1. Staehelin,T., Maglott,D.M. and Monro,R.E. (1969) On the catalytic center of peptidyl transfer: a part of the 50 S ribosome structure. Cold Spring Harb. Symp. Quant. Biol., 34, 39–48.
2. Haller,A., Soulière,M.F. and Micura,R. (2011) The Dynamic Nature of RNA as Key to Understanding Riboswitch Mechanisms. Acc. Chem. Res., 44, 1339–1348.
3. Serganov,A., Huang,L. and Patel,D.J. (2009) Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch. Nature, 458, 233–237.
4. Talini,G., Branciamore,S. and Gallori,E. (2011) Ribozymes: Flexible molecular devices at work. Biochimie, 93, 1998–2005.
5. Hoogstraten,C.G. and Sumita,M. (2007) Structure–function relationships in RNA and RNP enzymes: Recent advances. Biopolymers, 87, 317–328.
6. Ikawa,Y., Tsuda,K., Matsumura,S. and Inoue,T. (2004) De novo synthesis and development of an RNA enzyme. Proc. Natl. Acad. Sci. U. S. A., 101, 13750–5.
7. Munoz-Tello,P., Rajappa,L., Coquille,S. and Thore,S. (2015) Polyuridylation in Eukaryotes: A 3’-End Modification Regulating RNA Life. Biomed Res. Int., 2015, 968127.
8. Li,S.-C., Tsai,K.-W., Pan,H.-W., Jeng,Y.-M., Ho,M.-R. and Li,W.-H. (2012) MicroRNA 3’ end nucleotide modification patterns and arm selection preference in liver tissues. BMC Syst. Biol., 6 Suppl 2, S14.
9. Grimm,D., Pandey,K. and Kay,M.A. (2005) Adeno-Associated Virus Vectors for Short Hairpin RNA Expression. In Methods in enzymology.Vol. 392, pp. 381–405.
10. Lehninger Principles of Biochemistry (9781464126116) | Macmillan Learning.
11. Salazar,M., Fedoroff,O.Y., Miller,J.M., Ribeiro,N.S. and Reid,B.R. (1993) The DNA strand in DNA.cntdot.RNA hybrid duplexes is neither B-form nor A-form in solution. Biochemistry, 32, 4207–4215.
12. Berg,J.M. (Jeremy M., Tymoczko,J.L., Stryer,L. and Stryer,L. (2002) Biochemistry W.H. Freeman.
13. Butcher,S.E. and Pyle,A.M. (2011) The Molecular Interactions That Stabilize RNA Tertiary Structure: RNA Motifs, Patterns, and Networks. Acc. Chem. Res., 44, 1302–1311.
14. Zemora,G. and Waldsich,C. (2010) RNA folding in living cells. RNA Biol., 7, 634– 41.
15. Higgs,P.G. (2000) RNA secondary structure: physical and computational aspects. Q. Rev. Biophys., 33, 199–253.
16. Leontis,N.B. and Westhof,E. (2001) Geometric nomenclature and classification of RNA base pairs. RNA, 7, 499–512.
17. Lee,J.C. and Gutell,R.R. (2004) Diversity of Base-pair Conformations and their Occurrence in rRNA Structure and RNA Structural Motifs. J. Mol. Biol., 344, 1225–1249.
18. Ishikawa,J., Furuta,H. and Ikawa,Y. (2013) RNA Tectonics (tectoRNA) for RNA nanostructure design and its application in synthetic biology. Wiley Interdiscip. Rev. RNA, 4, 651–664.
19. Pyle,A. (2002) Metal ions in the structure and function of RNA. JBIC J. Biol. Inorg. Chem., 7, 679–690.
20. DOTY,P., BOEDTKER,H., FRESCO,J.R., HALL,B.D. and HASELKORN,R. (1959) Configurational studies of polynucleotides and ribonucleic acid. Ann. N. Y. Acad. Sci., 81, 693–708.
21. Moore,P.B. (1999) Structural Motifs in RNA. Annu. Rev. Biochem., 68, 287–300.
22. Leontis,N.B. and Westhof,E. (2003) Analysis of RNA motifs. Curr. Opin. Struct. Biol., 13, 300–8.
23. SenGupta,D.J., Zhang,B., Kraemer,B., Pochart,P., Fields,S. and Wickens,M. (1996) A three-hybrid system to detect RNA-protein interactions in vivo. Proc. Natl. Acad. Sci. U. S. A., 93, 8496–501.
