignee; Modified T7-related RNA polymerases and methods of use thereof","author":"Martin","year":"2015","journal-title":"U. S. Pat. 9045740 B2"},{"key":"B122","doi-asserted-by":"publisher","first-page":"4281","DOI":"10.1021\/BI00067A017","article-title":"Kinetic analysis of T7 RNA polymerase transcription initiation from promoters containing single-stranded regions","volume":"32","author":"Maslak","year":"1993","journal-title":"Biochemistry"},{"key":"B123","doi-asserted-by":"publisher","first-page":"6918","DOI":"10.1021\/BI00188A022","article-title":"Effects of solution conditions on the steady-state kinetics of initiation of transcription by T7 RNA polymerase","volume":"33","author":"Maslak","year":"1994","journal-title":"Biochemistry"},{"key":"B124","doi-asserted-by":"publisher","first-page":"620","DOI":"10.1007\/BF00160407","article-title":"Evolutionary role of abortive transcript as a primer for DNA replication","volume":"39","author":"Matsumoto","year":"1994","journal-title":"J. Mol. Evol."},{"key":"B125","first-page":"385","article-title":"Structure and function of the bacteriophage T7 RNA polymerase (or, the virtues of simplicity)","volume":"39","author":"McAllister","year":"1993","journal-title":"Cell. Mol. Biol. Res."},{"key":"B126","doi-asserted-by":"publisher","first-page":"4821","DOI":"10.1093\/NAR\/8.20.4821","article-title":"Regulation of promoter selection by the bacteriophage T7 RNA polymerase in vitro","volume":"8","author":"Mcallister","year":"1980","journal-title":"Nucleic Acids Res."},{"key":"B127","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/J.1365-2958.1993.TB00897.X","article-title":"The phage RNA polymerases are related to DNA polymerases and reverse transcriptases","volume":"10","author":"McAllister","year":"1993","journal-title":"Mol. Microbiol."},{"key":"B128","doi-asserted-by":"publisher","first-page":"6753","DOI":"10.1093\/NAR\/13.18.6753","article-title":"Sequence and analysis of the gene for bacteriophage T3 RNA polymerase","volume":"13","author":"Mcgraw","year":"1985","journal-title":"Nucleic Acids Res."},{"key":"B129","doi-asserted-by":"publisher","first-page":"1049","DOI":"10.1006\/JMBI.2000.4114","article-title":"Characterization of halted T7 RNA polymerase elongation complexes reveals multiple factors that contribute to stability","volume":"302","author":"Mentesana","year":"2000","journal-title":"J. Mol. Biol."},{"key":"B130","doi-asserted-by":"publisher","first-page":"7480","DOI":"10.1093\/NAR\/GKV734","article-title":"Transcription yield of fully 2\u2032-modified RNA can be increased by the addition of thermostabilizing mutations to T7 RNA polymerase mutants","volume":"43","author":"Meyer","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"B131","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1039\/D4FD00023D","article-title":"An engineered T7 RNA polymerase for efficient co-transcriptional capping with reduced dsRNA byproducts in mRNA synthesis","volume":"252","author":"Miller","year":"2024","journal-title":"Faraday Discuss."},{"key":"B132","article-title":"inventors; Codexis, Inc, assignee; T7 RNA polymerase variants","author":"Miller","year":"2022"},{"key":"B133","doi-asserted-by":"publisher","first-page":"4101","DOI":"10.1038\/s41596-020-00410-3","article-title":"Phage-assisted continuous and non-continuous evolution","volume":"15","author":"Miller","year":"2020","journal-title":"Nat. Protoc."},{"key":"B134","doi-asserted-by":"publisher","first-page":"8783","DOI":"10.1093\/nar\/15.21.8783","article-title":"Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates","volume":"15","author":"Milligan","year":"1987","journal-title":"Nucleic Acids Res."},{"key":"B135","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1016\/0022-2836(84)90194-3","article-title":"Nucleotide sequence of the gene for bacteriophage T7 RNA polymerase","volume":"173","author":"Moffatt","year":"1984","journal-title":"J. Mol. Biol."