Switchable DNA‐Based Peroxidases Controlled by a Chaotropic Ion**

Hoog, Tanner G.; Pawlak, Matthew R.; Aufdembrink, Lauren M.; Bachan, Benjamin F.; Galles, Matthew B.; Bense, Nicholas; Adamala, Katarzyna P.; Engelhart, Aaron E.

doi:10.1002/cbic.202200090

Cited by 6 publications

(5 citation statements)

References 48 publications

(78 reference statements)

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“…This structure can bind heme (Extended Data Fig. 5a), catalyzing the same peroxidase reactions as HRP, which we have previously demonstrated in high-perchlorate solutions using DNA 41 . We observed these reactions also occur in the RNA context with the RNA G quadruplex rPS2.M ( Extended Data Fig.…”

Section: Resultsmentioning

confidence: 68%

Emergent functional behaviors of ribozymes in oxychlorine brines indicate Mars could host a unique niche for molecular evolution

Hoog,

Pawlak,

Gaut

et al. 2023

Preprint

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Mars is a particularly attractive candidate among known astronomical objects to potentially host life. Results from space exploration missions have provided insights into Martian geochemistry indicating oxychlorine species, particularly perchlorate, are ubiquitous features of the Martian geochemical landscape. Perchlorate presents potential obstacles for known forms of life due to its toxicity. However, it can also provide potential benefits, such as producing brines by deliquescence, like those thought to exist on present-day Mars. Here we show perchlorate brines support folding and catalysis of functional RNAs, while inactivating representative protein enzymes. Additionally, we show perchlorate and other oxychlorine species enable new ribozyme functions, including homeostasis-like regulatory behavior, copying of structured RNAs, and the first ribozyme-catalyzed chlorination of organic molecules. We suggest nucleic acids are uniquely well-suited to hypersaline Martian environments. Furthermore, Martian near-or subsurface oxychlorine brines, and brines found in potential lifeforms, could provide a unique niche for biomolecular evolution.

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Section: Resultsmentioning

confidence: 68%

Emergent functional behaviors of ribozymes in oxychlorine brines indicate Mars could host a unique niche for molecular evolution

Hoog,

Pawlak,

Gaut

et al. 2023

Preprint

Self Cite

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“…We observed that these reactions also occur in the RNA context with the RNA G quadruplex rPS2.M even in near-saturated perchlorate solutions of 8 M (Supplementary Fig. 7b) 46,47 . Motivated by these findings, we hypothesized that this same RNAzyme could also catalyze halogenation reactions.…”

Section: Perchlorate (Clo 4 -mentioning

confidence: 72%

Emergent ribozyme behaviors in oxychlorine brines indicate a unique niche for molecular evolution on Mars

Hoog,

Pawlak,

Gaut

et al. 2024

Nat Commun

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Mars is a particularly attractive candidate among known astronomical objects to potentially host life. Results from space exploration missions have provided insights into Martian geochemistry that indicate oxychlorine species, particularly perchlorate, are ubiquitous features of the Martian geochemical landscape. Perchlorate presents potential obstacles for known forms of life due to its toxicity. However, it can also provide potential benefits, such as producing brines by deliquescence, like those thought to exist on present-day Mars. Here we show perchlorate brines support folding and catalysis of functional RNAs, while inactivating representative protein enzymes. Additionally, we show perchlorate and other oxychlorine species enable ribozyme functions, including homeostasis-like regulatory behavior and ribozyme-catalyzed chlorination of organic molecules. We suggest nucleic acids are uniquely well-suited to hypersaline Martian environments. Furthermore, Martian near- or subsurface oxychlorine brines, and brines found in potential lifeforms, could provide a unique niche for biomolecular evolution.

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“…In conclusion, it is possible that iron porphyrins already played a role in prebiotic times on the early Earth, possibly as ROS (and RSS)-degrading enzyme-like systems formed with amphiphile aggregates, well before the suggested formation of the more complex hemin-G-quadruplex RNA structures. 26b, 169 Obviously, micelle-forming amphiphiles are chemically much simpler than oligonucleotides with a specific sequence.…”

Section: Prebiological Considerationsmentioning

confidence: 99%

Optimization and Enhancement of the Peroxidase-like Activity of Hemin in Aqueous Solutions of Sodium Dodecylsulfate

Cvjetan,

Schuler,

Ishikawa

et al. 2023

ACS Omega

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Iron porphyrins play several important roles in present-day living systems and probably already existed in very early life forms. Hemin (= ferric protoporphyrin IX = ferric heme b), for example, is the prosthetic group at the active site of heme peroxidases, catalyzing the oxidation of a number of different types of reducing substrates after hemin is first oxidized by hydrogen peroxide as the oxidizing substrate of the enzyme. The active site of heme peroxidases consists of a hydrophobic pocket in which hemin is embedded noncovalently and kept in place through coordination of the iron atom to a proximal histidine side chain of the protein. It is this partially hydrophobic local environment of the enzyme which determines the efficiency with which the sequential reactions of the oxidizing and reducing substrates proceed at the active site. Free hemin, which has been separated from the protein moiety of heme peroxidases, is known to aggregate in an aqueous solution and exhibits low catalytic activity. Based on previous reports on the use of surfactant micelles to solubilize free hemin in a nonaggregated state, the peroxidase-like activity of hemin in the presence of sodium dodecyl sulfate (SDS) at concentrations below and above the critical concentration for SDS micelle formation (critical micellization concentration (cmc)) was systematically investigated. In most experiments, 3,3′,5,5′-tetramethylbenzidine (TMB) was applied as a reducing substrate at pH = 7.2. The presence of SDS clearly had a positive effect on the reaction in terms of initial reaction rate and reaction yield, even at concentrations below the cmc. The highest activity correlated with the cmc value, as demonstrated for reactions at three different HEPES concentrations. The 4-(2-hydroxyethyl)-1-piperazineethanesulfonate salt (HEPES) served as a pH buffer substance and also had an accelerating effect on the reaction. At the cmc, the addition of l-histidine (l-His) resulted in a further concentration-dependent increase in the peroxidase-like activity of hemin until a maximal effect was reached at an optimal l-His concentration, probably corresponding to an ideal mono-l-His ligation to hemin. Some of the results obtained can be understood on the basis of molecular dynamics simulations, which indicated the existence of intermolecular interactions between hemin and HEPES and between hemin and SDS. Preliminary experiments with SDS/dodecanol vesicles at pH = 7.2 showed that in the presence of the vesicles, hemin exhibited similar peroxidase-like activity as in the case of SDS micelles. This supports the hypothesis that micelle- or vesicle-associated ferric or ferrous iron porphyrins may have played a role as primitive catalysts in membranous prebiotic compartment systems before cellular life emerged.

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Switchable DNA‐Based Peroxidases Controlled by a Chaotropic Ion**

Cited by 6 publications

References 48 publications

Emergent functional behaviors of ribozymes in oxychlorine brines indicate Mars could host a unique niche for molecular evolution

Emergent functional behaviors of ribozymes in oxychlorine brines indicate Mars could host a unique niche for molecular evolution

Emergent ribozyme behaviors in oxychlorine brines indicate a unique niche for molecular evolution on Mars

Optimization and Enhancement of the Peroxidase-like Activity of Hemin in Aqueous Solutions of Sodium Dodecylsulfate

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