24. Hermann,T. and Patel,D.J. (2000) Adaptive recognition by nucleic acid aptamers. Science, 287, 820–5.
25. Denesyuk,N.A. and Thirumalai,D. (2015) How do metal ions direct ribozyme folding? Nat. Chem., 7, 793–801.
26. Cate,J.H. and Doudna,J.A. (1996) Metal-binding sites in the major groove of a large ribozyme domain. Structure, 4, 1221–9.
27. Qin,H., Sosnick,T.R. and Pan,T. (2001) Modular construction of a tertiary RNA structure: the specificity domain of the Bacillus subtilis RNase P RNA. Biochemistry, 40, 11202–10.
28. Holbrook,S.R. (2005) RNA structure: the long and the short of it. Curr. Opin. Struct. Biol., 15, 302–308.
29. Tinoco,I. and Bustamante,C. (1999) How RNA folds. J. Mol. Biol., 293, 271–281.
30. Greenleaf,W.J., Frieda,K.L., Foster,D.A.N., Woodside,M.T. and Block,S.M. (2008) Direct observation of hierarchical folding in single riboswitch aptamers. Science, 319, 630–3.
31. Jaeger,L. and Chworos,A. (2006) The architectonics of programmable RNA and DNA nanostructures. Curr. Opin. Struct. Biol., 16, 531–543.
32. Batey, Rambo and Doudna (1999) Tertiary Motifs in RNA Structure and Folding. Angew. Chem. Int. Ed. Engl., 38, 2326–2343.
33. Hendrix,D.K., Brenner,S.E. and Holbrook,S.R. (2005) RNA structural motifs: building blocks of a modular biomolecule. Q. Rev. Biophys., 38, 221–243.
34. Li,M., Zheng,M., Wu,S., Tian,C., Liu,D., Weizmann,Y., Jiang,W., Wang,G. and Mao,C. (2018) In vivo production of RNA nanostructures via programmed folding of single-stranded RNAs. Nat. Commun., 9, 1–9.
35. Laing,C., Jung,S., Iqbal,A. and Schlick,T. (2009) Tertiary motifs revealed in analyses of higher-order RNA junctions. J. Mol. Biol., 393, 67–82.
36. Tan,Z.-J. and Chen,S.-J. (2011) Importance of diffuse metal ion binding to RNA. Met. Ions Life Sci., 9, 101–24.
37. Hermann,T. Drugs targeting the ribosome. 10.1016/j.sbi.2005.05.001.
38. Frederiksen,J.K. and Piccirilli,J.A. (2009) Identification of catalytic metal ion ligands in ribozymes. Methods, 49, 148–66.
39. Johnson-Buck,A.E., McDowell,S.E. and Walter,N.G. (2011) Metal ions: supporting actors in the playbook of small ribozymes. Met. Ions Life Sci., 9, 175–96.
40. Zhang,J., Lau,M.W. and Ferré-D’Amaré,A.R. (2010) Ribozymes and Riboswitches: Modulation of RNA Function by Small Molecules. Biochemistry, 49, 9123–9131.
41. Ishikawa,J., Fujita,Y., Maeda,Y., Furuta,H. and Ikawa,Y. (2011) GNRA/receptor interacting modules: Versatile modular units for natural and artificial RNA architectures. Methods, 54, 226–238.
42. LESCOUTE,A. and WESTHOF,E. (2006) The A-minor motifs in the decoding recognition process. Biochimie, 88, 993–999.
43. Nissen,P., Ippolito,J.A., Ban,N., Moore,P.B. and Steitz,T.A. (2001) RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc. Natl. Acad. Sci. U. S. A., 98, 4899–903.
44. Geary,C., Baudrey,S. and Jaeger,L. (2008) Comprehensive features of natural and in vitro selected GNRA tetraloop-binding receptors. Nucleic Acids Res., 36, 1138–52.
45. Doherty,E.A., Batey,R.T., Masquida,B. and Doudna,J.A. (2001) A universal mode of helix packing in RNA. Nat. Struct. Biol., 8, 339–343.
46. Xin,Y., Laing,C., Leontis,N.B. and Schlick,T. (2008) Annotation of tertiary interactions in RNA structures reveals variations and correlations. RNA, 14, 2465– 77.
47. Principles of Nucleic Acid Structure (2008) Elsevier.
48. Laing,C., Wen,D., Wang,J.T.L. and Schlick,T. (2012) Predicting coaxial helical stacking in RNA junctions. Nucleic Acids Res., 40, 487.
