Protocells and RNA Self-Replication

The first demonstration of nonenzymatic template copying within fatty acid vesicles was achieved by copying an RNA template with 5'-activated 2'-aminonucleotides.

“The first demonstration of nonenzymatic template copying within fatty acid vesicles was achieved by copying an RNA template with 5 ′ -activated 2 ′ -aminonucleotides.”

• cites Mansy et al. 2008 sourceDisputed

  The copying experiment in the passage labeled Abstract used an oligo-dC DNA template, not an RNA template. The Methods likewise specify a DNA template and confirm nonenzymatic synthesis of phosphoramidate-linked DNA inside fatty acid vesicles. The nucleotide description is consistent with the claim, but the stated template identity is contrary to the source. (LLM, conf=0.90)

  Checked by a reasoning model — may be wrong.

  Experimental — accuracy not yet measured

When the reaction is performed in the eutectic phase of water ice, even longer polymers can be obtained because of increased concentration of reactants and reduced rate of RNA degradation under near-frozen conditions.

“When the reaction is performed in the eutectic phase of water ice, even longer polymers can be obtained because of the increased concentration of reactants and reduced rate of RNA degradation under these near-frozen conditions”

• cites Attwater et al. 2013 sourceDisputed

  The Results section, “Synthesis of long RNAs in ice and at ambient temperatures” (page not available), reports products up to 118 nucleotides in ice, versus 206 nucleotides at 17°C, and says frozen synthesis was slower and less efficient. Although the paper says the eutectic phase concentrates solutes and ice can enhance ribozyme stability, its measured product lengths contradict the claim that this reaction yielded longer polymers in ice. (LLM, conf=0.88)

  Checked by a reasoning model — may be wrong.

  Experimental — accuracy not yet measured

Even without replication, chemical and physical factors will control and alter the sequences that are generated and persist.

“Even without replication, chemical and physical factors will control and alter the sequences that are generated and persist (Chen and Nowak 2012).”

• cites Chen and Nowak 2012 sourceSupported

The best studied pathways involve Fischer-Tropsch-type chemistry, in which carbon monoxide and hydrogen react under high temperature and pressure on the surface of transition metal minerals to generate terminally oxygenated, saturated linear chains.

“The best studied pathways involve Fischer-Tropsch-type chemistry, in which carbon monoxide and hydrogen react under high temperature and pressure on the surface of transition metal minerals to generate terminally oxygenated, saturated linear chains (Rushdi and Simoneit 2001).”

• cites Rushdi and Simoneit 2001 sourcePartly supported

  Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

  Experimental — accuracy not yet measured

Gentle agitation is sufficient to bring about vesicle division without loss of the vesicle contents.

“Gentle agitation is sufficient to bring about vesicle division without loss of the vesicle contents.”

• cites Zhu and Szostak 2009 sourcePartly supported

  The Results (Vesicle Growth and Division) show that gentle agitation divided vesicles after micelle-induced growth into elongated or sphere-tail shapes, and that most encapsulated contents were retained. The same section says spherical vesicles without micelle addition could not divide by gentle agitation alone. The claim omits that growth condition and states no loss of contents more absolutely than the observation supports. (LLM, conf=0.86)

  Experimental — accuracy not yet measured

Vesicle growth has been observed directly by video microscopy, following the addition of oleate to larger multilamellar vesicles ∼4 μm in diameter.

“More recently, vesicle growth has been observed directly by video microscopy, following the addition of oleate to larger multilamellar vesicles ∼4 µm in diameter (Zhu and Szostak 2009).”

• cites Zhu and Szostak 2009 sourceSupported

Laboratory experiments using glass capillaries as analogs of porous rock channels have shown the simultaneous concentration of dilute fatty acids and DNA, leading to the assembly of vesicles with encapsulated DNA near the bottom of the capillary tube.

