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V 迷你螺旋起源更早，参见：Sun, F.-J.; Caetano-Anollés, G. (2007). The origin and evolution of tRNA inferred from phy logenetic analysis of structure.Journal of Molecular Evolution, 66(1): 21–35; Fujishima, K.; Sugahara, J.; Tomita, M.; Kanai,A.(2008). Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 5’and 3’ tRNA halves.PLoS ONE, 3: e1622。
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VI 迷你螺旋独立结合aaRS参见：Frugier, M.; Florentz, C.; Giegé, R.(1994). Eficient aminoacylation of resected RNA helices by class II aspartyl-tRNA synthetase dependent on a single nucleotide.The EMBO Journal, 13: 2218–2226; Saks, M.E.;Sampson, J.R.(1996). Variant minihelix RNAs reveal sequence-specific recognition of the helical tRNASer acceptor stem by E. coli seryl-tRNA synthetase.The EMBO Journal, 15: 2843–2849。
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VII 迷你螺旋的非经典碱基对决定aaRS的结合能力参见：McClain, W. H.; Foss, K.(1988). Changing the identity of a tRNA by introducing a G-U wobble pair near the 3’ acceptor end.Science, 240(4853): 793-6; Schimmel, P.; Ribas de Pouplana,L.(1995). Transfer RNA: from minihelix to genetic code.Cell, 81(7): 983-6。
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VIII aaRS的3’端域比反密码子域更古老，参见：Shimizu, M.; Asahara, H.; Tamura, K.; Hasegawa, T.; Himeno, H.(1992).The role of anticodon bases and the discriminator nucleotide in the recognition of some E. coli tRNAs by their aminoacyl-tRNA synthetases.Journal of molecular evolution, 35(5): 436-43; Francklyn, C.; Schimmel, P.(1990). Enzymatic aminoacylation of an eight-base-pair microhelix with histidine.Proceedings of the National Academy of Sciences, 87(21): 8655–8659。
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IX 基因组标签假说参见：Weiner, A. M.; Maizels, N.(1999). The genomic tag hypothesis: modern viruses as molecular fossils of ancient strategies for genomic replication, and clues regarding the origin of protein synthesis.Biological Bulletin, 196(3)
:327-8; discussion 329-30; 2, Phylogeny from Function: The Origin of tRNA Is in Replication, not Translation, In
:National Academy of Sciences (US); Fitch, W. M.; Ayala, F. J.(editors)(1995).Tempo And Mode In Evolution: Genetics AndPaleontology 50 Years After Simpson. Washington (DC): National Academies Press (US). Available from: https://www.ncbi.nlm. nih.gov/books/NBK232211/。
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X 转运RNA在三域中的多样性参见：Fujishima, K.; Kanai, A.(2014). tRNA gene diversity in the three domains of life.Frontiers in Genetics, 5: 142.。
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XI CCA添加酶给病毒添加CCA尾，参见：Hema, M.; Gopinath, K.; Kao, C.(2005). Repair of the tRNA-like CCA se quence in a multipartite positive-strand RNA virus.Journal of virology, 79(3): 1417‐1427。
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XII 两种CCA添加酶，参见：Neuenfeldt, A.; Just, A.; Betat, H.; Mörl. M.(2008). Evolution of tRNA nucleotidyltransfer ases: A small deletion generated CC-adding enzymes.Proceedings of the National Academy of Sciences, 105 (23): 7953-7958;Bralley, P.; Chang, S. A.; Jones, G. H.(2005). A phylogeny of bacterial RNA nucleotidyltransferases: bacillus halodurans con tains Two tRNA nucleotidyltransferases.Journal of bacteriology, 187 (17) : 5927-5936。
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XIII 忒修斯的船假说参见：White, H. B. 3rd.(1976). Coenzymes as fossils of an earlier metabolic state.Journal of molecularevolution, 7(2)
:101‐104; Graham, D. E.; White, R. H.(2002). Elucidation of methanogenic coenzyme biosyntheses: from spec troscopy to genomics.Natural product reports, 19(2): 133-47。
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XIV 剪接体进化自内含子参见：Seetharaman, M.; Eldho, N. V.; Padgett, R. A.; Dayie, K. T.(2006). Structure of a self-splic ing group II intron catalytic efector domain 5: parallels with spliceosomal U6 RNA.RNA, 12 (2): 235–47; Valadkhan, S.(2010). Role of the snRNAs in spliceosomal active site.RNA Biology, 7 (3): 345–53。
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XV aaRS进化关系与协同进化假说的匹配参见：Kim, Y.; Opron, K.; Burton, Z.F.(2019). A tRNA- and Anticodon-Centric View of the Evolution of Aminoacyl-tRNA Synthetases, tRNAomes, and the Genetic Code.Life, 9(2): 37。
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XVI 多肽催化氨基酸连接转运RNA假说参见：Chatterjee, S.; Yadav, S.(2019). The origin of prebiotic information system in the peptide/RNA world: a simulation model of the evolution of translation and the genetic code.Life, 9(1): 25; Kunnev, D.;Gospodinov, A.(2018). Possible emergence of sequence specific RNA aminoacylation via peptide intermediary to initiate dar winian evolution and code through origin of life.Life, 8(4)
:44。
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XVII 蛋白质自我复制参见：Rout, S. K.; Friedmann, M. P.; Riek, R.; Greenwald. J.(2018). A prebiotic template-directed pep tide synthesis based on amyloids.Nature communications, 9 (1)。
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XVIII 双发夹假说参见：Di Giulio, M.(2004). The origin of the tRNA molecule: implications for the origin of protein synthe sis.Journal of theoretical biology, 226(1): 89‐93; Chatterjee, S.; Yadav, S.(2019). The origin of prebiotic information system in the peptide/RNA world: a simulation model of the evolution of translation and the genetic code.Life, 9(1)
:25。
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XIX 三重迷你螺旋假说参见：Burton, Z. F.(2020). The 3-Minihelix tRNA evolution theorem.Journal of molecular evolution, 88: 234–242。
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XX 手性选择氨酰化假说参见：Tamura, K.; Schimmel, P.(2004). Chiral-selective aminoacylation of an RNA minihelix.Science, 305(5688): 1253.