49. Tyagi,R. and Mathews,D.H. (2007) Predicting helical coaxial stacking in RNA multibranch loops. RNA, 13, 939–51.
50. Kim,S.H., Suddath,F.L., Quigley,G.J., McPherson,A., Sussman,J.L., Wang,A.H.J., Seeman,N.C. and Rich,A. (1974) Three-Dimensional Tertiary Structure of Yeast Phenylalanine Transfer RNA. Science (80-. )., 185, 435–440.
51. Jaeger,L., Verzemnieks,E.J. and Geary,C. (2009) The UA_handle: a versatile submotif in stable RNA architectures. Nucleic Acids Res., 37, 215–30.
52. Forsdyke,D.R. (1995) A stem-loop "kissing" model for the initiation of recombination and the origin of introns. Mol. Biol. Evol., 12, 949–58.
53. Ennifar,E., Walter,P., Ehresmann,B., Ehresmann,C. and Dumas,P. (2001) Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site. Nat. Struct. Biol., 8, 1064–1068.
54. Quigley,G.J. and Rich,A. (1976) Structural domains of transfer RNA molecules. Science, 194, 796–806.
55. Batey,R.T., Gilbert,S.D. and Montange,R.K. (2004) Structure of a natural guanine- responsive riboswitch complexed with the metabolite hypoxanthine. Nature, 432, 411–415.
56. Chi,Y.-I., Martick,M., Lares,M., Kim,R., Scott,W.G. and Kim,S.-H. (2008) Capturing Hammerhead Ribozyme Structures in Action by Modulating General Base Catalysis. PLoS Biol., 6, e234.
57. Dufour,D., de la Peña,M., Gago,S., Flores,R. and Gallego,J. (2009) Structure– function analysis of the ribozymes of chrysanthemum chlorotic mottle viroid: a loop–loop interaction motif conserved in most natural hammerheads. Nucleic Acids Res., 37, 368–381.
58. Lehnert,V., Jaeger,L., Michel,F. and Westhof,E. (1996) New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme. Chem. Biol., 3, 993–1009.
59. Kim,N.-K., Zhang,Q., Zhou,J., Theimer,C.A., Peterson,R.D. and Feigon,J. (2008) Solution Structure and Dynamics of the Wild-type Pseudoknot of Human Telomerase RNA. J. Mol. Biol., 384, 1249–1261.
60. Woese,C. (1967) The genetic code Harper and Row, New York.
61. RIBOZYMES: NUCLEIC ACID ENZYMES WITH POTENTIAL PHARMACEUTICAL APPLICATIONS - A REVIEW -Pharmacophore.
62. Gaughan,D.J. and Whitehead,A.S. (1999) Function and biological applications of catalytic nucleic acids. Biochim. Biophys. Acta, 1445, 1–20.
63. Kruger,K., Grabowski,P.J., Zaug,A.J., Sands,J., Gottschling,D.E. and Cech,T.R. (1982) Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena. Cell, 31, 147–157.
64. Robinson,R. (2003) Genetics Macmillan Reference USA.
65. Lee,K.-Y. and Lee,B.-J. (2017) Structural and Biochemical Properties of Novel Self-Cleaving Ribozymes. Molecules, 22, 678.
66. Fong,N., Öhman,M. and Bentley,D.L. (2009) Fast ribozyme cleavage releases transcripts from RNA polymerase II and aborts co-transcriptional pre-mRNA processing. Nat. Struct. Mol. Biol., 16, 916–922.
67. Chadalavada,D.M., Gratton,E.A. and Bevilacqua,P.C. (2010) The Human HDV-like CPEB3 Ribozyme Is Intrinsically Fast-Reacting. Biochemistry, 49, 5321–5330.
68. de la Cruz,J., Karbstein,K. and Woolford,J.L. (2015) Functions of Ribosomal Proteins in Assembly of Eukaryotic Ribosomes In Vivo. Annu. Rev. Biochem., 84, 93–129.
69. Jaeger,L. (1997) The New World of ribozymes. Curr. Opin. Struct. Biol., 7, 324–35.
70. Loria,A. and Pan,T. (1996) Domain structure of the ribozyme from eubacterial ribonuclease P. RNA, 2, 551–63.
71. Campbell,T.B. and Cech,T.R. (1996) Mutations in the Tetrahymena Ribozyme Internal Guide Sequence: Effects on Docking of the P1 Helix into the Catalytic Core and Correlation with Catalytic Activity †. Biochemistry, 35, 11493–11502.
