Hydrolysis of N-glycosidic Bonds in Nucleosides, Nucleotides, and their Derivatives

Kochetkov, N. K.; Budovskii, E. I.

doi:10.1007/978-1-4684-2973-2_4

Cited by 28 publications

(38 citation statements)

References 90 publications

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“…The ␤-Glycosidic Bond-The stability of the ␤-glycosidic bond in nucleosides in water was determined in pioneering studies under several conditions (24). We describe here the effect of formamide on the stability of this bond.…”

Section: The Stability Of the ␤-Glycosidic And 3-and 5-phosphoester Bmentioning

confidence: 98%

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: The Stability Of the ␤-Glycosidic And 3-and 5-phosphoester Bmentioning

confidence: 98%

Origin of Informational Polymers

Saladino

Crestini

Busiello

et al. 2005

Journal of Biological Chemistry

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“…The ␤-Glycosidic Bond-The stability of the ␤-glycosidic bond of nucleosides in water was determined in early studies under several conditions (13). We describe here the effect of formamide on the stability of this bond.…”

Section: The Stability Of the ␤-Glycosidic And Of The 3-and 5-phosphomentioning

confidence: 99%

Origin of Informational Polymers

Saladino

Crestini

Ciciriello

et al. 2006

Journal of Biological Chemistry

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We have measured the stabilities of the bonds that are critical for determining the half-life of ribonucleotides and the ␤-glycosidic and 3-and 5-phosphoester bonds. Stabilities were measured under a wide range of temperatures and water/formamide ratios. The stability of phosphodiester bonds in oligoribonucleotides was determined in the same environments. The comparison of bond stabilities in the monomer versus the polymer forms of the ribo compounds revealed that physico-chemical conditions exist in which polymerization is thermodynamically favored. These conditions were compared with those determining a similar behavior for 2-deoxyribonucleosides, deoxyribonucleotides, and deoxyribooligonucleotides and were shown to profoundly differ. The implications of these facts on the origin of informational polymers are discussed.Minimal requirements for informational polymers to have originated under prebiotic conditions are a unitary chemical frame for the synthesis of nucleobases and a favorable thermodynamic energy balance for the polymerization of nucleotides to oligonucleotides.A Formamide-based Unitary Chemistry-To gather into a single reaction milieu all the precursors necessary for the assembly of the first informational polymers, a unitary chemical frame is needed. A series of observations suggest that formamide (NH 2 CHO) chemistry might have provided such a frame.To summarize the evidence: the one-carbon compound formamide is a highly versatile building block for the syntheses of all the necessary precursor nucleic bases. We have reported (Refs. 1-4 and references therein) the synthesis of purine, N 9 -formylpurine, adenine, N 9 , N6-diformyladenine, hypoxanthine, cytosine, hydroxypyrimidine, 4(3H)-pyrimidinone, uracil, 5,6-dihydrouracil, thymine, 5-hydroxymethyluracil, AICA (5-aminoimidazole-4-carboxamide), FAICA (5-formylaminoimidazole-4-carboxamide), and urea. These compounds are obtained from formamide heated in the presence of simple inorganic catalysts such as silica, alumina, zeolites, CaCO 3 , TiO 2 , common clays, kaolin, montmorillonites, olivines, and cosmic dust analogues of olivines. In all cases and for each catalyst several compounds were simultaneously formed, as summarized in Ref. 4.The richest yields were obtained in the presence of clays, TiO 2 , and cosmic dust analogues. Guanine is conspicuously absent, but a possible efficient substitute in base pairing might have been provided by hypoxanthine. Notably, formamide also yields purine acyclonucleosides through a formose-like condensation of N-formyl derivatives (2), providing a solution to the long-standing problem of the lack of reactivity between nucleobases and ribose or 2Ј-deoxyribose. In addition, formamide is an efficient activator of nucleoside transphosphorylation (Refs. 5-7), 2 further supporting its possible relevance in the prebiotic polymerization reactions that did lead to pregenetic informational macromolecules.Formamide is easily formed by hydrolysis of HCN and is stable in liquid form over a wide range of temperatures (2.5-2...