},{"key":"B136","doi-asserted-by":"publisher","first-page":"6305","DOI":"10.1021\/bi00239a032","article-title":"Processivity of T7 RNA polymerase requires the C-terminal phe882-ala883-COO- or \u201cfoot.\u201d","volume":"30","author":"Mookhtiar","year":"1991","journal-title":"Biochemistry"},{"key":"B137","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1016\/0378-1119(86)90098-3","article-title":"Cloning and expression of the bacteriophage T3 RNA polymerase gene","volume":"41","author":"Morris","year":"1986","journal-title":"Gene"},{"key":"B138","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1042\/BST20180499","article-title":"Mechanisms of antibiotics inhibiting bacterial RNA polymerase","volume":"47","author":"Mosaei","year":"2019","journal-title":"Biochem. Soc. Trans."},{"key":"B139","doi-asserted-by":"publisher","first-page":"5239","DOI":"10.1093\/nar\/gky177","article-title":"An origin of the immunogenicity of in vitro transcribed RNA","volume":"46","author":"Mu","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"B140","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1016\/S0092-8674(02)00815-2","article-title":"Structural transitions mediating transcription initiation by T7 RNA polymerase","volume":"110","author":"Mukherjee","year":"2002","journal-title":"Cell."},{"key":"B141","unstructured":"Processivity of proteolytically modified forms of T7 RNA Polymerase1\n          \n          \n            \n              Muller\n              D. K.\n            \n            \n              Martin\n              C. T.\n            \n            \n              Coleman\n              J. E.\n            \n          \n          \n          1988"},{"key":"B142","doi-asserted-by":"publisher","first-page":"3306","DOI":"10.1021\/BI00434A028","article-title":"T7 RNA polymerase interacts with its promoter from one side of the DNA helix","volume":"28","author":"Muller","year":"1989","journal-title":"Biochemistry"},{"key":"B143","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1007\/978-1-0716-3770-8_16","article-title":"Quality by digital design for developing platform RNA vaccine and therapeutic manufacturing processes","volume":"2786","author":"Nair","year":"2024","journal-title":"Methods Mol. Biol."},{"key":"B144","doi-asserted-by":"publisher","first-page":"490","DOI":"10.1016\/j.jmb.2007.05.070","article-title":"Functional architecture of T7 RNA polymerase transcription complexes","volume":"371","author":"Nayak","year":"2007","journal-title":"J. Mol. Biol."},{"key":"B145","doi-asserted-by":"publisher","first-page":"eaaz6893","DOI":"10.1126\/SCIADV.AAZ6893","article-title":"Impact of mRNA chemistry and manufacturing process on innate immune activation","volume":"6","author":"Nelson","year":"2020","journal-title":"Sci. Adv."},{"key":"B146","doi-asserted-by":"publisher","first-page":"3904","DOI":"10.1021\/bi00716a014","article-title":"Purification and physical characterization of T7 RNA polymerase from T7-infected escherichia coli B","volume":"13","author":"Niles","year":"1974","journal-title":"Biochemistry"},{"key":"B147","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1021\/acssynbio.2c00609","article-title":"Low resource integrated platform for production and analysis of capped mRNA","volume":"12","author":"Nwokeoji","year":"2023","journal-title":"ACS Synth. Biol."