Synthesis of hypermodified nucleosides and examination of nucleic acid templated stereoselective peptide formation in an RNA-peptide world

Węgrzyn, Ewa (2024): Synthesis of hypermodified nucleosides and examination of nucleic acid templated stereoselective peptide formation in an RNA-peptide world. Dissertation, LMU München: Fakultät für Chemie und Pharmazie

Abstract

Life on Earth in its full complexity could not exist without the ability to replicate and maintain its essential genetic and metabolic functions. The question of “how” and “when” life emerged, is one of the biggest unsolved mysteries of humankind. We can follow the evolution of living species by analysing the fossils excavated by scientist around the globe, but tracing back the beginnings of life to understand the transition from abiotic Earth to living matter is a much more difficult riddle to address. Modern life is based on the interactions between the nucleic acids (DNA and RNA) and the proteins, also known as the “central dogma of molecular biology”. One of the most important processes of contemporary biology is the translation, which can be seen as a link between the genotype and phenotype. In this process, the genetic information is decoded and translated into a chain of amino acids, which, upon folding, forms catalytically active proteins. The translation itself poses a chicken-and-egg conundrum, since it involves both nucleic acids and proteins in form of tRNA and the ribosome (a nucleic acid-protein hybrid). The RNA-world hypothesis suggests that initially the RNA molecule carried the dual function of being the keeper of genetic information as well as a catalyst. It is suspected that this versatility was supported by the presence of an extended genetic alphabet of modified nucleosides. Interestingly, a collection of modified nucleosides such as t6A, m6t6A and (m)nm5U, which may be considered to be “molecular fossils”, can be found in close proximity of the anticodon loop of modern tRNA. Another burning question in the prebiotic science field is the emergence and maintenance of biological homochirality. Modern life, with the complex protein folding and specific interactions, would not be able to maintain its functions if the building blocks were composed of mixed diastereomers. Life requires the molecules of life to be homochiral, with RNA built exclusively out of D-ribose and the proteins out of L-amino acids. In this work, I address the chicken-and-egg problem, postulating an RNA-peptide world, in which RNA can self-decorate with peptides. I show that the nucleoside-amino acid hybrid structure (m6)aa6A, (analogous to (m6)t6A), can be formed by loading an amino acid onto N6-methylurea adenosine under prebiotically plausible conditions. The modified nucleosides (m6)aa6A and (m)nm5U can be incorporated into RNA, forming strands that can act as a donor and an acceptor, respectively. The complementary oligonucleotides hybridise through hydrogen bonds, which brings the modified nucleosides into close proximity and facilitates peptide bond formation after prior activation of the amino acid. Subsequently, the formed RNA-peptide hairpin strand can be thermally cleaved at the urea moiety, releasing the amino acid-loaded acceptor strand. Upon encounter with another amino acid-carrying donor strand, the cycle can be repeated and the peptide will grow longer. This iterative cycle can be conducted under one-pot conditions, imitating a prebiotic world where the separation of the intermediates was not required. I present results with a range of different amino acid and various activation methods, leading to the formation of up to decapeptides on RNA. I demonstrate in my thesis that the peptide coupling reaction in RNA, but also in DNA, exhibits high stereoselectivity towards the naturally occurring L-amino acids. I report that the close proximity of the amino acid to RNA has strong influence on the stereoselectivity, which indicates that the D-ribose sugar present in RNA induces the L-homochirality of peptides. This stereochemical preference is based on the kinetic rather than thermodynamic aspects of the reactions, since the rate constants are the highest for the L-L amino acid coupling. The transfer of di- and tri- peptides is also possible with clear preference for homochirality. I also show a temperature-driven one-pot peptide synthesis with clear selectivity to form the homo-L-peptides. This thesis provides data that suggests a plausible alternative to the RNA world, namely the RNA-peptide world, in which RNA can self-decorate with peptides and these hybrids can then perform a peptide synthesis cycle, selectively transferring L-amino acids. The repetition of this cycle leads to the growth of longer peptides and can be a considered a prototype of a prebiotic, primitive, stereoselective translation mechanism, leading to homochiral peptides.

• Dokumententyp: Dissertationen (Dissertation, LMU München)
• Themengebiete: 500 Naturwissenschaften und Mathematik ; 500 Naturwissenschaften und Mathematik > 540 Chemie
• Fakultäten: Fakultät für Chemie und Pharmazie
• Sprache der Hochschulschrift: Englisch
• Datum der mündlichen Prüfung: 18. Oktober 2024
• 1. Bericht­erstatter:in: Carell, Thomas