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

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F17%3A00486066" target="_blank" >RIV/68081707:_____/17:00486066 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/61989592:15310/17:73584385

Výsledek na webu

<a href="http://dx.doi.org/10.1039/c6cp07993h" target="_blank" >http://dx.doi.org/10.1039/c6cp07993h</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1039/c6cp07993h" target="_blank" >10.1039/c6cp07993h</a>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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 a prebiotic pool. Here we performed ab initio molecular dynamics simulations at various temperatures in formamide and water to study the relative stabilities of the 20,30 and 30,50 isomers of cyclic nucleotides. The computations show that in an aqueous environment 20,30 cyclic nucleotides are more stable than their 30,50 counterparts at all temperatures up to the boiling point. In contrast, in formamide higher temperatures favor the accumulation of the 30,50 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 30,50 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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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 a prebiotic pool. Here we performed ab initio molecular dynamics simulations at various temperatures in formamide and water to study the relative stabilities of the 20,30 and 30,50 isomers of cyclic nucleotides. The computations show that in an aqueous environment 20,30 cyclic nucleotides are more stable than their 30,50 counterparts at all temperatures up to the boiling point. In contrast, in formamide higher temperatures favor the accumulation of the 30,50 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 30,50 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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10403 - Physical chemistry

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2017

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Physical Chemistry Chemical Physics

ISSN

1463-9076

e-ISSN

—

Svazek periodika

19

Číslo periodika v rámci svazku

3

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

9

Strana od-do

1817-1825

Kód UT WoS článku

000394426400014

EID výsledku v databázi Scopus

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