},{"key":"B148","doi-asserted-by":"publisher","first-page":"528","DOI":"10.1021\/BI00570A023","article-title":"T7 RNA polymerase: promoter structure and polymerase binding","volume":"18","author":"Oakley","year":"1979","journal-title":"Biochemistry"},{"key":"B149","doi-asserted-by":"publisher","first-page":"4266","DOI":"10.1073\/pnas.74.10.4266","article-title":"Structure of a promoter for T7 RNA polymerase","volume":"74","author":"Oakley","year":"1977","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B150","doi-asserted-by":"publisher","first-page":"4684","DOI":"10.1021\/BI00692A019","article-title":"T7 RNA polymerase: conformation, functional groups, and promotor binding","volume":"14","author":"Oakley","year":"1975","journal-title":"Biochemistry"},{"key":"B151","article-title":"RNA polymerase mutant with improved functions","author":"Oe","year":"2013"},{"key":"B152","article-title":"Inventors; new england biolabs, inc, assignee; thermostable variants of T7 RNA polymerase","author":"Ong","year":"2019"},{"key":"B153","article-title":"Inventors; new england biolabs, inc, assignee; thermostable variants of T7 RNA polymerase","author":"Ong","year":"2022","journal-title":"U. S. Pat. Appl. U. S. 2022\/0275352 A1"},{"key":"B154","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1038\/nrg3927","article-title":"Methods for the directed evolution of proteins","volume":"16","author":"Packer","year":"2015","journal-title":"Nat. Rev. Genet."},{"key":"B155","doi-asserted-by":"publisher","first-page":"e138","DOI":"10.1093\/NAR\/GNF138","article-title":"A Y639F\/H784A T7 RNA polymerase double mutant displays superior properties for synthesizing RNAs with non-canonical NTPs","volume":"30","author":"Padilla","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"B156","doi-asserted-by":"publisher","first-page":"6950","DOI":"10.1016\/s0021-9258(18)34522-8","article-title":"Molecular mechanism of promoter selection in gene transcription. II. Kinetic evidence for promoter search by a one-dimensional diffusion of RNA polymerase molecule along the DNA template","volume":"257","author":"Park","year":"1982","journal-title":"J. Biol. Chem."},{"key":"B157","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1016\/S0378-1119(96)00682-8","article-title":"Hypermutagenic in vitro transcription employing biased NTP pools and manganese cations","volume":"186","author":"Pezo","year":"1997","journal-title":"Gene"},{"key":"B158","doi-asserted-by":"publisher","first-page":"2783","DOI":"10.1038\/s41388-023-02780-w","article-title":"Going circular: history, present, and future of circRNAs in cancer","volume":"42","author":"Pisignano","year":"2023","journal-title":"Oncogene"},{"key":"B159","doi-asserted-by":"publisher","first-page":"114247","DOI":"10.1016\/J.EJPB.2024.114247","article-title":"Effect of in vitro transcription conditions on yield of high quality messenger and self-amplifying RNA","volume":"198","author":"Popova","year":"2024","journal-title":"Eur. J. Pharm. Biopharm."},{"key":"B160","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1002\/bit.28299","article-title":"Increasing yield of in vitro transcription reaction with at-line high pressure liquid chromatography monitoring","volume":"120","author":"Pregeljc","year":"2023","journal-title":"Biotechnol. Bioeng."},{"key":"B161","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1016\/j.omtn.2023.06.002","article-title":"Forging the future of circRNA therapeutics: unleashing synthetic potential and conquering challenges","volume":"33","author":"Qi","year":"2023","journal-title":"Mol. Ther. Nucleic Acids"},{"key":"B162","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1038\/s41392-022-01007-w","article-title":"mRNA-based therapeutics: powerful and versatile tools to combat diseases","volume":"7","author":"Qin","year":"2022","journal-title":"Signal Transduct. Target. Ther."},{"key":"B163","article-title":"inventors; ModernaTX, assignee; RNA polymerase variants","author":"Rabideau","year":"2019"},{"key":"B164","doi-asserted-by":"publisher","first-page":"37352","DOI":"10.1074\/JBC.M112.370643","article-title":"New insights into the mechanism of initial transcription: the T7 RNA polymerase mutant P266L transitions to elongation at longer RNA lengths than wild type","volume":"287","author":"Ram\u00edrez-Tapia","year":"2012","journal-title":"J. Biol. Chem."},{"key":"B165","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/9783527836895.CH1","article-title":"Introduction to directed evolution and rational design as protein engineering techniques","author":"Reetz","year":"2023","journal-title":"Enzyme Eng."