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III 关于逆转录酶与RNA聚合酶的相似性，参见：Gupta. S. P. (eds.)(2019).Viral polymerases: Structures, functions androles as antiviral drug targets. Academic Press, 1-42。
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IV 关于福泰尔的DNA酶系统起源假说，参见：Forterre, P.(2001). Genomics and early cellular evolution. The origin of the DNA world.Comptes Rendus de l’Académie des Sciences-Series III-Sciences de la Vie, 324(12): 1067–1076; Forterre, P.; Filée,J.; Myllykallio, H.( 2000-2013) Origin and evolution of DNA and DNA replication machineries. In
:Madame curie biosciencedatabase[Internet]. Austin (TX): Landes Bioscience. https://www.ncbi.nlm.nih.gov/books/NBK6360/; Forterre, P.( 2005). The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells.Biochimie, 87(9-10)
:793-803; For terre, P.; Krupovic, M.(2012). The origin of virions and virocells: The escape hypothesis revisited. In: Witzany G. (eds)Viruses: Essential agents of life. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-4899-6_3。
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V 关于内源性逆转录病毒，参见：Voisset, C.; Blancher, A.; Perron, H.; et al.(1999). Phylogeny of a novel family of human endogenous retrovirus sequences, HERV-W, in humans and other primates.AIDS research and human retroviruses, 15(17): 1529–1533; Lavialle, C.; Cornelis, G.; Dupressoir, A.; et al.(2013). Paleovirology of ‘syncytins’, retroviral env genes exapted for a role in placentation.Philosophical transactions of the Royal Society B Biological Sciences, 368 (1626): 20120507; Lander, E. S.; Linton, L. M.; Birren, B.; Nusbaum, C.(2001). International Human Genome Sequencing Consortium. Initial se quencing and analysis of the human genome.Nature, 409 (6822): 860–921。
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VI 关于噬菌体使用U碱基DNA，参见：Pérez‐Lago, L.; Serrano‐Heras, G.; Baños, B.; et al.(2011). Characterization of Bacillus subtilis uracil‐DNA glycosylase and its inhibition by phage φ29 protein p56.Molecular microbiology, 80(6)
:1657-66。
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VII 关于合成5-羟甲基胞嘧啶的酶的结构，参见：Song, H. K.; Sohn, S. H.; Suh, S. W.(1999). Crystal structure of deoxy cytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing com plex.The EMBO journal, 18(5)
:1104‐1113。
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VIII 关于5-羟甲基胞嘧啶出现在哺乳动物大脑中，参见：Kriaucionis, S.; Heintz, N.(2009). The nuclear DNA base 5-hy droxymethylcytosine is present in Purkinje neurons and the brain.Science, 324 (5929): 929–930。
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IX 关于对流式PCR，参见：Braun, D.; Goddard, N. L.; Libchaber, A.(2003). Exponential DNA replication by laminar con vection.Physical review letters, 91(15)
:158103。
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X 关于用乙醛等小分子从头合成DNA单体，参见：Teichert, J. S.; Kruse, F. M.; Trapp, O.(2019). Direct prebiotic pathway to DNA nucleosides.Angewandte chemie, 58(29)。
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XI 关于真核细胞RNA催化机制，参见：Torrents, E.(2014). Ribonucleotide reductases: essential enzymes for bacterial life.Frontiers in cellular and infection microbiology, 4
:52。
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XII 关于RNR制造自由基，参见：Kang, G.; Taguchi, A. T.; Stubbe, J.; Drennan, C. L.(2020). Structure of a trapped radical transfer pathway within a ribonucleotide reductase holocomplex. Science, 368(6489): 424-427。
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XIII 关于RNR自由基攻击核糖，参见：Cerqueira, N. M.; Fernandes, P. A.; Eriksson, L. A.; Ramos, M. J.(2006). Dehydra tion of ribonucleotides catalyzed by ribonucleotide reductase: the role of the enzyme.Biophysical journal, 90(6)
:2109‐2119。
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XIV 关于RNR类型，参见：Tomtera, A. B.; Zoppellaroa, G.; Andersena, N. H.; et al.(2013). Ribonucleotide reductase class I with diferent radical generating clusters,Coordination chemistry reviews, 257(1): 3-26。
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XV 关于RNR进化关系，参见：Poole, A. M.; Logan, D. T.; Sjöberg, B.-M.(2002). The evolution of ribonucleotide reduc tase: much ado about oxygen.Journal of molecular evolution, 55(2): 180–196。
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XVI 福泰尔关于RNR的病毒起源，参见：Forterre, P.; Filée, J.; Myllykallio, H.( 2000-2013) Origin and evolution of DNA and DNA replication machineries. In
:Madame curie bioscience database[Internet]. Austin (TX): Landes Bioscience. https://www.ncbi.nlm.nih.gov/books/NBK6360/。
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第十六章
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I 克里克的论文文献：Crick F.H. The origin of the genetic code. J. Mol. Biol. 1968;38
:367–379. doi: 10.1016/0022-2836(68) 90392-6.