“Laboratory experiments using glass capillaries as analogs of porous rock channels have shown the simultaneous concentration of dilute fatty acids and DNA, leading to the assembly of vesicles with encapsulated DNA near the bottom of the capillary tube (Budin et al. 2009).”

• cites Budin et al. 2009 sourceSupported

Over time, this filament grew in length, and equilibration with inner bilayers resulted in a filamentous multilamellar vesicle under conditions in which surface area growth is much faster than volume growth owing to osmotic constraints.

“Over time, this filament grew in length, and equilibration with inner bilayers resulted in a filamentous multilamellar vesicle under conditions in which surface area growth is much faster than volume growth owing to osmotic constraints.”

• cites Zhu and Szostak 2009 sourcePartly supported

  The Results (Vesicle Growth and Division; Mechanism of Initiation of Filamentous Vesicle Growth, pages unavailable) report tails growing into long thread-like vesicles while surface area increases rapidly and volume is constrained by slowly permeating buffer solutes. They propose that inner membrane layers may later grow and spread through the thread, but do not establish the claimed equilibration with inner bilayers as the mechanism. (LLM, conf=0.84)

  Experimental — accuracy not yet measured

Vesicle growth proceeded through the extrusion of a thin filament from the outermost bilayer.

“Surprisingly, vesicle growth proceeded through the extrusion of a thin filament from the outermost bilayer.”

• cites Zhu and Szostak 2009 sourceSupported

A special exception involves a remarkable set of reactions and fractionation processes that amplify a slight chiral imbalance, even to the level of local homochirality.

“A special exception involves a remarkable set of reactions and fractionation processes that amplify a slight chiral imbalance, even to the level of local homochirality (Kondepudi et al. 1990;Soai et al. 1995;Viedma 2005;Klussmann et al. 2006;Noorduin et al. 2008;Viedma et al. 2008).”

• cites Kondepudi et al. 1990 sourceNot checked — no full text of the source
• cites Soai et al. 1995 sourceNot checked — no full text of the source
• cites Viedma 2005 sourceSupported

Glycolaldehyde and glyceraldehyde can react with 2-aminothiazole to give the corresponding aminals, which selectively precipitate to give crystalline reservoirs of these key intermediates.

“However, glycolaldehyde and glyceraldehyde can react with 2-aminothiazole to give the corresponding aminals, which selectively precipitate to give crystalline reservoirs of these key intermediates (Islam et al. 2017).”

• cites Islam et al. 2017 sourceSupported

All detectable primer extension with 2-aminoimidazole (2AI)-activated monomers occurs via the 2-aminoimidazolium intermediate and not through direct reaction of a primer with an activated monomer.

“all detectable primer extension occurs via the 2-aminoimidazolium intermediate and not through the reaction of a primer with an activated monomer”

• cites Walton and Szostak 2017 sourceSupported

The catalytic effect reflects, at least in part, the greater stability of the 2-aminoimidazolium-bridged dinucleotide intermediate compared with the relatively unstable 2-methylimidazolium intermediate.

“This effect is now understood to reflect, at least in part, the greater stability of the 2-aminoimidazolium-bridged dinucleotide intermediate compared with the relatively unstable 2-methylimidazolium intermediate.”

• cites Walton and Szostak 2017 sourceSupported

The process can be iterated to replace labile 2',5' linkages with a progressively higher proportion of the more stable 3',5' linkages.

“This process can be iterated to replace labile 2 ′ ,5 ′ linkages, which lead to strand cleavage by transesterification, with a progressively higher proportion of the more stable 3 ′ ,5 ′ linkages”

• cites Mariani and Sutherland 2017 sourceSupported

The slow ligation is explained by primer extension with monomers proceeding through the highly reactive imidazolium-bridged dinucleotide intermediate.