},{"key":"B166","doi-asserted-by":"publisher","first-page":"515","DOI":"10.1073\/PNAS.95.2.515","article-title":"Promoter specificity determinants of T7 RNA polymerase","volume":"95","author":"Rong","year":"","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B167","doi-asserted-by":"publisher","first-page":"10253","DOI":"10.1074\/JBC.273.17.10253","article-title":"Template strand switching by T7 RNA polymerase","volume":"273","author":"Rong","year":"","journal-title":"J. Biol. Chem."},{"key":"B168","doi-asserted-by":"publisher","first-page":"3127","DOI":"10.1002\/BIT.28216","article-title":"Maximizing mRNA vaccine production with Bayesian optimization","volume":"119","author":"Rosa","year":"2022","journal-title":"Biotechnol. Bioeng."},{"key":"B169","article-title":"inventors; New England Biolabs, Inc, assignee; Methods and compositions for increasing capping efficiency of transcribed RNA","author":"Roy","year":"2021"},{"key":"B170","article-title":"Inventors; new england biolabs, inc, assignee; use of thermostable RNA polymerases to produce RNAs having reduced immunogenicity","author":"Roy","year":"2022","journal-title":"United Sates Pat. Appl. U. S. 2022\/0288240 A1"},{"key":"B171","doi-asserted-by":"publisher","first-page":"1723","DOI":"10.1096\/FASEBJ.3.6.2649403","article-title":"Promoter specificity and modulation of RNA polymerase II transcription","volume":"3","author":"Saltzman","year":"1989","journal-title":"FASEB J."},{"key":"B172","doi-asserted-by":"publisher","first-page":"333","DOI":"10.12688\/f1000research.75677.1","article-title":"Design-of-experiments in vitro transcription yield optimization of self-amplifying RNA","volume":"11","author":"Samnuan","year":"2022","journal-title":"F1000Res"},{"key":"B173","doi-asserted-by":"publisher","first-page":"9655","DOI":"10.1038\/s41598-024-59978-5","article-title":"Comprehensive evaluation of T7 promoter for enhanced yield and quality in mRNA production","volume":"14","author":"Sari","year":"2024","journal-title":"Sci. Rep."},{"key":"B174","doi-asserted-by":"publisher","first-page":"9870","DOI":"10.1039\/C2CC35028A","article-title":"Screening mutant libraries of T7 RNA polymerase for candidates with increased acceptance of 2\u2032-modified nucleotides","volume":"48","author":"Siegmund","year":"2012","journal-title":"Chem. Commun."},{"key":"B175","doi-asserted-by":"publisher","first-page":"3239","DOI":"10.1074\/jbc.M310471200","article-title":"Promoter binding, initiation, and elongation by bacteriophage T7 RNA polymerase: a single-molecule view of the transcription cycle","volume":"279","author":"Skinner","year":"2004","journal-title":"J. Biol. Chem."},{"key":"B176","doi-asserted-by":"publisher","first-page":"1928","DOI":"10.1002\/cite.202200133","article-title":"Gram-scale mRNA production using a 250-mL single-use bioreactor","volume":"94","author":"Skok","year":"","journal-title":"Chem. Ing. Tech."},{"key":"B177","article-title":"inventors; Roche Diagnostics Operations, Inc. assignee; T7 RNA polymerase variants with enhanced thermostability","author":"Sobek","year":"2016","journal-title":"U. S. Pat. Appl. U. S. 2016\/0032261 A1"},{"key":"B178","doi-asserted-by":"publisher","first-page":"4202","DOI":"10.1093\/nar\/gki688","article-title":"The involvement of the aspartate triad of the active center in all catalytic activities of multisubunit RNA polymerase","volume":"33","author":"Sosunov","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"B179","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1016\/S0968-0004(96)10023-2","article-title":"Structural and mechanistic relationships between nucleic acid polymerases","volume":"21","author":"Sousa","year":"1996","journal-title":"Trends Biochem. Sci."