Template-determined, variable rate of RNA chain elongation - PubMed (original) (raw)
Template-determined, variable rate of RNA chain elongation
D R Mills et al. Cell. 1978 Oct.
Abstract
Q beta replicase polymerizes MDV-1 RNA at a markedly variable rate. Electrophoretic analyses of partially synthesized strands showed that a few of the elongation intermediates are much more abundant than others, reflecting a variable rate of chain elongation. Our data suggest that at a relatively small number of specific sites in the sequence of this RNA, the progress of the replicase is temporarily interrupted, and then resumes spontaneously, with a finite probability. Since the time spent between these pause sites is negligible compared with the time spent at pause sites, the mean time of chain elongation is well approximated by the sum of the mean times spent at each pause site. Nucleotide sequence analysis of the most prominent elongation intermediates indicated that they all have the potential to form a 3' terminal hairpin structure. This suggests that the marked variability in the rate of chain elongation is due to the formation of terminal hairpins in the product strand, or the reformation of hairpins in the template strand. A survey of the literature shows that this phenomenon occurs with most, if not all, nucleic acid polymerases. Structure-induced pauses may play a role in the regulation of nucleic acid synthesis.
Similar articles
- RNA replication: required intermediates and the dissociation of template, product, and Q beta replicase.
Dobkin C, Mills DR, Kramer FR, Spiegelman S. Dobkin C, et al. Biochemistry. 1979 May 15;18(10):2038-44. doi: 10.1021/bi00577a030. Biochemistry. 1979. PMID: 107965 - Localization of the Q beta replicase recognition site in MDV-1 RNA.
Nishihara T, Mills DR, Kramer FR. Nishihara T, et al. J Biochem. 1983 Mar;93(3):669-74. doi: 10.1093/jb/93.3.669. J Biochem. 1983. PMID: 6192124 - Modification of cytidines in a Q beta replicase template: analysis of conformation and localization of lethal nucleotide substitutions.
Mills DR, Kramer FR, Dobkin C, Nishihara T, Cole PE. Mills DR, et al. Biochemistry. 1980 Jan 8;19(1):228-36. doi: 10.1021/bi00542a034. Biochemistry. 1980. PMID: 6986163 - RNA replication: function and structure of Qbeta-replicase.
Blumenthal T, Carmichael GG. Blumenthal T, et al. Annu Rev Biochem. 1979;48:525-48. doi: 10.1146/annurev.bi.48.070179.002521. Annu Rev Biochem. 1979. PMID: 382992 Review. No abstract available. - Towards an experimental analysis of molecular self-organization and precellular Darwinian evolution.
Küppers B. Küppers B. Naturwissenschaften. 1979 May;66(5):228-43. doi: 10.1007/BF00571603. Naturwissenschaften. 1979. PMID: 381944 Review.
Cited by
- Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation.
Wang D, Yang X, Ren Z, Hu B, Zhao H, Yang K, Shi P, Zhang Z, Feng Q, Nawenja CV, Obanda V, Robert K, Nalikka B, Waruhiu CN, Ochola GO, Onyuok SO, Ochieng H, Li B, Zhu Y, Si H, Yin J, Kristiansen K, Jin X, Xu X, Xiao M, Agwanda B, Ommeh S, Li J, Shi ZL. Wang D, et al. Microbiome. 2024 Apr 10;12(1):72. doi: 10.1186/s40168-024-01782-4. Microbiome. 2024. PMID: 38600530 Free PMC article. - Recombination between coronaviruses and synthetic RNAs and biorisk implications motivated by a SARS-CoV-2 FCS origin controversy.
Mueller S. Mueller S. Front Bioeng Biotechnol. 2023 Aug 4;11:1209054. doi: 10.3389/fbioe.2023.1209054. eCollection 2023. Front Bioeng Biotechnol. 2023. PMID: 37600318 Free PMC article. - Experimental evidence for the correlation between RNA structural fluctuations and the frequency of beneficial mutations.
Maeda Y, Mizuuchi R, Shigenobu S, Shibai A, Kotani H, Furusawa C, Ichihashi N. Maeda Y, et al. RNA. 2022 Dec;28(12):1659-1667. doi: 10.1261/rna.079291.122. Epub 2022 Oct 4. RNA. 2022. PMID: 36195345 Free PMC article. - Structural transition of replicable RNAs during in vitro evolution with Qβ replicase.
Mizuuchi R, Usui K, Ichihashi N. Mizuuchi R, et al. RNA. 2020 Jan;26(1):83-90. doi: 10.1261/rna.073106.119. Epub 2019 Nov 5. RNA. 2020. PMID: 31690585 Free PMC article. - Surveillance of Bat Coronaviruses in Kenya Identifies Relatives of Human Coronaviruses NL63 and 229E and Their Recombination History.
Tao Y, Shi M, Chommanard C, Queen K, Zhang J, Markotter W, Kuzmin IV, Holmes EC, Tong S. Tao Y, et al. J Virol. 2017 Feb 14;91(5):e01953-16. doi: 10.1128/JVI.01953-16. Print 2017 Mar 1. J Virol. 2017. PMID: 28077633 Free PMC article.