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RNA polymerase spoiled for choice as transcription begins. Proc Natl Acad Sci U S A 2021; 118:2110640118. [PMID: 34301880 DOI: 10.1073/pnas.2110640118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Goldman SR, Sharp JS, Vvedenskaya IO, Livny J, Dove SL, Nickels BE. NanoRNAs prime transcription initiation in vivo. Mol Cell 2011; 42:817-25. [PMID: 21700226 DOI: 10.1016/j.molcel.2011.06.005] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Revised: 04/18/2011] [Accepted: 06/08/2011] [Indexed: 11/16/2022]
Abstract
It is often presumed that, in vivo, the initiation of RNA synthesis by DNA-dependent RNA polymerases occurs using NTPs alone. Here, using the model Gram-negative bacterium Pseudomonas aeruginosa, we demonstrate that depletion of the small-RNA-specific exonuclease, Oligoribonuclease, causes the accumulation of oligoribonucleotides 2 to ∼4 nt in length, "nanoRNAs," which serve as primers for transcription initiation at a significant fraction of promoters. Widespread use of nanoRNAs to prime transcription initiation is coupled with global alterations in gene expression. Our results, obtained under conditions in which the concentration of nanoRNAs is artificially elevated, establish that small RNAs can be used to initiate transcription in vivo, challenging the idea that all cellular transcription occurs using only NTPs. Our findings further suggest that nanoRNAs could represent a distinct class of functional small RNAs that can affect gene expression through direct incorporation into a target RNA transcript rather than through a traditional antisense-based mechanism.
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Affiliation(s)
- Seth R Goldman
- Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
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Nickels BE, Dove SL. NanoRNAs: a class of small RNAs that can prime transcription initiation in bacteria. J Mol Biol 2011; 412:772-81. [PMID: 21704045 DOI: 10.1016/j.jmb.2011.06.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 06/08/2011] [Accepted: 06/09/2011] [Indexed: 01/12/2023]
Abstract
It has been widely assumed that all transcription in cells occur using NTPs only (i.e., de novo). However, it has been known for several decades that both prokaryotic and eukaryotic RNA polymerases can utilize small (2 to ∼5 nt) RNAs to prime transcription initiation in vitro, raising the possibility that small RNAs might also prime transcription initiation in vivo. A new study by Goldman et al. has now provided the first evidence that priming with so-called "nanoRNAs" (i.e., 2 to ∼5 nt RNAs) can, in fact, occur in vivo. Furthermore, this study provides evidence that altering the extent of nanoRNA-mediated priming of transcription initiation can profoundly influence global gene expression. In this perspective, we summarize the findings of Goldman et al. and discuss the prospect that nanoRNA-mediated priming of transcription initiation represents an underappreciated aspect of gene expression in vivo.
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Affiliation(s)
- Bryce E Nickels
- Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA.
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Wettich A, Biebricher CK. RNA species that replicate with DNA-dependent RNA polymerase from Escherichia coli. Biochemistry 2001; 40:3308-15. [PMID: 11258950 DOI: 10.1021/bi002756g] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An RNA that replicates with core RNA polymerase from E. coli and the substrates ATP, CTP, ITP, and UTP, was selected from a random poly(A,U,I,C) library and named EcorpI. Another replicating RNA, EcorpG, was obtained by template-free incubation of holo RNA polymerase and the substrates ATP, CTP, GTP, and UTP. Both RNA species showed typical autocatalytic RNA amplification profiles with replication rates in the range of other RNA replicons. The replication products were heterogeneous in length; the different lengths appeared to be different replication intermediates. Both RNA were single-stranded with much internal base-pairing but low melting points. Their sequences were composed by permutations of certain sequence motives in both polarities separated by short oligo(A) and oligo(U) clusters. There was evidence for 3'-terminal elongation on an intramolecular template. No double-stranded RNA was found, even though base-pairing is certainly the underlying basis of the replication process. The reaction was highly sensitive: a few RNA strands were sufficient to trigger an amplification avalanche.
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Affiliation(s)
- A Wettich
- Max-Planck-Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
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Baric RS, Shieh CK, Stohlman SA, Lai MM. Analysis of intracellular small RNAs of mouse hepatitis virus: evidence for discontinuous transcription. Virology 1987; 156:342-54. [PMID: 3027983 PMCID: PMC7130593 DOI: 10.1016/0042-6822(87)90414-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have previously shown the presence of multiple small leader-containing RNA species in mouse hepatitis virus (MHV)-infected cells. In this paper, we have analyzed the origin, structure, and mechanism of synthesis of these small RNAs. Using cDNA probes specific for leader RNA and genes A, D, and F, we demonstrate that subsets of these small RNAs were derived from the various viral genes. These subsets have discrete and reproducible sizes, varying with the gene from which they are derived. The size of each subset correlates with regions of secondary structure, whose free energy ranges from -1.6 to -77.1 kcal/mol, in each of the mRNAs examined. In addition, identical subsets were detected on the replicative intermediate (RI) RNA, suggesting that they represent functional transcriptional intermediates. The biological significance of these small RNAs is further supported by the detection of leader-containing RNAs of 47, 50, and 57 nucleotides in length, which correspond to the crossover sites in two MHV recombinant viruses. These data, coupled with the high frequency of RNA recombination during MHV infection, suggest that the viral polymerase may pause in or around regions of secondary structure, thereby generating pools of free leader-containing RNA intermediates which can reassociate with the template, acting as primers for the synthesis of full-length or recombinant RNAs. These data suggest that MHV transcription uses a discontinuous and nonprocessive mechanism in which RNA polymerase allows the partial RNA products to be dissociated from the template temporarily during the process of transcription.