72. Emerick,V.L., Pan,J. and Woodson,S.A. (1996) Analysis of Rate-Determining Conformational Changes during Self-Splicing of the Tetrahymena Intron †. Biochemistry, 35, 13469–13477.
73. Jaeger,L., Michel,F. and Westhof,E. (1996) The Structure of Group I Ribozymes. In. Springer, Berlin, Heidelberg, pp. 33–51.
74. Walter,N.G. and Perumal,S. The Small Ribozymes: Common and Diverse Features Observed Through the FRET Lens. In Non-Protein Coding RNAs. Springer Berlin Heidelberg, Berlin, Heidelberg, pp. 103–127.
75. Cooper,G.M. (2000) The Central Role of Enzymes as Biological Catalysts.
76. Tang,J. and Breaker,R.R. (2000) Structural diversity of self-cleaving ribozymes. Proc. Natl. Acad. Sci. U. S. A., 97, 5784.
77. Saito,H., Kourouklis,D. and Suga,H. (2001) An in vitro evolved precursor tRNA with aminoacylation activity. EMBO J., 20, 1797–806.
78. Lan,P., Tan,M., Zhang,Y., Niu,S., Chen,J., Shi,S., Qiu,S., Wang,X., Peng,X., Cai,G., et al. (2018) Structural insight into precursor tRNA processing by yeast ribonuclease P. Science, 362, eaat6678.
79. Esakova,O. and Krasilnikov,A.S. (2010) Of proteins and RNA: the RNase P/MRP family. RNA, 16, 1725–47.
80. Evans,D., Marquez,S.M. and Pace,N.R. (2006) RNase P: interface of the RNA and protein worlds. Trends Biochem. Sci., 31, 333–341.
81. Stams,T., Niranjanakumari,S., Fierke,C.A. and Christianson,D.W. (1998) Ribonuclease P Protein Structure: Evolutionary Origins in the Translational Apparatus. Science (80-. )., 280, 752–755.
82. Kazantsev,A. V. and Pace,N.R. (2006) Bacterial RNase P: a new view of an ancient enzyme. Nat. Rev. Microbiol., 4, 729–740.
83. Pan,T. (1995) Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P. Biochemistry, 34, 902–909.
84. Torres-Larios,A., Swinger,K.K., Pan,T. and Mondragón,A. (2006) Structure of ribonuclease P — a universal ribozyme. Curr. Opin. Struct. Biol., 16, 327–335.
85. Nakano,S., Miyoshi,D. and Sugimoto,N. (2014) Effects of Molecular Crowding on the Structures, Interactions, and Functions of Nucleic Acids. Chem. Rev., 114, 2733–2758.
86. Kilburn,D., Roh,J.H., Guo,L., Briber,R.M. and Woodson,S.A. (2010) Molecular Crowding Stabilizes Folded RNA Structure by the Excluded Volume Effect. J. Am. Chem. Soc., 132, 8690–8696.
87. Rahman,M.M., Matsumura,S. and Ikawa,Y. (2018) Effects of molecular crowding on a bimolecular group I ribozyme and its derivative that self-assembles to form ribozyme oligomers. Biochem. Biophys. Res. Commun., 507, 136–141.
88. Tagami,S., Attwater,J. and Holliger,P. (2017) Simple peptides derived from the ribosomal core potentiate RNA polymerase ribozyme function. Nat. Chem., 9, 325–332.
89. Jasinski,D., Haque,F., Binzel,D.W. and Guo,P. (2017) Advancement of the Emerging Field of RNA Nanotechnology. ACS Nano, 11, 1142–1164.
90. Guo,P., Haque,F., Hallahan,B., Reif,R. and Li,H. (2012) Uniqueness, advantages, challenges, solutions, and perspectives in therapeutics applying RNA nanotechnology. Nucleic Acid Ther., 22, 226–45.
91. Winfree,E., Liu,F., Wenzler,L.A. and Seeman,N.C. (1998) Design and self- assembly of two-dimensional DNA crystals. Nature, 394, 539–544.
92. Rothemund,P.W.K. (2006) Folding DNA to create nanoscale shapes and patterns. Nature, 440, 297–302.
93. Severcan,I., Geary,C., Chworos,A., Voss,N., Jacovetty,E. and Jaeger,L. (2010) A polyhedron made of tRNAs. Nat. Chem., 2, 772–779.
