- Alemi, M. 2020. From the Big Bang to Living Cells. In M. Alemi (Ed.), The Amazing Journey of Reason: from DNA to Artificial Intelligence (pp. 11-28). Cham: Springer International Publishing.
- Altman, S. 1989. Ribonuclease P: an enzyme with a catalytic RNA subunit. Advanced Enzymology and Related Areas of Moleular Biology, 62:1-36.
- Anthea, M., Hopkins, J., Johnson, S., LaHart, D., Warner, M. Q., Wright, J. 1997. Cells Building Blocks of Life. New Jersey: Prentice Hall.
- Attwater, J., Wochner, A., Pinheiro, V. B., Coulson , Holliger, P. 2010. Ice as a protocellular medium for RNA replication. Natural Community, 1(1):1-9.
- Bada, J. L., Lazcano, A. 2003. Prebiotic soup-revisiting the Miller experiment. Science, 300(5620):745-746.
- Ban, E., Kim, A. 2022. Coacervates: recent developments as nanostructure delivery platforms for therapeutic biomolecules. International Journal of Pharmaceutics, 624:122058.
- Bartel, D.P., Szostak, J.W. 1993. Isolation of new ribozymes from a large pool of random sequences. Science, 261(5127):1411-1418.
- Becker, S., Feldmann, J., Wiedemann, S., Okamura, H., Schneider, C., Iwan, K., Carell, T. (2019. Unified prebiotically plausible synthesis of pyrimidine and purine RNA ribonucleotides. Science, 366(6461):76-82.
- Biswajit, S., Joyce, G.F. 2017. A reverse transcriptase ribozyme. eLife, 6:e31153.
- Brown, T. A. 2018. Genomes. New York: Garland Science, 538 pp.
- Butlerow, A. 1861. Formation synthétique d’une substance sucrée. Comptes Rendus de l'Académie des Sciences, 53:145-147.
- Cech, T.R. 2000. The ribosome is a ribozyme. Science, 289(5481):878-879.
- Chen, Y., Qi, F., Gao, F., Cao, H., Xu, D., Salehi-Ashtiani, K., Kapranov, P. 2021. Hovlinc is a recently evolved class of ribozyme found in human lncRNA. Nature chemical biology, 17(5):601-607.
- Cojocaru, R., Unrau, P. 2021. Processive RNA polymerization and promoter recognition in an RNA World. Science, 371:1225-1232.
- Cornell, C. E., Black, R. A., Xue, M., Litz, H. E., Ramsay, A., Gordon, M., Lee, K.K. 2019. Prebiotic amino acids bind to and stabilize prebiotic fatty acid membranes. Proceedings of the National Academy of Sciences, 116(35): 17239-17244.
- Deamer, D. 2017. The role of lipid membranes in life’s origin. Life, 7(1):5.
- Decatur, W., Einvik, , Johansen, S., Vogt, V. 1995. Two group I ribozymes with different functions in a nuclear rDNA intron. The EMBO Journal, 14(18):558-4568.
- Deng, J., Shi, Y., Peng, X., He, Y., Chen, X., Li, M., Huang, L. 2023. Ribocentre: a database of Nucleic Acids Research, 51(D1):D262-D268.
- Ekland, E. H., Bartel, D. P. 1996. RNA-catalysed RNA polymerization using nucleoside triphosphates. Nature, 382(6589):373-376.
- Ferris, J. P., Hill, A. R., Liu, R., Orgel, L. E. (1996). Synthesis of long prebiotic oligomers on mineral surfaces. Nature, 381(6577):59-61.
- Fiore, M., Strazewski, P. 2016. Prebiotic lipidic amphiphiles and condensing agents on the early Earth. Life, 6(2):17.
- Fiore, M. 2018. The synthesis of mono-alkyl phosphates and their derivatives: an overview of their nature, preparation and use, including synthesis under plausible prebiotic conditions. Organic and Biomolecular Chemistry, 16(17):3068-3086.