“This is now explained by the fact that primer extension with monomers proceeds through the highly reactive imidazolium-bridged dinucleotide intermediate discussed above”

• cites Walton and Szostak 2017 sourcePartly supported

  The Conclusions (page not available) state that primer extension with activated cytidine monomers predominantly involves reaction with the imidazolium-bridged dinucleotide Cp*pC, whose reactivity is enhanced relative to the monomer. The cited passages do not explain slow ligation or establish that this mechanism is the reason ligation is slow. (LLM, conf=0.86)

  Experimental — accuracy not yet measured

The catalytic effect of a downstream, activated nucleotide is much stronger for an oligonucleotide than a mononucleotide at the downstream position.

“this effect is much stronger for an oligonucleotide than a mononucleotide at the downstream position”

• cites Prywes et al. 2016 sourceSupported

The intermediate could bind to the template through two adjacent Watson-Crick base pairs.

“The template specificity of primer extension suggested that the intermediate could bind to the template through two adjacent Watson-Crick base pairs”

• cites Walton and Szostak 2016 sourceSupported

Acetylation of the 3'-phosphate by N-acetyl-imidazole or other acetylating reagents preferentially transfers the acetyl group to the 2'-hydroxyl, partially avoiding cyclic phosphate formation.

“if the 3 ′ -phosphate is first acetylated by reaction with N-acetyl-imidazole or other acetylating reagents, in which case the acetyl group is preferentially transferred to the 2 ′ -hydroxyl”

• cites Bowler et al. 2013 sourceSupported

2AI can be generated in the same reaction mixture as the related heterocycle 2-aminooxazole, a precursor of the pyrimidine nucleotides.

“it can be generated in the same reaction mixture as the related heterocycle 2-aminooxazole, a precursor of the pyrimidine nucleotides”

• cites Fahrenbach et al. 2017 sourceSupported

Chemistry that would reactivate hydrolyzed substrates, such as EDC and an N-alkyl imidazole, could lead to a high ligation yield.

“This suggests that chemistry that would reactivate hydrolyzed substrates, such as the combination of EDC and an N-alkyl imidazole explored by the Richert laboratory (Jauker et al. 2015), could lead to a high ligation yield.”

• cites Jauker et al. 2015 sourceSupported

The rate of ligation of a primer to a 5'-imidazole-activated oligonucleotide is very slow compared with the rate of primer extension with similarly activated monomers.

“the rate of ligation of a primer to a 5 ′ -imidazole-activated oligonucleotide is very slow compared with the rate of primer extension with similarly activated monomers”

• cites Prywes et al. 2016 sourceSupported

Most errors in RNA-templated polymerization of imidazole-activated nucleotides result from G•U wobble pairing.

“most errors result from G•U wobble pairing”

• cites Rajamani et al. 2010 sourceCould not verify

  The Introduction and Results and Discussion describe experiments with DNA templates and deoxy-nucleotide monomers, not RNA-templated polymerization. The Mutation Rate section says misincorporations occurred predominantly when copying A and T, but does not identify G•U wobble pairing as their cause. The Choice of Experimental Model System section cautions that these data may not represent mutations in RNA. (LLM, conf=0.78)

  Experimental — accuracy not yet measured

Replacement of U by 2-thio-U also results in faster and more efficient copying of templates that contain A residues.

“Replacement of U by 2-thio-U also results in faster and more efficient copying of templates that contain A residues.”

• cites Heuberger et al. 2015 sourceSupported

It has been possible to copy short RNA templates inside fatty acid vesicles following the addition of activated monomers and trimers to the outside of the vesicles.

“it has been possible to copy short RNA templates inside fatty acid vesicles following the addition of activated monomers and trimers to the outside of the vesicles”

• cites O'Flaherty et al. 2018 sourceSupported

This model had the advantage of rapid primer extension in the absence of Mg2+.

“This model had the advantage of rapid primer extension in the absence of Mg 2+”

• cites Mansy et al. 2008 sourceSupported

This replication system uses a pair of ligase ribozymes that each catalyze the formation of the other, using a mixture of four different substrate oligonucleotides.