94. Severcan,I., Geary,C., Verzemnieks,E., Chworos,A. and Jaeger,L. (2009) Square-Shaped RNA Particles from Different RNA Folds. Nano Lett., 9, 1270–1277.
95. Geary,C., Chworos,A., Verzemnieks,E., Voss,N.R. and Jaeger,L. (2017) Composing RNA Nanostructures from a Syntax of RNA Structural Modules. Nano Lett., 17, 7095–7101.
96. Chworos,A., Severcan,I., Koyfman,A.Y., Weinkam,P., Oroudjev,E., Hansma,H.G. and Jaeger,L. (2004) Building Programmable Jigsaw Puzzles with RNA. Science (80-. )., 306, 2068–2072.
97. Boerneke,M.A., Dibrov,S.M. and Hermann,T. (2016) Crystal-Structure-Guided Design of Self-Assembling RNA Nanotriangles. Angew. Chemie Int. Ed., 55, 4097–4100.
98. Guo,P., Zhang,C., Chen,C., Garver,K. and Trottier,M. (1998) Inter-RNA interaction of phage phi29 pRNA to form a hexameric complex for viral DNA transportation. Mol. Cell, 2, 149–55.
99. Leontis,N.B., Stombaugh,J. and Westhof,E. (2002) The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res., 30, 3497–3531.
100. Shu,D., Shu,Y., Haque,F., Abdelmawla,S. and Guo,P. (2011) Thermodynamically stable RNA three-way junction for constructing multifunctional nanoparticles for delivery of therapeutics. Nat. Nanotechnol., 6, 658–667.
101. Benenson,Y. (2012) Synthetic biology with RNA: progress report. Curr. Opin. Chem. Biol., 16, 278–84.
102. McDaniel,R. and Weiss,R. (2005) Advances in synthetic biology: On the path from prototypes to applications. Curr. Opin. Biotechnol., 16, 476–483.
103. Khalil,A.S. and Collins,J.J. (2010) Synthetic biology: Applications come of age. Nat. Rev. Genet., 11, 367–379.
104. Bachellerie,J.P., Cavaillé,J. and Hüttenhofer,A. (2002) The expanding snoRNA world. Biochimie, 84, 775–790.
105. Blumenberg,M. and Yanofsky,C. (1982) Regulatory region of the Klebsiella aerogenes tryptophan operon. J. Bacteriol., 152, 49–56.
106. Ferapontova,E.E., Olsen,E.M. and Gothelf,K. V. (2008) An RNA aptamer-based electrochemical biosensor for detection of theophylline in serum. J. Am. Chem. Soc., 130, 4256–4258.
107. Lilley,D.M.J. (2003) The origins of RNA catalysis in ribozymes. Trends Biochem. Sci., 28, 495–501.
108. Ban,N., Nissen,P., Hansen,J., Moore,P.B. and Steitz,T.A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science (80-. )., 289, 905–920.
109. Cate,J.H., Gooding,A.R., Podell,E., Zhou,K., Golden,B.L., Kundrot,C.E., Cech,T.R. and Doudna,J.A. (1996) Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science (80-. )., 273, 1678–1685.
110. Yusupov,M.M., Yusupova,G.Z., Baucom,A., Lieberman,K., Earnest,T.N., Cate,J.H. and Noller,H.F. (2001) Crystal structure of the ribosome at 5.5 A resolution. Science, 292, 883–96.
111. Afonin,K.A., Grabow,W.W., Walker,F.M., Bindewald,E., Dobrovolskaia,M.A., Shapiro,B.A. and Jaeger,L. (2011) Design and self-assembly of siRNA- functionalized RNA nanoparticles for use in automated nanomedicine. Nat. Protoc., 6, 2022–2034.
112. Zhang,Y., Peng,L., Mumper,R.J. and Huang,L. (2013) Combinational delivery of c-myc siRNA and nucleoside analogs in a single, synthetic nanocarrier for targeted cancer therapy. Biomaterials, 34, 8459–68.
113. Jaeger,L., Michel,F. and Westhof,E. (1996) The Structure of Group I Ribozymes. In.pp. 33–51.
114. Jaeger,L., Wright,M.C., Joyce,G.F. and Inoue,T. (1999) A complex ligase ribozyme evolved in vitro from a group I ribozyme domain. Proc. Natl. Acad. Sci. U. S. A., 96, 14712–7.
115. Yoshioka,W., Ikawa,Y., Jaeger,L., Shiraishi,H. and Inoue,T. (2004) Generation of a catalytic module on a self-folding RNA. RNA, 10, 1900–1906.