- Fiore, M., Chieffo, C., Lopez, A., Fayolle, D., Ruiz, J., Soulère, L., Buchet, R. 2022. Synthesis of Phospholipids Under Plausible Prebiotic Conditions and Analogies with Phospholipid Biochemistry for Origin of Life Studies. Astrobiology, 22(5):598-627.
- Fraccia, T.P., Smith, G.P., Zanchetta, G., Paraboschi, E., Yi, Y., Walba, D. M., Bellini, T. 2015. Abiotic ligation of DNA oligomers templated by their liquid crystal ordering. Nature Communications, 6(1):6424.
- Fraccia, T.P., Martin, N. 2021. Non-enzymatic oligonucleotide ligation in photoswitchable coacervate protocells sustains compartment-content coupling. Polymere Science.
- Gregory, T. R. 2009. Artificial Selection and Domestication: Modern Lessons from Darwin’s Enduring Analogy. Evolution: Education and Outreach, 2(1):5-27.
- Guseva, E., Zuckermann, R.N., Dill, K.A. 2017. Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers. Proceedings of the National Academy of Sciences, 114.
- Hampel, A., Tritz, R. 1989. RNA catalytic properties of the minimum (-) sTRSV sequence. Biochemistry, 28(12):4929-4933.
- Han, K., Li, Z.F., Peng, R., Zhu, L.p., Zhou, T., Wang, L.G., Wu, Z.H. 2013. Extraordinary expansion of a Sorangium cellulosum genome from an alkaline milieu. Scientific Reports, 3(1):1-7.
- Hanczyc, M. M., Fujikawa, S. M., Szostak, J.W. 2003. Experimental models of primitive cellular compartments: encapsulation, growth, and division. Science, 302(5645):618-22.
- Hargreaves, W.R., Deamer, D.W. 1978. Liposomes from ionic, single-chain amphiphiles. Biochemistry, 17(18):3759-3768.
- Hashizume, H., Theng, B. K., Gaast, S. v. d., Fujii, K. 2019. Formation of nucleosides and nucleotides in chemical evolution Evolution, Origin of Life, Concepts and Methods, pp:31-42.
- Hud, N.V., Fialho, D.M. 2019. RNA nucleosides built in one prebiotic pot. Science, 366(6461):32-33.
- Ishida, S., Terasaka, N., Katoh, T., Suga, H. 2020. An aminoacylation ribozyme evolved from a natural tRNA-sensing T-box riboswitch. Nature Chemical Biology, 16(6):702-709.
- Jia, T. Z., Bellini, T., Clark, N., Fraccia, T. P. 2022. A liquid crystal world for the origins of life. Emerging Topics in Life Sciences, 6(6):557-569.
- Jin, L., Kamat, N. P., Jena, S., Szostak, J. W. 2018. Fatty acid/phospholipid blended membranes: a potential intermediate state in protocellular evolution. Small, 14(15):1704077.
- Johnson A. P., Cleaves, H. J., Dworkin, J. P., Glavin, D. P., Lazcano, A., Bada, J. L. (2008). The Miller volcanic spark discharge experiment. Science, 322(5900):404-404.
- Johnson, B.R., Lam, S.K. 2010. Self-organization, Natural Selection, and Evolution: Cellular Hardware and Genetic Software. BioScience, 60(11): 879.
- Johnston, W. K., Unrau, P. J., Lawrence, M. S., Glasner, M. E., Bartel, D. P. 2001. RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension. Science, 292(5520):1319-1325.
- Jordan, S. F., Rammu, H., Zheludev, I. N., Hartley, A. M., Maréchal, A., Lane, N. 2019. Promotion of protocell self-assembly from mixed amphiphiles at the origin of life. Nature Ecology and Evolution, 3(12):1705-1714.
- Kim, H. J., Kim, J. 2019. A Prebiotic Synthesis of Canonical Pyrimidine and Purine Ribonucleotides. Astrobiology, 19(5):669-674.
- Kindt, J. T., Szostak, J. W., Wang, A. 2020. Bulk self-assembly of giant, unilamellar vesicles. ACS Nano, 14(11):14627-14634.