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XXI 甘氨酸起始假说参见：Bernhardt, H. S.; Tate, W. P.(2008). Evidence from glycine transfer RNA of a frozen accident at the dawn of the genetic code.Biology direct, 3
:53; Bernhardt, H. S.; Tate, W. P.(2010). The transition from noncoded to coded protein synthesis: did coding mRNAs arise from stability-enhancing binding partners to tRNA?Biology direct, 5
:16。
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XXII 受体臂折叠假说参见：Puglisi, E. V.; Puglisi, J. D.; Williamson, J. R.; RajBhandary, U. L.(1994). NMR analysis of tRNA acceptor stem microhelices: discriminator base change afects tRNA conformation at the 3’ end.Proceedings of the National Academy of Sciences, 91(24): 11467‐11471。
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XXIII 芜菁黄花叶病毒争夺缬氨酸参见：Colussi, T. M.; Costantino, D. A.; Hammond, J. A.; Ruehle, G. M.; Nix, J.C.; Kieft, J. S.(2014). The structural basis of transfer RNA mimicry and conformational plasticity by a viral RNA.Nature, 511(7509): 366‐369。
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XXIV 芜菁黄花叶病毒结合其他氨基酸参见：Dreher, T. W.(2009). Role of tRNA-like structures in controlling plant virus replication.Virus research, 139(2): 217‐229; Tsai, C. H.; Dreher, T. W.(1991). Turnip yellow mosaic virus RNAs with anti codon loop substitutions that result in decreased valylation fail to replicate eficiently.Journal of virology, 65(6): 3060‐3067;Wientges, J.; Putz, J.; Giege, R.; Florentz, C.; Schwienhorst, A.(2000). Selection of viral RNA-derived tRNA-like structures with improved valylation activities.Biochemistry, 39: 6207–18; Dreher, T. W.; Tsai, C. H.; Skuzeski, J. M.(1996). Aminoacyla tion identity switch of turnip yellow mosaic virus RNA from valine to methionine results in an infectious virus.Proceedings ofthe National Academy of Sciences, 93
:12212–6。
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XXV 转运RNA样结构加快翻译速度参见：Osman,T.; Hemenway, C. L.; Buck, K. W.(2000). Role of the 3’tRNA-Like Structure in Tobacco Mosaic Virus Minus-Strand RNA Synthesis by the Viral RNA-Dependent RNA Polymerase In Vitro.Journal of virology, 74(24): 11671-11680; Gallie, D. R.; Feder, J. N.; Schimke, R. T.; Walbot, V.(1991). Functional analysis of the tobacco mosaic virus tRNA-like structure in cytoplasmic gene regulation,Nucleic acids research, 19(18): 5031–5036。
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XXVI 病毒转运RNA样结构只凭假结就可以结合aaRS，参见：Schimmel, P.; Alexander. R.(1998). Diverse RNA sub strates for aminoacylation: Clues to origins? Proceedings of the National Academy of Sciences, 95(18): 10351-10353。
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XXVII 粉红面包霉菌逆转录质粒参见：Kuiper，M. T.；Lambowitz, A. M.(1988). A novel reverse transcriptase activity associated with mitochondrial plasmids of neurospora.Cell, 55(4): 693-704; Chen, B.; Lambowitz, A. M.(1997). De novo and DNA primer-mediated initiation of cDNA synthesis by the mauriceville retroplasmid reverse transcriptase involve recognition of a 3’ CCA sequence.Journal of molecular biology, 271(3): 311-32。
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XXVIII 关于逆转录质粒的自我剪切参见：Saville, B. J.; Collins, R. A.(1990). A site-specific self-cleavage reaction per formed by a novel RNA in Neurospora mitochondria.Cell, 61(4): 685-696。
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XXIX 逆转录质粒的逆转录酶逆转录转运RNA参见：Chiang, C. C.; Lambowitz, A. M.(1997). The Mauriceville ret roplasmid reverse transcriptase initiates cDNA synthesis de novo at the 3’ end of tRNAs.Molecular and cellular biology, 17(8): 4526‐4535。
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