DNA Catalysis: Potential, Limitations, Open Questions

Peracchi, Alessio

doi:10.1002/cbic.200500098

Cited by 77 publications

(36 citation statements)

References 74 publications

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“…DNA catalytic potentialities and versatility are well established (recently reviewed in Ref. 30). Translation remains a unique property of RNA at present and a support for RNA being an older information carrier than DNA.…”

Section: Comparison Of the Bond Stabilities In Ribo-and In 2ј-deoxyrimentioning

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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Section: Comparison Of the Bond Stabilities In Ribo-and In 2ј-deoxyrimentioning

confidence: 99%

Origin of Informational Polymers

Saladino

Crestini

Ciciriello

et al. 2006

Journal of Biological Chemistry

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“…In recent years, the powerful methodologies of in vitro selection ("SELEX") from large random-sequence DNA and RNA libraries have significantly facilitated such explorations. [7][8][9] To date, a substantially broader catalytic repertoire for RNA and DNA [as ribozymes and deoxyribozymes (DNAzymes) [10][11][12][13] than is found in naturally occurring ribozymes has been reported. [1][2][3]14 We have been interested in investigating whether reactions that utilize the energy of light can be catalyzed by ribozymes or DNAzymes.…”

Section: Introductionmentioning

confidence: 99%

A Deoxyribozyme, Sero1C, Uses Light and Serotonin to Repair Diverse Pyrimidine Dimers in DNA

Thorne

Chinnapen

Sekhon

et al. 2009

Journal of Molecular Biology

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“…[6][7][8][9][10] Since first report in 1994, 11 DNAzymes have been proposed to cleave mRNA. [12][13][14] DNAzymes can execute the same catalytic function as ribozymes but are more stable, cost-effective and easier to label. [6][7][8][9][10] In 1997, Santoro and Joyce reported two general-purpose RNA-cleaving DNAzymes that cleave all-RNA substrates with efficiency comparable to that of protein enzymes.…”

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confidence: 99%

“…For example, when an rAC junction was used, barely any cleavage was observed even with 500 mM Mg 2+ ( Figure S1, ESI). Therefore, it is also true for the [10][11][12][13][14][15][16][17][18][19][20][21][22][23] DNAzyme that its cleavage activity for every junction is not the same.…”

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confidence: 99%