},{"key":"B180","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-3-642-60691-5_1","article-title":"Fundamental aspects of T7 RNA polymerase structure and mechanism","author":"Sousa","year":"1997","journal-title":"Nucleic Acids Mol. Biol."},{"key":"B181","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1016\/B978-0-12-378630-2.00267-X","article-title":"T7 RNA polymerase","volume-title":"Encyclopedia of biological chemistry","author":"Sousa","year":"2013"},{"key":"B182","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1038\/364593A0","article-title":"Crystal structure of bacteriophage T7 RNA polymerase at 3.3 A resolution","volume":"364","author":"Sousa","year":"1993","journal-title":"Nature"},{"key":"B183","volume-title":"Methods for using mutant RNA polymerases with reduced discrimination between non-canonical and canonical nucleoside triphosphates","author":"Sousa","year":"2000"},{"key":"B184","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S0079-6603(03)01001-8","article-title":"T7 RNA polymerase","volume":"73","author":"Sousa","year":"2003","journal-title":"Prog. Nucleic Acid. Res. Mol. Biol."},{"key":"B185","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1002\/PROT.340050403","article-title":"Single crystals of bacteriophage T7 RNA polymerase","volume":"5","author":"Sousa","year":"1989","journal-title":"Proteins"},{"key":"B186","doi-asserted-by":"publisher","first-page":"37292","DOI":"10.1074\/jbc.M201600200","article-title":"The +2 NTP binding drives open complex formation in T7 RNA polymerase","volume":"277","author":"Stano","year":"2002","journal-title":"J. Biol. Chem."},{"key":"B187","doi-asserted-by":"publisher","first-page":"1009","DOI":"10.1006\/jmbi.2001.5313","article-title":"The intercalating beta-hairpin of T7 RNA polymerase plays a role in promoter DNA melting and in stabilizing the melted DNA for efficient RNA synthesis","volume":"315","author":"Stano","year":"2002","journal-title":"J. Mol. Biol."},{"key":"B188","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1016\/J.SBI.2009.09.001","article-title":"The structural changes of T7 RNA polymerase from transcription initiation to elongation","volume":"19","author":"Steitz","year":"2009","journal-title":"Curr. Opin. Struct. Biol."},{"key":"B189","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1016\/0006-291X(60)90110-8","article-title":"Incorporation of the adenine ribonucleotide into RNA by cell fractions from E. coli B","volume":"3","author":"Stevens","year":"1960","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"B190","doi-asserted-by":"publisher","first-page":"2636","DOI":"10.1002\/BIT.28699","article-title":"Mechanistic modeling of in vitro transcription incorporating effects of magnesium pyrophosphate crystallization","volume":"121","author":"Stover","year":"2024","journal-title":"Biotechnol. Bioeng."},{"key":"B191","article-title":"inventors; Universit\u00e4t Hamburg, assignee; Novel single-subunit RNA polymerase","author":"Streit","year":"2023","journal-title":"Eur. Pat. Appl. EP 4 265 718 A1"},{"key":"B192","article-title":"inventors; Boehringer Ingelheim RCV GmbH and Co KG, assignee; Transcription terminator sequences","author":"Striedner","year":"2019"},{"key":"B193","doi-asserted-by":"publisher","first-page":"1074","DOI":"10.1021\/bi00547a005","article-title":"Promoter melting by T7 ribonucleic acid polymerase as detected by single-stranded endonuclease digestion","volume":"19","author":"Strothkamp","year":"1980","journal-title":"Biochemistry"},{"key":"B194","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1016\/0022-2836(86)90385-2","article-title":"Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes","volume":"189","author":"Studier","year":"1986","journal-title":"J. Mol. Biol."