116. Ikawa,Y., Fukada,K., Watanabe,S.I., Shiraishi,H. and Inoue,T. (2002) Design, construction, and analysis of a novel class of self-folding RNA. Structure, 10, 527– 534.
117. Fujita,Y., Furuta,H. and Ikawa,Y. (2009) Tailoring RNA modular units on a common scaffold: A modular ribozyme with a catalytic unit for β-nicotinamide mononucleotide-activated RNA ligation. RNA, 15, 877–888.
118. Nozawa,Y., Hagihara,M., Rahman,M.S., Matsumura,S. and Ikawa,Y. (2019) Rational Design of an Orthogonal Pair of Bimolecular RNase P Ribozymes through Heterologous Assembly of Their Modular Domains. Biology (Basel)., 8.
119. Kuznetsova,I.M., Turoverov,K.K. and Uversky,V.N. (2014) What macromolecular crowding can do to a protein. Int. J. Mol. Sci., 15, 23090–23140.
120. Mittal,S., Chowhan,R.K. and Singh,L.R. (2015) Macromolecular crowding: Macromolecules friend or foe. Biochim. Biophys. Acta, 1850, 1822–31.
121. Teraoka,H. and Tsukada,K. (1987) Influence of polyethylene glycol on the ligation reaction with calf thymus DNA ligases I and II. J. Biochem., 101, 225–31.
122. Wu,Q., Huang,L. and Zhang,Y. (2009) The structure and function of catalytic RNAs. Sci. China. Ser. C, Life Sci., 52, 232–44.
123. Lilley,D.M.J. and Eckstein,F. eds. (2007) Ribozymes and RNA Catalysis Royal Society of Chemistry, Cambridge.
124. Hervé,G., Tobé,S., Heams,T., Vergne,J. and Maurel,M.C. (2006) Hydrostatic and osmotic pressure study of the hairpin ribozyme. Biochim. Biophys. Acta - Proteins Proteomics, 1764, 573–577.
125. Nakano,S.I., Karimata,H.T., Kitagawa,Y. and Sugimoto,N. (2009) Facilitation of RNA enzyme activity in the molecular crowding media of cosolutes. J. Am. Chem. Soc., 131, 16881–16888.
126. Strulson,C.A., Yennawar,N.H., Rambo,R.P. and Bevilacqua,P.C. (2013) Molecular crowding favors reactivity of a human ribozyme under physiological ionic conditions. Biochemistry, 52, 8187–97.
127. Desai,R., Kilburn,D., Lee,H.-T. and Woodson,S.A. (2014) Increased ribozyme activity in crowded solutions. J. Biol. Chem., 289, 2972–7.
128. Krasilnikov,A.S., Yang,X., Pan,T. and Mondragón,A. (2003) Crystal structure of the specificity domain of ribonuclease P. Nature, 421, 760–4.
129. Krasilnikov,A.S., Xiao,Y., Pan,T. and Mondragón,A. (2004) Basis for structural diversity in homologous RNAs. Science, 306, 104–7.
130. Van Der Horst,G., Christian,A. and Inoue,T. (1991) Reconstitution of a group I intron self-splicing reaction with an activator RNA. Proc. Natl. Acad. Sci. U. S. A., 88, 184–188.
131. Doudna,J.A. and Cech,T.R. (1995) Self-assembly of a Group I intron active site from its component tertiary structural domains. RNA, 1, 36–45.
132. Ikawa,Y., Shiraishi,H. and Inoue,T. (1998) Trans-activation of the Tetrahymena ribozyme by its P2-2.1 domains. J. Biochem., 123, 528–533.
133. Pan,T. (1995) Higher Order Folding and Domain Analysis of the Ribozyme from Bacillus subtilis Ribonuclease P. Biochemistry, 34, 902–909.
134. Mondragón,A. (2013) Structural Studies of RNase P. Annu. Rev. Biophys., 42, 537–557.
135. Nozawa,Y., Hagihara,M., Matsumura,S. and Ikawa,Y. (2018) Modular Architecture of Bacterial RNase P Ribozymes as a Structural Platform for RNA Nanostructure Design. Chimia (Aarau)., 72, 882–887.
136. Walczyk,D., Willkomm,D.K. and Hartmann,R.K. (2016) Bacterial type B RNase P: Functional characterization of the L5.1-L15.1 tertiary contact and antisense inhibition. RNA, 22, 1699–1709.