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“…Depyrimidination is much slower and occurs at rates 100 times lower than depurination (4). Exposure of cells to a variety of carcinogens leads to the formation of modified bases, some of which are converted to AP sites either because of enhanced spontaneous release (e.g., 7-methylguanine) (5) or by specific DNA glycosylases (e.g., 3-methyladenine) as part of the DNA repair processes (6). Specific DNA glycosylases form AP sites also by removing uracils or hypoxanthines misincorporated during replication or produced via deamination of cytosines or adenines, respectively (6).…”

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confidence: 99%

Bypass and termination at apurinic sites during replication of single-stranded DNA in vitro: a model for apurinic site mutagenesis.

Hevroni

Livneh

1988

Proc. Natl. Acad. Sci. U.S.A.

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Mutations produced in Escherichia coli by apurinic sites are believed to arise via SOS-assisted translesion replication. Analysis of replication products synthesized on depurinated single-stranded DNA by DNA polymerase Ill holoenzyme revealed that apurinic sites frequently blocked in vitro replication. Bypass frequency of an apurinic site was estimated to be 10-15%. Direct evidence for replicative bypass was obtained in a complete single-stranded -+ replicative form replication system containing DNA polymerase III holoenzyme, single-stranded DNA binding protein, DNA polymerase I, and DNA ligase, by demonstrating the sensitivity of fully replicated products to the apurinic endonuclease activity of E. coli exonuclease III. Termination at apurinic sites, like termination at pyrimidine photodimers, involved dissociation of the polymerase from the blocked termini, followed by initiations at available primer templates. When no regular primer templates were available, the polymerase underwent repeated cycles of dissociation and rebinding at the blocked termini and, while bound, carried out multiple polymerization-excision reactions opposite the apurinic sites, leading to turnover of dNTPs into dNMPs. From the in vitro turnover rates, we could predict with striking accuracy the specificity of apurinic site mutagenesis, as determined in vivo in depurinated single-stranded DNA from an M13-ac hybrid phage. This fimding is consistent with the view that DNA polymerase III holoenzyme carries out the mutagenic "misinsertion" step during apurinic site mutagenesis in vivo and that the specificity of the process is determined primarily by the polymerase. SOS-induced proteins such as UmuD/C might act as processivity-like factors to stabilize the polymerase-DNA complex, thus increasing the efficiency of the next stage of past-lesion polymerization required to complete the bypass reaction.Apurinic (AP) and apyrimidinic sites are common lesions in DNA and are believed to be important intermediates in chemical carcinogenesis by a variety of chemical agents (1,2). Depurination is the most frequent spontaneous alteration in DNA under physiological conditions and occurs in vitro at the rate of 3 x 10-11 per nucleotide per sec (3). Extrapolation to the in vivo situation would suggest that 0.5 purine is lost from an Escherichia coli cell per generation, and as many as 10,000 purines are lost in each mammalian cell per day (3). Depyrimidination is much slower and occurs at rates 100 times lower than depurination (4). Exposure of cells to a variety of carcinogens leads to the formation of modified bases, some of which are converted to AP sites either because of enhanced spontaneous release (e.g., 7-methylguanine) (5) or by specific DNA glycosylases (e.g., 3-methyladenine) as part of the DNA repair processes (6). Specific DNA glycosylases form AP sites also by removing uracils or hypoxanthines misincorporated during replication or produced via deamination of cytosines or adenines, respectively (6).In E. coli, AP sites are highly mutag...

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Hydrolysis of N-glycosidic Bonds in Nucleosides, Nucleotides, and their Derivatives

Cited by 28 publications

References 90 publications

Origin of Informational Polymers

Origin of Informational Polymers

Origin of Informational Polymers

Bypass and termination at apurinic sites during replication of single-stranded DNA in vitro: a model for apurinic site mutagenesis.

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