},{"key":"B195","article-title":"assignee; RNA polymerase mutants with increased thermostability","author":"Sugiyama","year":"2009"},{"key":"B196","doi-asserted-by":"publisher","first-page":"1160","DOI":"10.1038\/2281160a0","article-title":"Transcription of late phage RNA by T7 RNA polymerase","volume":"228","author":"Summers","year":"1970","journal-title":"Nature"},{"key":"B197","doi-asserted-by":"publisher","first-page":"732","DOI":"10.1016\/J.SBI.2009.10.009","article-title":"RNA polymerase fidelity and transcriptional proofreading","volume":"19","author":"Sydow","year":"2009","journal-title":"Curr. Opin. Struct. Biol."},{"key":"B198","doi-asserted-by":"publisher","first-page":"1850","DOI":"10.1016\/J.YMTHE.2022.02.016","article-title":"COVID-19 mRNA vaccines: platforms and current developments","volume":"30","author":"Szab\u00f3","year":"2022","journal-title":"Mol. Ther."},{"key":"B199","doi-asserted-by":"publisher","first-page":"1074","DOI":"10.1073\/PNAS.82.4.1074","article-title":"A bacteriophage T7 RNA polymerase\/promoter system for controlled exclusive expression of specific genes","volume":"82","author":"Tabor","year":"1985","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B200","doi-asserted-by":"publisher","first-page":"e91859","DOI":"10.1371\/JOURNAL.PONE.0091859","article-title":"Relaxed rotational and scrunching changes in P266L mutant of T7 RNA polymerase reduce short abortive RNAs while delaying transition into elongation","volume":"9","author":"Tang","year":"2014","journal-title":"PLoS One"},{"key":"B201","doi-asserted-by":"publisher","first-page":"4947","DOI":"10.1021\/bi052292s","article-title":"Rapid binding of T7 RNA polymerase is followed by simultaneous bending and opening of the promoter DNA","volume":"45","author":"Tang","year":"","journal-title":"Biochemistry"},{"key":"B202","doi-asserted-by":"publisher","first-page":"4936","DOI":"10.1021\/BI0522910","article-title":"T7 RNA polymerase-induced bending of promoter DNA is coupled to DNA opening","volume":"45","author":"Tang","year":"","journal-title":"Biochemistry"},{"key":"B203","doi-asserted-by":"publisher","first-page":"22175","DOI":"10.1073\/pnas.0906979106","article-title":"Real-time observation of the transition from transcription initiation to elongation of the RNA polymerase","volume":"106","author":"Tang","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B204","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1016\/J.MOLCEL.2008.04.003","article-title":"Transcription initiation in a single-subunit RNA polymerase proceeds through DNA scrunching and rotation of the N-terminal subdomains","volume":"30","author":"Tang","year":"2008","journal-title":"Mol. Cell."},{"key":"B205","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1016\/S0092-8674(04)00059-5","article-title":"Structural basis for substrate selection by T7 RNA polymerase","volume":"116","author":"Temiakov","year":"2004","journal-title":"Cell."},{"key":"B206","doi-asserted-by":"publisher","first-page":"12709","DOI":"10.1021\/BI0486987","article-title":"Topological and conformational analysis of the initiation and elongation complex of t7 RNA polymerase suggests a new twist","volume":"43","author":"Theis","year":"2004","journal-title":"Biochemistry"},{"key":"B207","doi-asserted-by":"publisher","first-page":"2423","DOI":"10.1529\/BIOPHYSJ.107.125096","article-title":"T7 RNA polymerase studied by force measurements varying cofactor concentration","volume":"95","author":"Thomen","year":"2008","journal-title":"Biophys. J."},{"key":"B208","article-title":"RNA polymerase for synthesis of modified RNA","author":"Thompson","year":"2022"},{"key":"B209","doi-asserted-by":"publisher","first-page":"6298","DOI":"10.1074\/JBC.270.11.6298","article-title":"Self-coded 3\u2032-extension of run-off transcripts produces aberrant products during in vitro transcription with T7 RNA polymerase","volume":"270","author":"Triana-Alonso","year":"1995","journal-title":"J. Biol. Chem."