137. Guerrier-Takada,C., Haydock,K., Allen,L. and Altman,S. (1986) Metal Ion Requirements and Other Aspects of the Reaction Catalyzed by M1 RNA, the RNA Subunit of Ribonuclease P from Escherichia coli. Biochemistry, 25, 1509–1515.
138. Kazantsev,A. V. and Pace,N.R. (2006) Bacterial RNase P: a new view of an ancient enzyme. Nat. Rev. Microbiol., 4, 729–740.
139. Tanaka,T., Furuta,H. and Ikawa,Y. (2014) Installation of orthogonality to the interface that assembles two modular domains in the Tetrahymena group I ribozyme. J. Biosci. Bioeng., 117, 407–12.
140. Marszalkowski,M., Willkomm,D.K. and Hartmann,R.K. (2008) Structural basis of a ribozyme’s thermostability: P1-L9 interdomain interaction in RNase P RNA. RNA, 14, 127–133.
141. Oi,H., Fujita,D., Suzuki,Y., Sugiyama,H., Endo,M., Matsumura,S. and Ikawa,Y. (2017) Programmable formation of catalytic RNA triangles and squares by assembling modular RNA enzymes. J. Biochem., 161, 451–462.
142. Tsuruga,R., Uehara,N., Suzuki,Y., Furuta,H., Sugiyama,H., Endo,M., Matsumura,S. and Ikawa,Y. (2019) Oligomerization of a modular ribozyme assembly of which is controlled by a programmable RNA-RNA interface between two structural modules. J. Biosci. Bioeng., 128, 410–415.
143. Higgs,P.G. and Lehman,N. (2015) The RNA World: molecular cooperation at the origins of life. Nat. Rev. Genet., 16, 7–17.
144. Joyce,G.F. and Szostak,J.W. (2018) Protocells and RNA Self-Replication. Cold Spring Harb. Perspect. Biol., 10.
145. Gillams,R.J. and Jia,T.Z. (2018) Mineral Surface-Templated Self-Assembling Systems: Case Studies from Nanoscience and Surface Science towards Origins of Life Research. Life (Basel, Switzerland), 8.
146. Rahman,M.M., Matsumura,S. and Ikawa,Y. (2018) Oligomerization of a Bimolecular Ribozyme Modestly Rescues its Structural Defects that Disturb Interdomain Assembly to Form the Catalytic Site. J. Mol. Evol., 86, 431–442.
147. Saha,R., Pohorille,A. and Chen,I.A. (2014) Molecular crowding and early evolution. Orig. Life Evol. Biosph., 44, 319–24.
148. Klemm,B.P., Wu,N., Chen,Y., Liu,X., Kaitany,K.J., Howard,M.J. and Fierke,C.A. (2016) The diversity of ribonuclease P: Protein and RNA catalysts with analogous biological functions. Biomolecules, 6.
149. Guerrier-Takada,C., Gardiner,K., Marsh,T., Pace,N. and Altman,S. (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell, 35, 849–857.
150. Loria,A. and Pan,T. (1996) Domain structure of the ribozyme from eubacterial ribonuclease P. RNA, 2, 551–63.
151. Loria,A. and Pan,T. (1997) Recognition of the T Stem−Loop of a Pre-tRNA Substrate by the Ribozyme from Bacillus subtilis Ribonuclease P †. Biochemistry, 36, 6317–6325.
152. Reiter,N.J., Osterman,A., Torres-Larios,A., Swinger,K.K., Pan,T. and Mondragón,A. (2010) Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA. Nature, 468, 784–791.
153. Steitz,T.A. and Steitz,J.A. (1993) A general two-metal-ion mechanism for catalytic RNA. Proc. Natl. Acad. Sci. U. S. A., 90, 6498–6502.
154. Ribozymes and RNA Catalysis - Google Books.
155. Massire,C., Jaeger,L. and Westhof,E. (1998) Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis. J. Mol. Biol., 279, 773–793.
156. Lai,L.B., Vioque,A., Kirsebom,L.A. and Gopalan,V. (2010) Unexpected diversity of RNase P, an ancient tRNA processing enzyme: Challenges and prospects. FEBS Lett., 584, 287–296.
157. Weiss,M.C., Sousa,F.L., Mrnjavac,N., Neukirchen,S., Roettger,M., Nelson- Sathi,S. and Martin,W.F. (2016) The physiology and habitat of the last universal common ancestor. Nat. Microbiol., 1.
