Influence of the Linkage between Leaving Group and Nucleoside on Substrate Efficiency for Incorporation in DNA Catalyzed by Reverse Transcriptase

Giraut, Anne; Herdewijn, Piet

doi:10.1002/cbic.201000128

Cited by 12 publications

(15 citation statements)

References 73 publications

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“…The substrate affinity is doubled and the maximum velocity is increased by a factor of 10 (Table 3 ). However, pausing is also observed here after incorporation of two to three nucleotides, indicating that this effect is not caused by the nature of the linker (P–O versus P–N) [38].…”

Section: Metabolic Accessible Leaving Groupssupporting

confidence: 52%

Redesigning the leaving group in nucleic acid polymerization

Herdewijn

Marlière²

2012

FEBS Letters

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a b s t r a c tArtificial nucleic acids have the potential to propagate genetic information in vivo purposefully insulated from the canonical replication and transcription processes of cells. Natural nucleic acids are synthesized using nucleoside triphosphates as building blocks and polymerases as catalysts, pyrophosphate functioning as the universal leaving group for DNA and RNA biosynthesis. In order to avoid entanglement between the propagation of artificial nucleic acids in vivo and the cellular information processes, we promote the biosynthesis of natural and xenobiotic nucleic acids (XNA) dependent on the involvement of leaving groups distinct from pyrophosphate. The feasibility of such radically novel biochemical systems relies on the systematic exploration of the chemical diversity of nucleic acid leaving groups that can undergo the catalytic mechanism of phosphotransfer in nucleic acid polymerization. Initial forays in this research area demonstrate the wide acceptance of polymerases and augur well for in vivo implementation and integration with canonical metabolism.

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Section: Metabolic Accessible Leaving Groupssupporting

confidence: 52%

Redesigning the leaving group in nucleic acid polymerization

Herdewijn

Marlière²

2012

FEBS Letters

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“…In contrast, these analogues were processed as substrates by other enzymes (HIV-1 RT, Taq). [7,9,11] Differences in the three-dimensional structures of the active site of Pol III a and other polymerases are likely to be responsible for the intolerance towards these candidates.…”

Section: Single Incorporation Of 2'-deoxyadenosine Triphosphate Analomentioning

confidence: 98%

2′‐Deoxyribonucleoside Phosphoramidate Triphosphate Analogues as Alternative Substrates for E. coli Polymerase III

et al. 2012

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Thermostable bacterial polymerases like Taq, Therminator and Vent exo(-) are able to perform DNA synthesis by using modified DNA precursors, a property that is exploited in several therapeutic and biotechnological applications. Viral polymerases are also known to accept modified substrates, and this has proven crucial in the development of antiviral therapies. However, non-thermostable polymerases of bacterial origin, or engineered variants, that have similar substrate tolerance and could be used for synthetic biology purposes remain to be identified. We have identified the α subunit of Escherichia coli polymerase III (Pol III α) as a bacterial polymerase that is able to recognise and process as substrates several pyrophosphate-modified dATP analogues in place of its natural substrate dATP for template-directed DNA synthesis. A number of dATP analogues featuring a modified pyrophosphate group were able to serve as substrates during enzymatic DNA synthesis by Pol III α. Features such as the presence of potentially chelating chemical groups and the size and spatial flexibility of the chemical structure seem to be of major importance for the modified leaving group to play its role during the enzymatic reaction. In addition, we could establish that if the pyrophosphate group is altered, deoxynucleotide incorporation proceeds with an efficiency varying with the nature of the nucleobase. Our results represent a great step towards the achievement of a system of artificial DNA synthesis hosted by E. coli and involving the use of altered nucleotide precursors for nucleic acid synthesis.

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“…The chemical interaction of free α-amino acids with activated phosphates can also yield phosphoramidate derivatives by nucleophilic reaction of the amino group (Figure 6). By contrast with the behaviour of carboxylic acid derivatives, phosphoramidates are more reactive than phosphate esters and correspond to an activated state of phosphate, which has been illustrated by the ability of some of them to behave as polymerase substrates for the synthesis of DNA [63,64,65,66,67,68]. In addition to that ability in enzyme reactions, N -phosphoryl amino acids proved to be capable of yielding both phosphate esters and polypeptides through spontaneous reactions in aqueous solution [69,70,71].…”

Section: Phosphoryl Transfer Pathwaysmentioning

confidence: 99%

How Prebiotic Chemistry and Early Life Chose Phosphate

Liu

Rossi

Pascal

2019

Life

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The very specific thermodynamic instability and kinetic stability of phosphate esters and anhydrides impart them invaluable properties in living organisms in which highly efficient enzyme catalysts compensate for their low intrinsic reactivity. Considering their role in protein biosynthesis, these properties raise a paradox about early stages: How could these species be selected in the absence of enzymes? This review is aimed at demonstrating that considering mixed anhydrides or other species more reactive than esters and anhydrides can help in solving the paradox. The consequences of this approach for chemical evolution and early stages of life are analysed.

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Influence of the Linkage between Leaving Group and Nucleoside on Substrate Efficiency for Incorporation in DNA Catalyzed by Reverse Transcriptase

Cited by 12 publications

References 73 publications

Redesigning the leaving group in nucleic acid polymerization

Redesigning the leaving group in nucleic acid polymerization

2′‐Deoxyribonucleoside Phosphoramidate Triphosphate Analogues as Alternative Substrates for E. coli Polymerase III

How Prebiotic Chemistry and Early Life Chose Phosphate

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