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II 标准密码子第一位的规律，参见：Wong, J. T.(1975). A co-evolution theory of the genetic code.Proceedings of theNational Academy of Sciences, 72 (5): 1909-1912; Taylor, F. J. R.; Coates, D. (1989). The code within the codons.BioSystems, 22(3): 177–187; Umbarger, H. E.(1978). Amino acid biosynthesis and its regulation.Annual review of biochemistry, 47: 533–606; Danmaliki, G. I.; Liu, P. B.; Hwang, P. M.(2017). Stereoselective deuteration in aspartate, asparagine, lysine, and methionine amino acid residues using fumarate as a carbon source for Escherichia coli in D2O.Biochemistry, 56(45)
:6015-6029。
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III 关于氨基酸侧链疏水性，参见：Wimley, W. C.; Creamer, T. P.; White, S. H.(1996). Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides.Biochemistry, 35 (16): 5109–5124。
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IV 库宁总结影响力最大的三个标准遗传密码起源假说，参见：Koonin, E. V.; Novozhilov, A. S.(2009). Origin and evolu tion of the genetic code: the universal enigma.IUBMB Life, 61(2)
:99‐111。
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V 伽莫夫的论文，参见：GAMOW, G. (1954). Possible relation between deoxyribonucleic acid and protein structures.Nature, 173, 318。
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VI 立体化学假说，参见：GAMOW, G. (1954). Possible relation between deoxyribonucleic acid and protein structures.Nature, 173, 318; Pelc, S.; Welton, M.(1966). Stereochemical relationship between coding triplets and amino-acids.Nature, 209: 868–870)；Ellington, A. D.; Khrapov, M.; Shaw, C. A.(2006). The scene of a frozen accident.RNA, 6(4)
:485‐498。
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VII 错误最小化假说，参见：Woese, C. R.(1965). On the evolution of the genetic code.PNAS, 54(6)
:1546-52；Sonneborn,T. M.(1965). Degeneracy of the genetic code: extent, nature, and genetic implications.Evolving genes and proteins, 377–397;Epstein, C. J.(1966). Role of the amino-acid “code” and of selection for conformation in the evolution of proteins.Nature, 210(5031)
:25-8。
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VIII 关于突变参考文献：Suzanne Clancy (2008). Genetic mutation.Nature education, 1 (1): 187；Wellstein, A.; Pitschner,H. F.(1988). Complex dose-response curves of atropine in man explained by diferent functions of M1- and M2-cholinoceptors.Naunyn-Schmiedeberg’s Archives of Pharmacology, 338 (1): 19–27。
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IX 标准遗传密码优越性，参见：Woese, C. R.; Dugre, D. H.; Saxinger, W. C.; et al.(1966). The molecular basis for the ge netic code.Proceedings of the National Academy of Sciences, 55(4): 966-74; Freeland, S. J.; Hurst, L. D.(1998). The genetic code is one in a million.Journal of molecular evolution, 47(3)
:238-48。
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X 协同进化假说，参见：Wong, J. T.(1975). A co-evolution theory of the genetic code.Proceedings of the NationalAcademy of Sciences, 72(5)
:1909‐1912; Wong, J. T.(2005). Coevolution theory of the genetic code at age thirty.Bioessays, 27(4)
:416-25。
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