- Kolev, N. G., Hartland, E. I., Huber, P. W. 2008. A manganese-dependent ribozyme in the 3′-untranslated region of Xenopus Vg1 mRNA. Nucleic Acids Research, 36(17):5530-5539.
- Kondepudi, D., Prigogine, I. 1998. Modern Thermodynamics. From heat Engines to Dissipative Structures (2nd ed.). John Wiley and Sons.
- Koshland, D.E. 1958. Application of a theory of enzyme specificity to protein synthesis. Proceedings of the National Academy of Sciences, 44(2):98-104.
- Kruger, K., Grabowski, P.J., Zaug, A.J., Sands, J., Gottschling, D.E., Cech, T.R. 1982. Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell, 31(1):147-157.
- Leslie E.O. 2004. Prebiotic chemistry and the origin of the RNA world. Critical Reviews in Biochemistry and Molecular Biology, 39(2):99-123.
- Lodish, H., Berk, A., Kaiser, C.A., Krieger, M., Bretscher, A., Ploegh, H., Martin, K.C. 2016. Loose-leaf Version for Molecular Cell Biology: W. H. Freeman, 1280 pp.
- Lopez, A., Fiore, M. 2019. Investigating prebiotic protocells for a comprehensive understanding of the origins of life: A prebiotic systems chemistry perspective. Life, 9(2):49.
- Lopez, A., Fayolle, D., Fiore, M., Strazewski, P. 2020. Chemical Analysis of Lipid Boundaries after Consecutive Growth and Division of Supported Giant Vesicles. Iscience, 23(11):101677.
- Margulis, L., Sagan, D. 1997. Microcosmos: Four billion years of microbial evolution. University of California Press, 304 pp.
- Mast, C. B., Schink, S., Gerland, U., Braun, D. 2013. Escalation of polymerization in a thermal gradient. Proceedings of the National Academy of Sciences, 110(20):8030-8035.
- Menor‐Salván, C., Marín‐Yaseli, M.R. 2013. A new route for the prebiotic synthesis of nucleobases and hydantoins in water/ice solutions involving the photochemistry of acetylene. Chemistry–A European Journal, 19(20):6488-6497.
- Monnard, P.A., Kanavarioti, A., Deamer, D.W . Eutectic phase polymerization of activated ribonucleotide mixtures yields quasi-equimolar incorporation of purine and pyrimidine nucleobases. Journal of the American Chemical Society, 125(45):13734-13740.
- Orgel, L.E. 1992. Molecular replication. Nature, 358:203-209.
- Ourisson, G., Nakatani, Y. 1994. The terpenoid theory of the origin of cellular life: the evolution of terpenoids to cholesterol. Chemistry and Biology, 1(1):11-23.
- Peebles, C. L., Perlman, P., Mecklenburg, K., Petrillo, M., Tabor, J., Jarrell, K., Cheng, H.-L. 1986. A self-splicing RNA excises an intron lariat. Cell, 44(2):213-223.
- Peretó, J., Bada, J. L., Lazcano, A. 2009. Charles Darwin and the origin of life. Origins of Life and Evolution of Biospheres, 39: 395-406.
- Prody, G. A., Bakos, J. T., Buzayan, J. M., Schneider, I. R., Bruening, G. 1986. Autolytic processing of dimeric plant virus satellite RNA. Science, 231(4745):1577-1580.
- Prosdocimi, F., Farias, S., José, M. 2022. Prebiotic chemical refugia: multifaceted scenario for the formation of biomolecules in primitive Earth. Theory in Biosciences, 141:1-9.
- Radakovic, A., DasGupta, S., Wright, T. H., Aitken, H.R., Szostak, J.W. 2022. Nonenzymatic assembly of active chimeric ribozymes from aminoacylated RNA oligonucleotides. Proceedings of the National Academy of Sciences, 119(7):e2116840119.