},{"key":"B210","doi-asserted-by":"publisher","first-page":"14574","DOI":"10.1021\/BI961165G","article-title":"Thermodynamic and kinetic measurements of promoter binding by T7 RNA polymerase","volume":"35","author":"\u00dajv\u00e1ri","year":"1996","journal-title":"Biochemistry"},{"key":"B211","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1006\/JMBI.1997.1350","article-title":"Identification of a minimal binding element within the T7 RNA polymerase promoter","volume":"273","author":"\u00dajv\u00e1ri","year":"1997","journal-title":"J. Mol. Biol."},{"key":"B212","doi-asserted-by":"publisher","first-page":"1173","DOI":"10.1006\/JMBI.1999.3418","article-title":"Evidence for DNA bending at the T7 RNA polymerase promoter","volume":"295","author":"\u00dajv\u00e1ri","year":"2000","journal-title":"J. Mol. Biol."},{"key":"B213","doi-asserted-by":"publisher","first-page":"7015","DOI":"10.1021\/BI200620Q","article-title":"Direct tests of the energetic basis of abortive cycling in transcription","volume":"50","author":"Vahia","year":"2011","journal-title":"Biochemistry"},{"key":"B214","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1038\/s41541-021-00322-7","article-title":"Quality by design modelling to support rapid RNA vaccine production against emerging infectious diseases","volume":"6","author":"van de Berg","year":"2021","journal-title":"npj Vaccines"},{"key":"B215","doi-asserted-by":"publisher","first-page":"958","DOI":"10.1006\/JMBI.1997.1358","article-title":"Role of open complex instability in kinetic promoter selection by bacteriophage T7 RNA polymerase","volume":"273","author":"Villemain","year":"1997","journal-title":"J. Mol. Biol."},{"key":"B216","article-title":"inventors; ModernaTX, Inc. assignee; Enzymes and polymerases for the synthesis of RNA. US patent 9790531 B2","author":"Wang","year":"2017"},{"key":"B217","doi-asserted-by":"publisher","first-page":"4118","DOI":"10.1021\/ja01524a087","article-title":"A mammalian system for the incorporation of cytidine triphosphate into ribonucleic acid","volume":"81","author":"Weiss","year":"1959","journal-title":"J. Am. Chem. Soc."},{"key":"B218","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1006\/JMBI.1997.1199","article-title":"Positioning of the start site in the initiation of transcription by bacteriophage T7 RNA polymerase","volume":"272","author":"Weston","year":"1997","journal-title":"J. Mol. Biol."},{"key":"B219","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1016\/J.TRSL.2021.11.009","article-title":"Development of mRNA manufacturing for vaccines and therapeutics: mRNA platform requirements and development of a scalable production process to support early phase clinical trials","volume":"242","author":"Whitley","year":"2022","journal-title":"Transl. Res."},{"key":"B220","article-title":"assignee; Methods and means for enhancing RNA production","author":"Wochner","year":"2015","journal-title":"WO 2015\/188933 Al"},{"key":"B221","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1021\/BI952037F","article-title":"Asp537 and Asp812 in bacteriophage T7 RNA polymerase as metal ion-binding sites studied by EPR, flow-dialysis, and transcription","volume":"35","author":"Woody","year":"1996","journal-title":"Biochemistry"},{"key":"B222","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1016\/0968-0004(90)90074-L","article-title":"RNA polymerase II: subunit structure and function","volume":"15","author":"Woychik","year":"1990","journal-title":"Trends Biochem. Sci."},{"key":"B223","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1080\/15476286.2021.1954808","article-title":"A single mutation attenuates both the transcription termination and RNA-dependent RNA polymerase activity of T7 RNA polymerase","volume":"18","author":"Wu","year":"2021","journal-title":"RNA Biol."},{"key":"B224","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1261\/RNA.073858.119","article-title":"Synthesis of low immunogenicity RNA with high-temperature in vitro transcription","volume":"26","author":"Wu","year":"2020","journal-title":"RNA"},{"key":"B225","doi-asserted-by":"publisher","first-page":"1130","DOI":"10.1080\/15476286.2022.2139113","article-title":"Psychrophilic phage VSW-3 RNA polymerase reduces both terminal and full-length dsRNA byproducts in in vitro transcription","volume":"19","author":"Xia","year":"2022","journal-title":"RNA Biol."