The “Strong” RNA World Hypothesis: Fifty Years Old

Neveu, Marc; Kim, Hyo‐Joong; Benner, Steven A.

doi:10.1089/ast.2012.0868

Cited by 188 publications

(148 citation statements)

References 66 publications

(69 reference statements)

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“…The first selfreplicating macromolecules must not necessarily have been RNA. Derivatives of RNA, especially with altered backbones, have been suggested as predecessors of RNA owing to more favorable chemistries/stabilities for spontaneous generation and persistence of oligomerization at the presumed planetary conditions (Joyce et al 1987;Schöning et al 2000;Zhang et al 2005;Powner et al 2009;Robertson and Joyce 2012;Neveu et al 2013). …”

Section: When Does Life Begin?mentioning

confidence: 99%

The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular Function

Brosius

2014

Cold Spring Harbor Perspectives in Biology

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Section: When Does Life Begin?mentioning

confidence: 99%

The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular Function

Brosius

2014

Cold Spring Harbor Perspectives in Biology

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“…Note, that formamide is considered to be the medium where phosphorylation chemistries could take place on the early Earth also in the "discontinuous synthesis model" elaborated by the Benner group. 17,18 As our computations suggest, at around 430 K in formamide solution, the 3',5' cyclic form is the thermodynamically favored one and thus it is reasonable to assume that it out-competes the 2',3' cyclic form on an extended time scale. However, upon an environmental stimulus, such as a sudden drop of the temperature (e.g.…”

Section: Prebiotic Implicationsmentioning

confidence: 90%

“…These are the two solvents most frequently considered in recent origin of life studies. [17][18][19][20][21][22] We will show that while aqueous solutions and lower temperatures could favor accumulation of 2',3' cyclic nucleotides over that of the 3',5' cyclic form, at higher temperatures and in formamide solvent 3',5' cyclic nucleotides are the thermodynamically preferred species. Thus, after a temperature drop, 23 initial cycles of polymerization leading to the first RNA molecules could indeed occur in a 3',5'-cyclic-nucleotide rich environment.…”

Section: Introductionmentioning

confidence: 89%

“…Indeed, the formamide-based synthesis experiments of prebiotic building blocks has commonly been conducted at 433 K. 7 More detailed explanation of the potential prebiotic relevance of the temperature range can be found, e.g., in our preceding review paper (see also below). 23 Note that such conditions are considered as a relevant context for prebiotic processes on early Earth not only by us 23 but also, e.g., by the so called "discontinuous synthesis model" of the origin of life advocated by the Benner group; 17,18 for another independent latest research highlight see Ref. 21.…”

Section: Stability Of Cyclic Nucleotides In Formamidementioning

confidence: 99%

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Stability of 2′,3′ and 3′,5′ cyclic nucleotides in formamide and in water: a theoretical insight into the factors controlling the accumulation of nucleic acid building blocks in a prebiotic pool

Cassone

Šponer

Saija

et al. 2017

Phys. Chem. Chem. Phys.

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Synthesis of the first RNAs represents one of the cornerstones of the emergence of life. Recent studies demonstrated powerful scenarios of prebiotic synthesis of cyclic nucleotides in aqueous and formamide environments. This raised a question about their thermodynamic stability, a decisive factor determining their accumulation in the prebiotic pool. Here we performed ab initio molecular dynamics simulations at various temperatures in formamide and water to study the relative stabilities of the 2',3' and 3',5' isomers of cyclic nucleotides. The computations show that in an aqueous environment 2',3' cyclic nucleotides are more stable than their 3',5' counterparts at all temperatures up to the boiling point. In contrast, in formamide higher temperatures favor accumulation of the 3',5' cyclic form, whereas below about 400 K the 2',3' cyclic form becomes more stable. The latter observation is consistent with a formamide-based origin scenario suggesting that 3',5' cyclic nucleotides accumulated at higher temperatures subsequently allowed oligomerization reactions after fast cooling to lower temperatures. A statistical analysis of the geometrical parameters of the solutes indicates that thermodynamics of cyclic nucleotides in aqueous and formamide environments are dictated by the floppiness of the molecules rather than by the ring strain of the cyclic phosphodiester linkages.

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“…Today, mutagenesis teaches us that in the water can, for example, take place more easily the deamination that converts cytosine into uracil, adenine into hypoxanthine and guanine into xanthine [3], all transformations that change, in a DNA or RNA, the genetic significance of the coded message, adding variability. From this point of view, water could be classified as the first archaic mutagen of evolution.…”

Section: Dear Editormentioning

confidence: 99%

Water: The First Archaic Mutagen of Evolution, the Adoptive Mother of Currently Nucleic Acids

Caradonna¹

2016

J Carcinog Mutagen

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It would be intuitive to think that for the evolutionary onset of nucleic acids, and even before of their monomeric constituents, the water was crucial.Within the series of evolutions which start from the origin of the universe and still cannot, by definition, be considered concluded, certainly among the geothermal evolution end and the beginning of the chemical one, on Earth, the moment was favorable for the arrival of the first proto-nucleotides: from underground deposits of methanehydrate [1] and phosphate, with the support of all known pre-biotic physical-chemical conditions, were made the monomeric components of nucleic acids. The cradle of nucleic acids does not seem to have been so fundamentally aqueous, but organic. In fact, thinking back that "all the major biopolymers are metastable in aqueous solution" [2], it is easy to conclude that in those days a proto-nucleotide, or better its carbohydrate, in the aqueous phase would have shown all its inadequacy. However, knowing how today is made a nucleic acid, it is evident that the fine evolutionary strategy has distinguished, for this event, two necessities and consequently has chosen two evolutionary times and two different environments to achieve them:1. To ensure the synthesis, the events have selected an underground environment basically non-aqueous and consequently not hostile to the nucleotides in general and to the carbohydrate component, in particular. Additionally, the evolutionary randomness system selected ribose as more stable pentose. 2. To guarantee the flexibility, in terms of information variability that the future nucleic acid must keep for not stop the subsequent biological evolution, it was necessary to introduce this new chemical molecule in an environment that can determine a controlled and controllable instability.In fact, with the advent of the ancestral rains, aqueous surface environment has triggered a sort of proto-mutation. Today, mutagenesis teaches us that in the water can, for example, take place more easily the deamination that converts cytosine into uracil, adenine into hypoxanthine and guanine into xanthine [3], all transformations that change, in a DNA or RNA, the genetic significance of the coded message, adding variability. From this point of view, water could be classified as the first archaic mutagen of evolution. Studies of the 80s of the last century also show that the water is able to exchange the chemical-physical parameters of the DNA double helix by moving it from a conformation to another one: for example, the DNA-A is assumed when it is in the presence of little water and instead form B is taken in the presence of a lot of water [4]; this is because the water modifies the strength of hydrogen bonds bridge and the Coulomb forces [5]. Since epigenomics and interactomics reporte today that several biomolecular meanings are associated with different conformations of DNA helix, we can say that the water has actually modulated and continues to modulate the structure and the function of a nucleic acid.Coming to the cur...

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The “Strong” RNA World Hypothesis: Fifty Years Old

Cited by 188 publications

References 66 publications

The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular Function

The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular Function

Stability of 2′,3′ and 3′,5′ cyclic nucleotides in formamide and in water: a theoretical insight into the factors controlling the accumulation of nucleic acid building blocks in a prebiotic pool

Water: The First Archaic Mutagen of Evolution, the Adoptive Mother of Currently Nucleic Acids

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