“This replication system uses a pair of ligase ribozymes that each catalyze the formation of the other, using a mixture of four different substrate oligonucleotides (Lincoln and Joyce 2009).”

• cites Lincoln and Joyce 2009 sourceSupported

In reaction mixtures containing only these RNA substrates, MgCl2, and buffer, a small starting number of ribozymes gives rise to many additional ribozymes through RNA-catalyzed exponential amplification.

“In reaction mixtures containing only these RNA substrates, MgCl 2 , and buffer, a small starting number of ribozymes gives rise to many additional ribozymes through RNA-catalyzed exponential amplification.”

• cites Lincoln and Joyce 2009 sourceSupported

The most highly optimized class I polymerase also has the ability to synthesize DNA polymers on an RNA template.

“This most highly optimized class I polymerase also has the ability to synthesize DNA polymers on an RNA template”

• cites Samanta and Joyce 2017 sourceSupported

The self-cleaving hammerhead ribozyme has activity within fatty acid-based vesicles.

“Such studies have generally used simple ribozymes, such as the self-cleaving hammerhead ribozyme, for which activity within fatty acid-based vesicles has been shown (Chen et al. 2005).”

• cites Chen et al. 2005 sourceSupported

Thus far, the properties of encapsulation and replication have not been combined within a single system.

“Thus far, however, the properties of encapsulation and replication have not been combined within a single system.”

These considerations imply that compartmentalization is an essential step on the path to biology.

“These considerations imply that compartmentalization is an essential step on the path to biology.”

Experimentally, even transient compartmentalization is sufficient to prevent extinction caused by parasites.

“Experimentally, even transient compartmentalization is sufficient to prevent extinction caused by parasites (Bansho et al. 2016;Matsumura et al. 2016).”

• cites Bansho et al. 2016 sourceNot checked — no full text of the source
• cites Matsumura et al. 2016 sourceNot checked — no full text of the source

Protocells were also membrane-bound structures, albeit with very different membranes than modern cells.

“Given that all modern cells are bounded by a semipermeable cell membrane, it is reasonable to postulate that protocells were also membrane-bound structures, albeit with very different membranes than modern cells (Deamer 1997).”

• cites Deamer 1997 sourceNot checked — no full text of the source

Repeated cycles of replication would be expected to shape the structure of a population by influencing base composition, template length, secondary structure, and other properties.

“Repeated cycles of replication would therefore be expected to shape the structure of a population by influencing base composition, template length, secondary structure, and other properties.”

Such a transition would have become increasingly difficult as the system of replicating and functional RNAs became more highly adapted to any prior form of compartmentalization.

“Such a transition would have become increasingly difficult as the system of replicating and functional RNAs became more highly adapted to any prior form of compartmentalization.”

Even without compartmentalization, RNAs can be obtained that bind a ligand or catalyze a self-modification reaction.

“Numerous in vitro selection experiments have shown that, even without compartmentalization, RNAs can be obtained that bind a ligand or catalyze a self-modification reaction.”

Bilayer membranes are a barrier to free access to the substrates needed for genome replication, most notably charged nucleotides.

“Chief among these is that bilayer membranes are a barrier to free access to the substrates needed for genome replication, most notably charged nucleotides.”

For more complex functions, such as RNA-catalyzed replicative or metabolic reactions, some form of compartmentalization becomes essential.

“However, for more complex functions, such as RNA-catalyzed replicative or metabolic reactions, some form of compartmentalization becomes essential.”

Replication of both the protocell and its encapsulated genetic material would have enabled natural selection to operate based on the differential fitness of competing cellular entities, ultimately giving rise to modern cellular life.

“Replication of both the protocell and its encapsulated genetic material would have enabled natural selection to operate based on the differential fitness of competing cellular entities, ultimately giving rise to modern cellular life.”

RNA was the dominant genetic and functional biopolymer at an early stage in the evolution of life.

