Mechanism of Degradation of Purine Nucleosides by Formamide. Implications for Chemical DNA Sequencing Procedures

Saladino, Raffaele; Mincione, Enrico; Crestini, Claudia; Negri, Rodolfo; Mauro, § Ernesto Di; Costanzo, Giovanna

doi:10.1021/ja953527y

Cited by 44 publications

(54 citation statements)

References 28 publications

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“…degradation of nucleobases by formamide becomes the operatively predominant process (21)(22)(23). Thus, the transition between the two different types of hydrolytic pathways shown in titration experiments in Figs.…”

Section: Discussionmentioning

confidence: 91%

“…At temperatures ϳ100°C or above and in the absence of water, formamide reacts with both purine and pyrimidine nucleobases by nucleophilic addition at position C (8) and the 5Ј-phosphoester bonds and the consequent cleavage of the polymer follow (21,22). The cleavage at 3Ј is faster than that at 5Ј (21)(22)(23). This reaction pathway can be referred to as Hydrolysis following Nucleobase Degradation (HND).…”

Section: Two Different Reaction Pathwaysmentioning

confidence: 99%

“…At apurinic sites in DNA, the deoxyribose residue occurs in equilibrium between the free aldehyde and the furanose form, leading to the cleavage of the phosphodiester bonds at both 5Ј-and 3Ј-positions (Ref. 21 and references therein). However, a systematic and comprehensive comparison of the stability of the phosphoester bonds in the precursor monomers (both ribo and 2Ј-deoxyribo) versus the stability of the same bonds when present in DNA and RNA was not performed.…”

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Origin of Informational Polymers

Saladino

Crestini

Busiello

et al. 2005

Journal of Biological Chemistry

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To survive, an informational macromolecule must solve the major problem set by its very polymeric nature: instability. This is especially true in prebiotic terms because of the presumed initial absence of protective structures (proteins, lipids, etc.). We have analyzed the stability of the ␤-glycosidic and of the 3-and 5-phosphoester bonds in both deoxy monomers and deoxy oligomers under a large set of conditions. The results show a strong dependence of the relative stability of these bonds on the physico-chemical environment. A set of conditions has been identified in which the stability of polymers becomes comparable with that of the precursor monomers. In certain instances the stability of the 5-phosphoester bond is even higher in the polymer than in the mononucleotide.If life on this planet had an early start as it seems (1-8), several conditions had to be satisfied at the same time: abundance of the starting biogenic materials, formation of precursors based on simple chemical processes, and simultaneous (or quasi so) presence of the building blocks to be used for the assembling of informational molecules. We have observed (Refs. 9 -11 and references therein) that the one-carbon compound formamide is an highly versatile building block for the synthetic processes yielding all the necessary precursor nucleic bases. In terms of its possible role in allowing or favoring the formation of informational nucleic polymers, formamide chemistry also provides a possible solution to the lack of reactivity between ribose/deoxyribose with bases through a formose-like reaction yielding acyclonucleosides (10). The reported activity of formamide as activator of transphosphorylation (see "Discussion") provides additional possible relevance to its role in prebiotic reactions leading to pre-genetic informational polymers. The plausibility of its prebiotic role is related to (i) its presence in interstellar medium, in comets and asteroids (12), hence on early Earth; (ii) the ease of its formation by hydrolysis of HCN and its stability in liquid form over a wide range of temperatures (2.5-210°C), thus favoring its concentration from dilute aqueous solutions; and (iii) the above mentioned catalyst-induced wealth of nucleic precursors.The question arises as to whether the physico-chemical conditions (moderately high temperature and varying concentration of formamide in water) allowing active synthesis and potentially leading to polymerization favor or impair the survival of the polymerized materials. In reconstructing the passage from monomers to the information-bearing polymers that we know at present, two major pieces of the mosaic are markedly missing: the knowledge of the mechanisms leading to the formation of the ␤-glycosidic and of the 3Ј-5Ј phosphodiester bonds and, once the polymer had been formed, the physico-chemical reason(s) leading to its very survival as a polymer. In other words, which is the Darwinian selective advantage that overcame the intrinsically higher instability of the polymeric form?The analysis presented h...

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Section: Discussionmentioning

confidence: 91%

Section: Two Different Reaction Pathwaysmentioning

confidence: 99%

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confidence: 99%

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Origin of Informational Polymers

Saladino

Crestini

Busiello

et al. 2005

Journal of Biological Chemistry

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“…At apurinic sites in DNA, the deoxyribose occurs both in the free-aldehyde and the furanose form, which leads to the cleavage of the phosphodiester bonds both at 5'-and at 3'-positions [128] (and refs. cit.…”

Section: Stability Of Informational Polymers In Formamidementioning

confidence: 99%

Formamide Chemistry and the Origin of Informational Polymers

Saladino

Crestini

Ciciriello

et al. 2007

Chemistry & Biodiversity

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Formamide (HCONH2) provides a chemical frame potentially affording all the monomeric components necessary for the formation of nucleic polymers. In the presence of the appropriate catalysts, and by moderate heating, formamide yields a complete set of nucleic bases, acyclonucleosides, and favors both phosphorylations and transphosphorylations. Physico-chemical conditions exist in which formamide favors the stability of the phosphoester bonds in nucleic polymers more than that of the same bonds in monomers. This property establishes 'thermodynamic niches' in which the polymeric forms are favored. The hypothesis that these specific attributes of formamide allowed the onset of prebiotic chemical equilibria capable of Darwinian evolution is discussed.

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“…This interpretation is supported by the genome recovery in the low-GCorganism P. heparinus being lower than in the other two organisms (Supplementary Figure S3). In addition, it has been shown that formamide can degrade purine nucleosides (Saladino et al, 1996). Small amounts of damage could explain the reduction in the genome recovered by the MDA.…”

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Effects of sample treatments on genome recovery via single-cell genomics

et al. 2014

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Single-cell genomics is a powerful tool for accessing genetic information from uncultivated microorganisms. Methods of handling samples before single-cell genomic amplification may affect the quality of the genomes obtained. Using three bacterial strains we show that, compared to cryopreservation, lower-quality single-cell genomes are recovered when the sample is preserved in ethanol or if the sample undergoes fluorescence in situ hybridization, while sample preservation in paraformaldehyde renders it completely unsuitable for sequencing.

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Mechanism of Degradation of Purine Nucleosides by Formamide. Implications for Chemical DNA Sequencing Procedures

Cited by 44 publications

References 28 publications

Origin of Informational Polymers

Origin of Informational Polymers

Formamide Chemistry and the Origin of Informational Polymers

Effects of sample treatments on genome recovery via single-cell genomics

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