Exotic DNAs Made of Nonnatural Bases and Natural Phosphodiester Bonds

Chiba, Junya; Inoûye, Masahiko

doi:10.1002/cbdv.200900282

Cited by 21 publications

(21 citation statements)

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“…[65] Alternative viewpoints have been put forward suggesting that selection of the native bases coincided with the emergence of RNA from the prebiotic environment. [10c,44] This scenario appears to offer a simpler explanation for the origin of the nucleic acid bases. However, in addition to the challenges mentioned in this review, the direct selection of the native bases from a prebiotic environment seems a little too elegant for evolutionary processes that were likely much more messy, complex and prolonged.…”

Section: Discussionmentioning

confidence: 99%

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On the Origin of the Canonical Nucleobases: An Assessment of Selection Pressures across Chemical and Early Biological Evolution

Rios

Tor

2013

Israel Journal of Chemistry

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The native bases of RNA and DNA are prominent examples of the narrow selection of organic molecules upon which life is based. How did nature “decide” upon these specific heterocycles? Evidence suggests that many types of heterocycles could have been present on the early Earth. It is therefore likely that the contemporary composition of nucleobases is a result of multiple selection pressures that operated during early chemical and biological evolution. The persistence of the fittest heterocycles in the prebiotic environment towards, for example, hydrolytic and photochemical assaults, may have given some nucleobases a selective advantage for incorporation into the first informational polymers. The prebiotic formation of polymeric nucleic acids employing the native bases remains, however, a challenging problem to reconcile. Hypotheses have proposed that the emerging RNA world may have included many types of nucleobases. This is supported by the extensive utilization of non-canonical nucleobases in extant RNA and the resemblance of many of the modified bases to heterocycles generated in simulated prebiotic chemistry experiments. Selection pressures in the RNA world could have therefore narrowed the composition of the nucleic acid bases. Two such selection pressures may have been related to genetic fidelity and duplex stability. Considering these possible selection criteria, the native bases along with other related heterocycles seem to exhibit a certain level of fitness. We end by discussing the strength of the N-glycosidic bond as a potential fitness parameter in the early DNA world, which may have played a part in the refinement of the alphabetic bases.

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Section: Discussionmentioning

confidence: 99%

“…[9] Note that we have not included newer synthetic base pairs that have recently been promoted for diverse molecular biological applications but are likely prebiotically irrelevant. [10] …”

Section: Introductionmentioning

confidence: 99%

On the Origin of the Canonical Nucleobases: An Assessment of Selection Pressures across Chemical and Early Biological Evolution

Rios

Tor

2013

Israel Journal of Chemistry

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“…Analyses of carbonaceous meteorites also suggest that both the extraterrestrial and early terrestrial environment may have been diversely populated with related heterocycles (Botta and Bada, 2002;Martins et al, 2008;Callahan et al, 2011). Furthermore, contributions illustrating that alternative bases and base pairs can both replace and expand the genetic alphabet continue to underscore the question as to why nature selected the native letters (Piccirilli et al, 1990;Benner, 2004;Benner and Sismour, 2005;Chiba and Inouye, 2010). The discovery of bacteriophages that employ modified bases completely replacing one of the native letters (Fig.…”

Section: Prebiotic Chemistry and Alternative Basesmentioning

confidence: 99%

Refining the Genetic Alphabet: A Late-Period Selection Pressure?

Rios

Tor

2012

Astrobiology

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The transition from genomic ribonucleic acid (RNA) to deoxyribonucleic acid (DNA) in primitive cells may have created a selection pressure that refined the genetic alphabet, resulting from the global weakening of the Nglycosyl bonds. Hydrolytic rupture of these bonds, termed deglycosylation, leaves an abasic site that is the single greatest threat to the stability and integrity of genomic DNA. The rates of deglycosylation are highly dependent on the identity of the nucleobases. Modifications made to the bases, such as deamination, oxidation, and alkylation, can further increase deglycosylation reaction rates, suggesting that the native bases provide optimum N-glycosyl bond stability. To protect their genomes, cells have evolved highly specific enzymes called glycosylases, associated with DNA repair, that detect and remove these damaged bases. In RNA, however, the occurrence of many of these modified bases is deliberate. The dichotomous behavior that cells exhibit toward base modifications may have originated in the RNA world. Modified bases would have been advantageous for the functional and structural repertoire of catalytic RNAs. Yet in an early DNA world, the utility of these heterocycles was greatly diminished, and their presence posed a distinct liability to the stability of cells' genomes. A natural selection for bases exhibiting the greatest resistance to deglycosylation would have ensured the viability of early DNA life, along with the recruitment of DNA repair.

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“…During the formation of this kind of complexes the typical hydrogen bonds of Watson-Crick type are replaced by metal-nitrogen base bonds [1][2][3][4][5][6]. Till now the DNA biosensors based on metal-specific oligonucleotide sequences have been used only for the determination of various metal ions.…”

Section: Introductionmentioning

confidence: 99%