- Rajamani, S., Vlassov, A., Benner, S., Coombs, A., Olasagasti, F., Deamer, D. 2008. Lipid-assisted synthesis of RNA-like polymers from mononucleotides. Origins of Life and Evolution of Biospheres, 38(1):57-74.
- Ray, S. 2017. Evolutionary computing to examine variation in proteins with evolution nature-inspired computing: concepts, methodologies, tools, and applications (pp. 187-202): IGI Global.
- Reece, J. B., Taylor, M. R., Simon, E. J., Dickey, J. L., Hogan. 2021. Campbell Biology (Vol. 4). Boston: Pearson
- Roberts, S. J., Liu, Z. 2022. Potentially Prebiotic Synthesis of Aminoacyl-RNA via a Bridging Phosphoramidate-Ester Intermediate. Journal of the American Chemical Society, 144(9):4254-4259.
- Roth, A., Weinberg, Z., Chen, A. G., Kim, P. B., Ames, T. D., Breaker, R. R. 2014. A widespread self-cleaving ribozyme class is revealed by bioinformatics. Nature Chemical Biology, 10(1):56-60.
- Salehi-Ashtiani, K., Lupták, A., Litovchick, A., Szostak, J.W. 2006. A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene. Science, 313(5794):1788-1792.
- Sanchez, R., Ferris, J., Orgel, L. 1966. Conditions for purine synthesis: did prebiotic synthesis occur at low temperatures? Science, 153(3731):72-73.
- Sanchez, R., Ferris, J., Orgel, L. 1966. Cyanoacetylene in prebiotic synthesis. Science, 154(3750):784-785.
- Saville, B.J., Collins, R.A. 1990. A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria. Cell, 61(4):685-696.
- Sharmeen, L., Kuo, M., Dinter-Gottlieb, G., Taylor, J. 1988. Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage. Journal of Virology, 62(8):2674-2679.
- Smith, G. P., Fraccia, T. P., Todisco, M., Zanchetta, G., Zhu, C., Hayden, E., Clark, N. A. 2018. Backbone-free duplex-stacked monomer nucleic acids exhibiting Watson–Crick selectivity. Proceedings of the National Academy of Sciences, 115(33):E7658-E7664.
- Šponer, J., Jurečka, P., Marchan, I., Luque, F. J., Orozco, M., Hobza, P. 2006. Nature of Base Stacking: Reference Quantum-Chemical Stacking Energies in Ten Unique B-DNA Base-Pair Steps. Chemistry-A European Journal, 12(10):2854-2865.
- Šponer, J.E., Šponer, J., Výravský, J., Šedo, O., Zdráhal, Z., Costanzo, G., Matyášek, R. 2021. Nonenzymatic, Template‐Free Polymerization of 3’, 5’Cyclic Guanosine Monophosphate on Mineral Surfaces. Chem SystemsChem, 3(6):e2100017.
- Teixeira, A., Tahiri-Alaoui, A., West, S., Thomas, B., Ramadass, A., Martianov, I., Akoulitchev, A. 2004. Autocatalytic RNA cleavage in the human β-globin pre-mRNA promotes transcription termination. Nature, 432(7016):526-530.
- Todisco, M., Fraccia, T. P., Smith, G. P., Corno, A., Bethge, L., Klussmann, S., Zanchetta, G. 2018. Nonenzymatic polymerization into long linear RNA templated by liquid crystal self-assembly. ACS Nano, 12(10):9750-9762.
- Vicens, Q., Cech, T. R. 2009. A natural ribozyme with 3′, 5′ RNA ligase activity. Nature Chemical Biology, 5(2):97-99.
- Weinberg, Z., Kim, P.B., Chen, T.H., Li, S., Harris, K.A., Lünse, C.E., Breaker, R.R. 2015. New classes of self-cleaving ribozymes revealed by comparative genomics analysis. Nature Chemical Biology, 11(8):606-610.
Winkler, W.C., Nahvi, A., Roth, A., Collins, J.A., Breaker, R.R. 2004. Control of gene expression by a natural metabolite-responsive ribozyme. Nature, 428(6980):281-286.
|