“The central role of RNA in modern cellular biochemistry, and especially the role of the large ribosomal RNA as the catalyst of protein synthesis (Steitz and Moore 2003), provides a powerful argument in support of RNA as the dominant genetic and functional biopolymer at an early stage in the evolution of life.”

• cites Steitz and Moore 2003 sourceNot checked — no full text of the source

The Mg2+-catalyzed degradation of RNA is prevented by citrate.

“As an added benefit, the Mg 2+ -catalyzed degradation of RNA is prevented by citrate.”

• cites Adamala and Szostak 2013aNot matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

In a population of small compartments, the emergence of a parasitic sequence in one compartment will not affect the population as a whole, even if it dooms the descendants of that compartment.

“In a population of small compartments, however, the emergence of a parasitic sequence in one compartment will not affect the population as a whole, even if it dooms the descendants of that compartment.”

Other forms of compartmentalization would have had to undergo a transition to membrane-based compartments.

“Other forms of compartmentalization would have had to undergo a transition to membrane-based compartments.”

Membranes formed from single-chain amphiphiles, such as fatty acids and their glycerol esters as well as fatty alcohols and related compounds, tend to be much more permeable than membranes composed of two-chain lipids.

“Membranes formed from single-chain amphiphiles, such as fatty acids and their glycerol esters as well as fatty alcohols and related compounds, tend to be much more permeable than membranes composed of two-chain lipids.”

Protocell membranes must be compatible with the physical and chemical conditions necessary for RNA chemistry.

“Protocell membranes must be compatible with the physical and chemical conditions necessary for RNA chemistry.”

The formation of compartments through the assembly of bilayer membranes has a major conceptual advantage over other types of compartments, namely, its continuity with known biology.

“The formation of compartments through the assembly of bilayer membranes has a major conceptual advantage over other types of compartments, namely, its continuity with known biology.”

Modern cell membranes, composed of phospholipids, sterols, and other complex lipids, are nearly complete barriers to the permeation of nucleotides and even divalent cations such as Mg2+.

“Modern cell membranes, composed of phospholipids, sterols, and other complex lipids, are nearly complete barriers to the permeation of nucleotides and even divalent cations such as Mg 2+ (Deamer 1997).”

• cites Deamer 1997 sourceNot checked — no full text of the source

Simple processes of natural selection can occur in solution.

“Simple processes of natural selection can occur in solution.”

In free solution, parasitic RNAs that are better templates will increase at the expense of functional replicase RNAs, leading to a population crash.

“In free solution, parasitic RNAs that are better templates will increase at the expense of functional replicase RNAs, leading to a population crash.”

An RNA replicase in free solution might replicate other surrounding RNAs, thus failing to benefit itself.

“A similar argument can be made with respect to an RNA replicase, which in free solution might replicate other surrounding RNAs, thus failing to benefit itself.”

Compartmentalization is essential to prevent system crashes caused by the evolution of parasites.

“Compartmentalization is also essential to prevent system crashes caused by the evolution of parasites.”

Because primitive cells would have lacked the sophisticated transport machinery that controls molecular trafficking in modern cells, protocells must have been bounded by simpler, more permeable membranes.

“Because primitive cells would have lacked the sophisticated transport machinery that controls molecular trafficking in modern cells, protocells must have been bounded by simpler, more permeable membranes.”

Fatty acid-based membranes become unstable in ≥4 mM Mg2+, indicating an apparent incompatibility between the two systems.

“In contrast, fatty acid-based membranes become unstable in ≥4 mM Mg 2+ , indicating an apparent incompatibility between the two systems.”

Montmorillonite clay can catalyze the polymerization of activated mononucleotides.

“The ability of montmorillonite clay to catalyze the polymerization of activated mononucleotides is well known (Ferris et al. 1996;Ferris 2002).”

