Template-directed nonenzymatic oligonucleotide synthesis: lessons  from synthetic chemistry

Fahrenbach, Albert C.

doi:10.1515/pac-2014-1004

Cited by 8 publications

(6 citation statements)

References 82 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Application of solution-phase techniques common for supramolecular and host–guest chemistry, in particular NMR spectroscopy, played an important role in developing the template-directed syntheses that led to a variety of complex macromolecular structures. 26 , 27 Accordingly, a thorough understanding of monomer–duplex binding interactions will provide a strong foundation 28 on which to optimize the template-directed polymerization of RNA. These same techniques can also be applied to experiments with structurally alternative polymers 29 that may have played a role in the early evolution of life.…”

Section: Discussionmentioning

confidence: 99%

Uncovering the Thermodynamics of Monomer Binding for RNA Replication

et al. 2015

Self Cite

View full text Add to dashboard Cite

The nonenzymatic replication of primordial RNA is thought to have been a critical step in the origin of life. However, despite decades of effort, the poor rate and fidelity of model template copying reactions have thus far prevented an experimental demonstration of nonenzymatic RNA replication. The overall rate and fidelity of template copying depend, in part, on the affinity of free ribonucleotides to the RNA primer–template complex. We have now used 1H NMR spectroscopy to directly measure the thermodynamic association constants, Kas, of the standard ribonucleotide monophosphates (rNMPs) to native RNA primer–template complexes. The binding affinities of rNMPs to duplexes with a complementary single-nucleotide overhang follow the order C > G > A > U. Notably, these monomers bind more strongly to RNA primer–template complexes than to the analogous DNA complexes. The relative binding affinities of the rNMPs for complementary RNA primer–template complexes are in good quantitative agreement with the predictions of a nearest-neighbor analysis. With respect to G:U wobble base-pairing, we find that the binding of rGMP to a primer–template complex with a 5′-U overhang is approximately 10-fold weaker than to the complementary 5′-C overhang. We also find that the binding of rGMP is only about 2-fold weaker than the binding of rAMP to 5′-U, consistent with the poor fidelity observed in the nonenzymatic copying of U residues in RNA templates. The accurate Ka measurements for ribonucleotides obtained in this study will be useful for designing higher fidelity, more effective RNA replication systems.

show abstract

Section: Discussionmentioning

confidence: 99%

Uncovering the Thermodynamics of Monomer Binding for RNA Replication

et al. 2015

Self Cite

View full text Add to dashboard Cite

show abstract

“…Imidazoles are thought to have played important roles in prebiotic chemistry prior to their current biological significance as components of the histidine residues in proteins, where they function as, for example, charge-relay agents in catalytic triads . One of the most important potential roles of imidazoles in prebiotic chemistry came to light through the efforts of Orgel and co-workers, , who demonstrated that nucleoside 5′-phosphoro-imidazolides, and especially nucleotides activated with 2-methylimidazole, allow for nonenzymatic template-directed , RNA synthesis yielding predominantly the canonical 3′-5′ phosphodiester linkage. These phosphoro-imidazolides are more reactive than nucleoside triphosphates as a result of their labile P–N bonds and their propensity to form a reactive imidazolium-bridged dinucleotide. In addition to prebiotic activation chemistry, imidazoles have also been suggested to play catalytic roles, assisting in the oligomerization of amino acids, phosphates , and nucleotides, , and a number of plausible mechanisms for the prebiotic synthesis of imidazoles have been reported , (further discussion in SI).…”

mentioning

confidence: 99%

Common and Potentially Prebiotic Origin for Precursors of Nucleotide Synthesis and Activation

et al. 2017

Self Cite

View full text Add to dashboard Cite

We have recently shown that 2-aminoimidazole is a superior nucleotide activating group for nonenzymatic RNA copying. Here we describe a prebiotic synthesis of 2-aminoimidazole that shares a common mechanistic pathway with that of 2-aminooxazole, a previously described key intermediate in prebiotic nucleotide synthesis. In the presence of glycolaldehyde, cyanamide, phosphate and ammonium ion, both 2-aminoimidazole and 2-aminooxazole are produced, with higher concentrations of ammonium ion and acidic pH favoring the former. Given a 1:1 mixture of 2-aminoimidazole and 2-aminooxazole, glyceraldehyde preferentially reacts and cyclizes with the latter, forming a mixture of pentose aminooxazolines, and leaving free 2-aminoimidazole available for nucleotide activation. The common synthetic origin of 2-aminoimidazole and 2-aminooxazole and their distinct reactivities are suggestive of a reaction network that could lead to both the synthesis of RNA monomers and to their subsequent chemical activation.

show abstract

“…Although nonenzymatic template-directed RNA polymerization with activated monomers has been studied since the 1960s, ,− basic thermodynamic aspects remain unclear. The proposed mechanisms start with a reversible noncovalent binding event in which the activated monomer associates with the template. These interactions can be aided by base stacking from either upstream − or downstream ,− adjacent mono- or oligonucleotides.…”

mentioning

confidence: 99%

Downstream Oligonucleotides Strongly Enhance the Affinity of GMP to RNA Primer–Template Complexes

et al. 2017

Self Cite

View full text Add to dashboard Cite

Origins of life hypotheses often invoke a transitional phase of nonenzymatic template-directed RNA replication prior to the emergence of ribozyme-catalyzed copying of genetic information. Here, using NMR and ITC, we interrogate the binding affinity of guanosine 5'-monophosphate (GMP) for primer-template complexes when either another GMP, or a helper oligonucleotide, can bind downstream. Binding of GMP to a primer-template complex cannot be significantly enhanced by the possibility of downstream monomer binding, because the affinity of the downstream monomer is weaker than that of the first monomer. Strikingly, GMP binding affinity can be enhanced by ca. 2 orders of magnitude when a helper oligonucleotide is stably bound downstream of the monomer binding site. We compare these thermodynamic parameters to those previously reported for T7 RNA polymerase-mediated replication to help address questions of binding affinity in related nonenzymatic processes.

show abstract

Template-directed nonenzymatic oligonucleotide synthesis: lessons from synthetic chemistry

Cited by 8 publications

References 82 publications

Uncovering the Thermodynamics of Monomer Binding for RNA Replication

Uncovering the Thermodynamics of Monomer Binding for RNA Replication

Common and Potentially Prebiotic Origin for Precursors of Nucleotide Synthesis and Activation

Downstream Oligonucleotides Strongly Enhance the Affinity of GMP to RNA Primer–Template Complexes

Contact Info

Product

Resources

About