},{"key":"B226","article-title":"inventors; Primordial Genetics, Inc, assignee; Methods and compositions for manufacturing polynucleotides","author":"Xu","year":"2020"},{"key":"B227","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1016\/J.MOLCEL.2006.03.013","article-title":"Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity","volume":"22","author":"Yang","year":"2006","journal-title":"Mol. Cell."},{"key":"B228","doi-asserted-by":"publisher","first-page":"1387","DOI":"10.1126\/science.1077464","article-title":"Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase","volume":"298","author":"Yin","year":"2002","journal-title":"Science"},{"key":"B229","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1016\/S0092-8674(04)00120-5","article-title":"The structural mechanism of translocation and helicase activity in T7 RNA polymerase","volume":"116","author":"Yin","year":"2004","journal-title":"Cell."},{"key":"B230","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1016\/0076-6879(89)80090-4","article-title":"Synthesis of long, capped transcripts in vitro by SP6 and T7 RNA polymerases","volume":"180","author":"Yisraeli","year":"1989","journal-title":"Methods Enzymol."},{"key":"B231","doi-asserted-by":"publisher","first-page":"783","DOI":"10.1038\/s41586-022-05604-1","article-title":"Structural basis for intrinsic transcription termination","volume":"613","author":"You","year":"2023","journal-title":"Nature"},{"key":"B232","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1002\/(SICI)1097-0290(19971020)56:2<210::AID-BIT10>3.0.CO;2-K","article-title":"Modeling and optimization of a batch process for in vitro RNA production","volume":"56","author":"Young","year":"1997","journal-title":"Biotechnol. Bioeng."},{"key":"B233","doi-asserted-by":"publisher","first-page":"10352","DOI":"10.1073\/pnas.0606306104","article-title":"Dissociation of halted T7 RNA polymerase elongation complexes proceeds via a forward-translocation mechanism","volume":"104","author":"Zhou","year":"2007","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B234","doi-asserted-by":"publisher","first-page":"e94","DOI":"10.1093\/NAR\/GKV367","article-title":"Synthesis of 2\u2032-fluoro RNA by Syn5 RNA polymerase","volume":"43","author":"Zhu","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"B235","doi-asserted-by":"publisher","first-page":"3545","DOI":"10.1074\/JBC.M112.442350","article-title":"The RNA polymerase of marine cyanophage Syn5","volume":"288","author":"Zhu","year":"2013","journal-title":"J. Biol. Chem."},{"key":"B236","doi-asserted-by":"publisher","first-page":"e33","DOI":"10.1093\/NAR\/GKT1193","article-title":"Syn5 RNA polymerase synthesizes precise run-off RNA products","volume":"42","author":"Zhu","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"B237","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1038\/s41419-022-05075-2","article-title":"RNA-based therapeutics: an overview and prospectus","volume":"13","author":"Zhu","year":"2022","journal-title":"Cell. Death and Dis."}],"container-title":["Frontiers in Molecular Biosciences"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmolb.2024.1504876\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,21]],"date-time":"2024-11-21T05:10:56Z","timestamp":1732165856000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmolb.2024.1504876\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,21]]},"references-count":237,"alternative-id":["10.3389\/fmolb.2024.1504876"],"URL":"https:\/\/doi.org\/10.3389\/fmolb.2024.1504876","relation":{},"ISSN":["2296-889X"],"issn-type":[{"value":"2296-889X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,11,21]]},"article-number":"1504876"}}