• cites Ferris et al. 1996 sourceNot checked — no full text of the source
• cites Ferris 2002 sourceNot checked — no full text of the source

There are examples of DNA origami that undergo self-replication based on growth and division processes analogous to those of membrane systems.

“There are examples of DNA origami that undergo self-replication based on growth and division processes analogous to those of membrane systems (Schulman et al. 2012).”

• cites Schulman et al. 2012 sourceNot checked — no full text of the source

Nucleic acids might provide the basis for their own compartmentalization.

“Finally, nucleic acids might provide the basis for their own compartmentalization.”

Competition results from the slower dissociation of fatty acid molecules from membranes that contain phospholipids, which results in growth of phospholipid-containing vesicles at the expense of vesicles that do not contain (or contain less) phospholipid.

“In this case, competition results from the slower dissociation of fatty acid molecules from membranes that contain phospholipids, which results in growth of phospholipidcontaining vesicles at the expense of vesicles that do not contain (or contain less) phospholipid.”

• cites Budin and Szostak 2011 sourceNot checked — no full text of the source

The addition of excess alkaline oleate micelles to preformed oleate vesicles, buffered at a lower pH, led to an increase in vesicle number.

“However, the addition of excess alkaline oleate micelles to preformed oleate vesicles, buffered at a lower pH, led to an increase in vesicle number.”

• cites Rasi et al. 2004 sourceNot checked — no full text of the source

This high-energy state can be relaxed by the incorporation of additional fatty acid molecules into the membrane.

“This high-energy state can be relaxed by the incorporation of additional fatty acid molecules into the membrane.”

The strong electrostatic interactions between polyanionic nucleic acids and various polycations leads to the formation of complex coacervates, which, depending on their composition and the ambient conditions, may remain as liquid droplets.

“The strong electrostatic interactions between polyanionic nucleic acids and various polycations leads to the formation of complex coacervates, which, depending on their composition and the ambient conditions, may remain as liquid droplets.”

Filamentous vesicles are subject to a pearling instability that likely contributes to the ease with which they are fragmented under mild shear stress.

“Filamentous vesicles are subject to a pearling instability that likely contributes to the ease with which they are fragmented under mild shear stress.”

As the heated vent fluids cool, dissolved minerals form precipitates and build up a network of interconnected microscale channels.

“As the heated vent fluids cool, dissolved minerals form precipitates and build up a network of interconnected microscale channels.”

Concentration as a result of thermophoresis can also preferentially enrich longer products relative to shorter ones, providing a means to overcome the replication bias that favors shorter templates.

“Concentration as a result of thermophoresis can also preferentially enrich longer products relative to shorter ones, providing a means to overcome the replication bias that favors shorter templates (Kreysing et al. 2015).”

• cites Kreysing et al. 2015 sourceNot checked — no full text of the source

Temperature gradients across narrow channels can concentrate oligonucleotides, facilitating the assembly of longer DNA strands.

“Subsequent experiments have shown that temperature gradients across narrow channels can concentrate oligonucleotides, facilitating the assembly of longer DNA strands (Mast et al. 2013).”

• cites Mast et al. 2013 sourceNot checked — no full text of the source

A small fraction of phospholipid in a largely fatty acid membrane can also lead to competitive growth.

“Subsequent studies revealed that a small fraction of phospholipid in a largely fatty acid membrane can also lead to competitive growth (Budin and Szostak 2011).”

• cites Budin and Szostak 2011 sourceNot checked — no full text of the source

Any vesicle that also contained a heritable catalyst of phospholipid synthesis would experience a strong selective advantage.

“Thus, any vesicle that also contained a heritable catalyst of phospholipid synthesis would experience a strong selective advantage.”

In an environment rich in organic thiols, photochemical oxidative processes that lead to disulfide formation can induce extreme pearling in such vesicles, resulting in spontaneous division into a large number of small daughter vesicles.

