Periodic Melting of Oligonucleotides by Oscillating Salt Concentrations Triggered by Microscale Water Cycles Inside Heated Rock Pores

Ianeselli, Alan; Mast, Christof B.; Braun, Dieter

doi:10.1002/anie.201907909

Cited by 35 publications

(54 citation statements)

References 18 publications

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“…The Sutherland group has reported that pH fluctuations can drive RNA separation (Mariani et al, 2018a), but this does not address the problem of rapid strand annealing following the return of the pH to more neutral values. The Braun group has recently shown that wet-dry cycles inside heated rock pores triggering salt concentration fluctuations can also lead to strand separation (Ianeselli et al, 2019). Although these latter two approaches are simple and prebiotically plausible, up till now no demonstration of non-enzymatic RNA copying has been reported with these methods.…”

Section: Introductionmentioning

confidence: 99%

Non-enzymatic primer extension with strand displacement

Zhou

Kim

et al. 2019

eLife

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Non-enzymatic RNA self-replication is integral to the emergence of the ‘RNA World’. Despite considerable progress in non-enzymatic template copying, demonstrating a full replication cycle remains challenging due to the difficulty of separating the strands of the product duplex. Here, we report a prebiotically plausible approach to strand displacement synthesis in which short ‘invader’ oligonucleotides unwind an RNA duplex through a toehold/branch migration mechanism, allowing non-enzymatic primer extension on a template that was previously occupied by its complementary strand. Kinetic studies of single-step reactions suggest that following invader binding, branch migration results in a 2:3 partition of the template between open and closed states. Finally, we demonstrate continued primer extension with strand displacement by employing activated 3′-aminonucleotides, a more reactive proxy for ribonucleotides. Our study suggests that complete cycles of non-enzymatic replication of the primordial genetic material may have been facilitated by short RNA oligonucleotides.

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Section: Introductionmentioning

confidence: 99%

Non-enzymatic primer extension with strand displacement

Zhou

Kim

et al. 2019

eLife

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“…We also tried to get kinetic measurements of the same samples by using Eva Green intercalation dye in temperature jump experiments with a thermocycler (SI‐10). Although such measurements were successful for kinetic FRET measurements, [40] the intercalating dye was unfortunately not suitable for kinetics measurements of the short DNA strands in our hands. The KMST‐measured on‐rates showed weak to no dependence on strand length and increased linearly with salt concentration by

(1.9 \pm 0.2) \times \frac{10^{6} M^{- 1} s^{- 1}}{\times PBS}

(Figure 4 a,b).…”

Section: Resultsmentioning

confidence: 98%

Kinetic Microscale Thermophoresis for Simultaneous Measurement of Binding Affinity and Kinetics

2021

Self Cite

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Microscale thermophoresis (MST) is a versatile technique to measure binding affinities of binder–ligand systems, based on the directional movement of molecules in a temperature gradient. We extended MST to measure binding kinetics as well as binding affinity in a single experiment by increasing the thermal dissipation of the sample. The kinetic relaxation fingerprints were derived from the fluorescence changes during thermodynamic re‐equilibration of the sample after local heating. Using this method, we measured DNA hybridization on‐rates and off‐rates in the range 104–106 m−1 s−1 and 10−4–10−1 s−1, respectively. We observed the expected exponential dependence of the DNA hybridization off‐rates on salt concentration, strand length and inverse temperature. The measured on‐rates showed a linear dependence on salt concentration and weak dependence on strand length and temperature. For biomolecular interactions with large enthalpic contributions, the kinetic MST technique offers a robust, cost‐effective and immobilization‐free determination of kinetic rates and binding affinity simultaneously, even in crowded solutions.

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“…Experimental models of such fluctuating environments have been studied extensively by Braun et al (Ianeselli et al 2019;Morasch et al 2019;Salditt et al 2020). Volcanic or impact related hydrothermally active settings have the potential to provide such rapidly fluctuating environments in nature.…”

Section: Emergence and Stability Of Virtual Circular Genomesmentioning

confidence: 99%

The virtual circular genome model for primordial RNA replication

Zhou

Ding

Szostak

2020

RNA

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We propose a model for the replication of primordial protocell genomes that builds upon recent advances in the nonenzymatic copying of RNA. We suggest that the original genomes consisted of collections of oligonucleotides beginning and ending at all possible positions on both strands of one or more virtual circular sequences. Replication is driven by feeding with activated monomers and by the activation of monomers and oligonucleotides in situ. A fraction of the annealed configurations of the protocellular oligonucleotides would allow for template-directed oligonucleotide growth by primer extension or ligation. Rearrangements of these annealed configurations, driven either by environmental fluctuations or occurring spontaneously, would allow for continued oligonucleotide elongation. Assuming that shorter oligonucleotides were more abundant than longer ones, replication of the entire genome could occur by the growth of all oligonucleotides by as little as one nucleotide on average. We consider possible scenarios that could have given rise to such protocell genomes, as well as potential routes to the emergence of catalytically active ribozymes and thus the more complex cells of the RNA World.

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Periodic Melting of Oligonucleotides by Oscillating Salt Concentrations Triggered by Microscale Water Cycles Inside Heated Rock Pores

Cited by 35 publications

References 18 publications

Non-enzymatic primer extension with strand displacement

Non-enzymatic primer extension with strand displacement

Kinetic Microscale Thermophoresis for Simultaneous Measurement of Binding Affinity and Kinetics

The virtual circular genome model for primordial RNA replication

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