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Burke RL, Munn M, Barry J, Alberts BM. Purification and properties of the bacteriophage T4 gene 61 RNA priming protein. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(18)89652-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Samuels M, Fire A, Sharp PA. Dinucleotide priming of transcription mediated by RNA polymerase II. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)43383-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Badaracco G, Plevani P, Cassani G. Stimulation of poly(dT) transcription by Bacillus subtilis RNA polymerase in the presence of adenosine monophosphate. Biochem Biophys Res Commun 1981; 99:23-9. [PMID: 6786288 DOI: 10.1016/0006-291x(81)91707-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Kumar SA. The structure and mechanism of action of bacterial DNA-dependent RNA polymerase. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1981; 38:165-210. [PMID: 6170089 DOI: 10.1016/0079-6107(81)90013-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Shaw PA, Saunders GF. Stimulation of RNA synthesis by dinucleotides with eukaryotic RNA polymerase. FEBS Lett 1979; 106:104-10. [PMID: 387440 DOI: 10.1016/0014-5793(79)80704-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Bernard O, Cory S, Adams JM. Synthesis of complementary RNA on RNA templates using the DNA-dependent RNA polymerase of Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA 1977; 478:407-16. [PMID: 334264 DOI: 10.1016/0005-2787(77)90096-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
It is shown that the DNA-dependent RNA polymerase of Escherichia coli can synthesize complementary RNA (cRNA) directly on rRNA and mRNA templates. Synthesis occurred preferentially in the presence of Mn2+ and at relatively high substrate and enzyme concentrations. No primer was required, and addition of oligo-U to a mRNA-dependent reaction gave no marked stimulation. Sedimentation analysis of cRNA made on different templates indicated that the products were mainly 2-4 S, but a fraction of the product was larger. Fingerprints of 32P-labelled cRNA made on 5 S rRNA and 18 S rRNA indicated that the complexity of the cRNAs was related to the size of the template, suggesting that a substantial portion of the templates were copied. This reaction provides a simple method for preparing cRNA of high specific activity for use in hybridisation studies, and possibly in sequence analysis. 32P-labelled cRNA made on 18 S and 28 S rRNA was a sensitive hybridisation probe for detection of the specific fragments of mouse DNA containing the rRNA genes.
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Initiation of synthesis of messenger RNA of deoxynucleotide kinase by oligoribonucleotides. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)40555-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Datta AK, Niyogi SK. Biochemistry and physiology of bacterial ribonucleases. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1976; 17:271-308. [PMID: 6997 DOI: 10.1016/s0079-6603(08)60073-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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In vitro transcription of the Escherichia coli histidine operon primed by dinucleotides. Effect of the first histidine biosynthetic enzyme. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)40768-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Niyogi SK, Datta AK. A novel oligoribonuclease of Escherichia coli. I. Isolation and properties. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)40945-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Lebowitz P, Bloodgood R. Transcription of simian virus 40 DNA by Escherichia coli RNA polymerase: synthesis of a DNA-RNA hybrid and discrete RNAs under restrictive transcription conditions. J Mol Biol 1975; 94:183-201. [PMID: 167179 DOI: 10.1016/0022-2836(75)90077-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
A sequence of 79 nucleotides from the lambda OR operator is obtained by primed transcription of repressor protected DNA fragments. The sequence contains the primary repressor binding site plus partial duplications which can be interpreted as secondary repressor binding sites.