“Alternatively, in an environment rich in organic thiols, photochemical oxidative processes that lead to disulfide formation can induce extreme pearling in such vesicles, resulting in spontaneous division into a large number of small daughter vesicles (Zhu et al. 2012).”

• cites Zhu et al. 2012 sourceNot checked — no full text of the source

The size of the newly formed vesicles was close to that of the original preformed vesicles.

“Strikingly, the size of the newly formed vesicles was close to that of the original preformed vesicles (Rasi et al. 2004).”

• cites Rasi et al. 2004 sourceNot checked — no full text of the source

The first experimental demonstration of competition between protocells arose from studies of osmotically driven growth.

“The first experimental demonstration of competition between protocells arose from studies of osmotically driven growth (Chen et al. 2004).”

• cites Chen et al. 2004 sourceNot checked — no full text of the source

Competition between vesicles for limiting membrane components could provide a simple scenario for protocell growth that obviates the need for periodic input of new amphiphilic material.

“Competition between vesicles for limiting membrane components could provide a simple scenario for protocell growth that obviates the need for periodic input of new amphiphilic material.”

Because thermophoresis is strongly inhibited by high salt concentrations, this concentration mechanism would only be operative in freshwater hydrothermal vents, such as those currently found in Lake Yellowstone.

“Because thermophoresis is strongly inhibited by high salt concen-trations, this concentration mechanism would only be operative in freshwater hydrothermal vents, such as those currently found in Lake Yellowstone (Inskeep et al. 2015).”

• cites Inskeep et al. 2015Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Because single-chain amphiphiles exchange rapidly between vesicles, fatty acid vesicles containing RNA grow in the presence of empty (relaxed) fatty acid vesicles.

“Because single-chain amphiphiles exchange rapidly between vesicles, fatty acid vesicles containing RNA grow in the presence of empty (relaxed) fatty acid vesicles.”

When this reaction is performed with a complex mixture of sugars, the ribose derivative strikingly crystallizes from aqueous solution, segregating it from the other sugars.

“When this reaction is performed with a complex mixture of sugars, the ribose derivative strikingly crystallizes from aqueous solution, segregating it from the other sugars (Springsteen and Joyce 2004).”

• cites Springsteen and Joyce 2004 sourceNot checked — no full text of the source

Experiments on the nonenzymatic template-directed polymerization of imidazole-activated mononucleotides suggest that the polymerization of the D-enantiomer is strongly inhibited by the L-enantiomer.

“This is a serious problem because experiments on the nonenzymatic template-directed polymerization of imidazole-activated mononucleotides suggest that the polymerization of the D-enantiomer is strongly inhibited by the L-enantiomer (Joyce et al. 1984).”

• cites Joyce et al. 1984 sourceNot checked — no full text of the source

These and similar studies suggest that there are many ways of linking together the nucleotide bases into chains that are capable of forming base-paired double helices.

“These and similar studies suggest that there are many ways of linking together the nucleotide bases into chains that are capable of forming base-paired double helices.”

There likely were biases in the inventory of compounds delivered to the Earth by comets and meteorites.

“There likely were biases in the inventory of compounds delivered to the Earth by comets and meteorites (Cronin and Pizzarello 1997;Engel and Macko 1997;Pizzarello et al. 2003;Glavin and Dworkin 2009).”

• cites Cronin and Pizzarello 1997 sourceNot checked — no full text of the source
• cites Engel and Macko 1997 sourceNot checked — no full text of the source
• cites Pizzarello et al. 2003 sourceNot checked — no full text of the source

Even chemical fractionation could not achieve on a macroscopic scale one desirable separation, the resolution of D-ribonucleotides from their L-enantiomers.

“Even chemical fractionation could not achieve on a macroscopic scale one desirable separation, the resolution of D-ribonucleotides from their L-enantiomers.”

For the purines, but not the pyrimidines, simply heating the nucleobase with ribose or ribose-phosphate results in the synthesis of the corresponding ribonucleoside or ribonucleotide, but in low yield.