158. Hartmann,R.K. and Erdmann,V.A. (1991) Analysis of the gene encoding the RNA subunit of ribonuclease P from T.Thermophilus HB8. Nucleic Acids Res., 19, 5957–5964.
159. Brown,J.W., Haas,E.S. and Pace,N.R. (1993) Characterization of ribonuclease P RNAs from thermophilic bacteria. Nucleic Acids Res., 21, 671–679.
160. Fang,X.W., Golden,B.L., Littrell,K., Shelton,V., Thiyagarajan,P., Pan,T. and Sosnick,T.R. (2001) The thermodynamic origin of the stability of a thermophilic ribozyme. Proc. Natl. Acad. Sci. U. S. A., 98, 4355–4360.
161. Marszalkowski,M., Teune,J.H., Steger,G., Hartmann,R.K. and Willkomm,D.K. (2006) Thermostable RNase P RNAs lacking P18 identified in the Aquificales. RNA, 12, 1915–1921.
162. Deckert,G., Warren,P. V., Gaasterland,T., Young,W.G., Lenox,A.L., Graham,D.E., Overbeek,R., Snead,M.A., Keller,M., Aujay,M., et al. (1998) The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature, 392, 353– 358.
163. Paul,R. (2001) Characterization of RNase P from Thermotoga maritima. Nucleic Acids Res., 29, 880–885.
164. Burcar,B.T., Barge,L.M., Trail,D., Watson,E.B., Russell,M.J. and McGown,L.B. (2015) RNA Oligomerization in Laboratory Analogues of Alkaline Hydrothermal Vent Systems. Astrobiology, 15, 509–522.
165. Kawamura,K. (2017) Hydrothermal microflow technology as a research tool for origin-of-life studies in extreme earth environments. Life, 7.
166. Gardiner,K.J., Marsh,T.L. and Pace,N.R. (1985) Ion dependence of the Bacillus subtilis RNase P reaction. J. Biol. Chem., 260, 5415–5419.
167. Partono,S. and Lewin,A.S. (1991) The rate and specificity of a group I ribozyme are inversely affected by choice of monovalent salt. Nucleic Acids Res., 19, 605– 609.
168. Basu,S., Rambo,R.P., Strauss-Soukup,J., Cate,J.H., Ferré-D’Amaré,A.R., Strobel,S.A. and Doudna,J.A. (1998) A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor. Nat. Struct. Biol., 5, 986–992.
169. Schlegl,J., Hardt,W.D., Erdmann,V.A. and Hartmann,R.K. (1994) Contribution of structural elements to Thermus thermophilus ribonuclease P RNA function. EMBO J., 13, 4863–9.
170. Hardt,W.D., Schlegl,J., Erdmann,V.A. and Hartmann,R.K. (1995) Kinetics and thermodynamics of the RNase P RNA cleavage reaction: Analysis of tRNA 3′-end variants. J. Mol. Biol., 247, 161–172.
171. Nozawa,Y., Hagihara,M., Rahman,M.S., Matsumura,S. and Ikawa,Y. (2019) Rational Design of an Orthogonal Pair of Bimolecular RNase P Ribozymes through Heterologous Assembly of Their Modular Domains. Biology (Basel)., 8.
172. Ikawa,Y. (2000) Structure-function relationships of two closely related group IC3 intron ribozymes from Azoarcus and Synechococcus pre-tRNA. Nucleic Acids Res., 28, 3269–3277.
173. Fang,X.-W., Srividya,N., Golden,B.L., Sosnick,T.R. and Pan,T. (2003) Stepwise conversion of a mesophilic to a thermophilic ribozyme. J. Mol. Biol., 330, 177–83.
174. Nishito,Y., Osana,Y., Hachiya,T., Popendorf,K., Toyoda,A., Fujiyama,A., Itaya,M. and Sakakibara,Y. (2010) Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data. BMC Genomics, 11, 243.
175. Ando,T., Tanaka,T., Hori,Y., Sakai,E. and Kikuchi,Y. (2001) Human tyrosine tRNA is also internally cleavable by E. coli ribonuclease P RNA ribozyme in vitro. Biosci. Biotechnol. Biochem., 65, 2798–801.
176. Ikawa,Y., Moriyama,S. and Furuta,H. (2008) Facile syntheses of BODIPY derivatives for fluorescent labeling of the 3’ and 5’ ends of RNAs. Anal. Biochem., 378, 166–70.
論文の公開元へ