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Sasaki Y, Goto H, Wake T, Sasaki R. Purine ribonucleotide homopolymer formation activity of RNA polymerase from cauliflower. BIOCHIMICA ET BIOPHYSICA ACTA 1974; 366:443-53. [PMID: 4473214 DOI: 10.1016/0005-2787(74)90042-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Rhodes G, Chamberlin MJ. Ribonucleic Acid Chain Elongation by Escherichia coli Ribonucleic Acid Polymerase. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(19)42207-2] [Citation(s) in RCA: 91] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Smith DA, Martinez AM. Initiation of in vitro RNA synthesis with deoxyribosyl oligomers. BIOCHIMICA ET BIOPHYSICA ACTA 1974; 353:475-86. [PMID: 4852489 DOI: 10.1016/0005-2787(74)90053-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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23
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Mangel WF, Chamberlin MJ. Studies of Ribonucleic Acid Chain Initiation by Escherichia coli Ribonucleic Acid Polymerase Bound to T7 Deoxyribonucleic Acid. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(19)42627-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Nath K, Hurwitz J. Covalent Attachment of Ribonucleotides at 3′-Hydroxyl Ends of Deoxyribonucleic Acid Catalyzed by Deoxyribonucleic Acid-dependent Ribonucleic Acid Polymerase of Escherichia coli. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(19)42774-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Chamberlin MJ. 10. Bacterial DNA-Dependent RNA Polymerase. ACTA ACUST UNITED AC 1974. [DOI: 10.1016/s1874-6047(08)60142-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
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Niyogi SK, Hoffman DJ. Elucidation of RNA initiation (DNA promoter?) sequences in T4 DNA transcription using Escherichia coli RNA polymerase and dinucleoside monophosphates. BASIC LIFE SCIENCES 1974; 3:81-92. [PMID: 4595845 DOI: 10.1007/978-1-4613-4529-9_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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van Kreijl CF. Optimal conditions for primer-dependent transcription of poly (dT) by RNA polymerase. Biochem Biophys Res Commun 1973; 54:17-24. [PMID: 4582375 DOI: 10.1016/0006-291x(73)90882-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Hoffman DJ, Niyogi SK. Differential effects of sigma factor, ionic strength, and ribonucleoside triphosphate concentration on the transcription of phage T4 DNA with ribonucleic acid polymerase of Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA 1973; 299:588-95. [PMID: 4575182 DOI: 10.1016/0005-2787(73)90231-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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31
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Association of an Endoribonuclease with the Avian Myeloblastosis Virus Deoxyribonucleic Acid Polymerase. J Biol Chem 1972. [DOI: 10.1016/s0021-9258(19)44626-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Wickner S, Hurwitz J, Nath K, Yarbrough L. DNA dependent RNA polymerase catalyzed synthesis of polyribonucleotide chains covalently linked to DNA. Biochem Biophys Res Commun 1972; 48:619-27. [PMID: 4558612 DOI: 10.1016/0006-291x(72)90393-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Niyogi SK. Effect of sigma factor and oligoribonucleotides on the transcription of well-defined templates with the ribonucleic acid polymerase of Escherichia coli. J Mol Biol 1972; 64:609-18. [PMID: 4553855 DOI: 10.1016/0022-2836(72)90086-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Straat PA, Pongs O, Ts'o PO. RNA polymerase from Micrococcus luteus: comparative effect of ribosyl and deoxyribosyl oligomers on the homopolymer. Directed reaction. Biochem Biophys Res Commun 1971; 44:905-11. [PMID: 5125233 DOI: 10.1016/0006-291x(71)90797-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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So AG, Downey KM. Studies on the mechanism of ribonucleic acid synthesis. II. Stabilization of the deoxyribonucleic acid-ribonucleic acid polymerase complex by the formation of a single phosphodiester bond. Biochemistry 1970; 9:4788-93. [PMID: 4320541 DOI: 10.1021/bi00826a024] [Citation(s) in RCA: 67] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Downey KM, So AG. Studies on the kinetics of ribonucleic acid chain initiation and elongation. Biochemistry 1970; 9:2520-5. [PMID: 4912487 DOI: 10.1021/bi00814a019] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Wilson RG, Russo JF, Steck TL. RNA synthesis: divalent cation-related specificity in the initiation step. BIOCHIMICA ET BIOPHYSICA ACTA 1970; 204:412-5. [PMID: 5441187 DOI: 10.1016/0005-2787(70)90161-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Pitha PM, Ts'o PO. The interactions of adenosine and adenine heptanucleoside hexaphosphate with polyuridylic acid. Biochemistry 1969; 8:5206-17. [PMID: 5365803 DOI: 10.1021/bi00840a075] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Niyogi SK, Wilton PE. Effect of temperature on the oligonucleotide stimulation of the RNA polymerase reaction. J Mol Biol 1969; 41:149-53. [PMID: 4896015 DOI: 10.1016/0022-2836(69)90132-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Krakow JS. Azotobacter vinelandii ribonucleic acid polymerase. V. Unprimed synthesis of poly A-poly U. BIOCHIMICA ET BIOPHYSICA ACTA 1968; 166:459-65. [PMID: 5680605 DOI: 10.1016/0005-2787(68)90233-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Steck TL, Caicuts MJ, Wilson RG. The Influence of Divalent Cations on the Activity of the Ribonucleic Acid Polymerase of Micrococcus lysodeikticus. J Biol Chem 1968. [DOI: 10.1016/s0021-9258(18)93439-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Adman R, Grossman L. Template properties of polyribonucleotides containing uracil or modified uracil in the RNA polymerase reaction. J Mol Biol 1967; 23:417-39. [PMID: 6032185 DOI: 10.1016/s0022-2836(67)80116-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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