“It has long been known for the purines, but not the pyrimidines, that simply heating the nucleobase with ribose or ribose-phosphate results in the synthesis of the corresponding ribonucleoside or ribonucleotide, but in low yield (Fuller et al. 1972).”

• cites Fuller et al. 1972 sourceNot checked — no full text of the source

Recent studies suggest that other routes may be more feasible, most notably those that involve the coassembly of the base and sugar phosphate.

“Recent studies, however, suggest that other routes may be more feasible, most notably those that involve the coassembly of the base and sugar phosphate.”

The gradual twist of p-RNA should make it easier to separate strands of p-RNA during replication.

“which should make it easier to separate strands of p-RNA during replication”

Arabinose amino-oxazoline in turn can react with cyanoacetylene, also in phosphate buffer, to form cytosine 2',3'-cyclic phosphate as the major product.

“Arabinose amino-oxazoline in turn can react with cyanoacetylene, also in phosphate buffer, to form cytosine 2 ′ ,3 ′ -cyclic phosphate as the major product.”

• cites Powner et al. 2009 sourceNot checked — no full text of the source

RAO also reacts with cyanoacetylene, generating the 2,2'-anhydro-ribonucleoside, but in this case as the α-anomer.

“(RAO) also reacts with cyanoacetylene, generating the 2,2 ′ -anhydro-ribonucleoside, but in this case as the αanomer.”

• cites Xu et al. 2017Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

p-RNAs are less likely than the corresponding RNAs to form multiple-strand competing structures.

“p-RNAs are less likely than the corresponding RNAs to form multiple-strand competing structures”

• cites Pitsch et al. 1993 sourceNot checked — no full text of the source
• cites Pitsch et al. 1995 sourceNot checked — no full text of the source
• cites Pitsch et al. 2003 sourceNot checked — no full text of the source

p-RNA helices twist much more gradually than those of standard nucleic acids.

“the helices twist much more gradually than those of standard nucleic acids”

• cites Pitsch et al. 1993 sourceNot checked — no full text of the source
• cites Pitsch et al. 1995 sourceNot checked — no full text of the source
• cites Pitsch et al. 2003 sourceNot checked — no full text of the source

Arabinose 3-phosphate reacts with cyanamide to give the corresponding amino-oxazoline.

“Like arabinose, arabinose 3-phosphate reacts with cyanamide to give the corresponding amino-oxazoline (Fig. 2C).”

• cites Ingar et al. 2003 sourceNot checked — no full text of the source

An RNA-like structure based on threose nucleotide analogs (TNA), although it involves a five-atom repeat, can still form a stable double-helical structure with standard RNA.

“an RNA-like structure based on threose nucleotide analogs (TNA; Fig. 4C), although it involves a five-atom repeat, can still form a stable double-helical structure with standard RNA”

• cites Schöning et al. 2000 sourceNot checked — no full text of the source

Many sugars, including the four pentoses, react readily with cyanamide to form stable bicyclic amino-oxazolines.

“Many sugars, including the four pentoses, react readily with cyanamide to form stable bicyclic amino-oxazolines (Fig. 2A) (Sanchez and Orgel 1970).”

• cites Sanchez and Orgel 1970 sourceNot checked — no full text of the source

Starting simply with glycolaldehyde and cyanamide, in the presence of 1 M phosphate at neutral pH, gives 2-amino-oxazole in excellent yield.

“Sutherland and colleagues (Ingar et al. 2003;Anastasi et al. 2007;Powner et al. 2009) avoided the complication of the separate synthesis of sugars by starting simply with glycolaldehyde and cyanamide, which in the presence of 1 M phosphate at neutral pH gives 2-amino-oxazole an excellent yield (Fig. 2B).”

• cites Ingar et al. 2003 sourceNot checked — no full text of the source
• cites Anastasi et al. 2007Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

• cites Powner et al. 2009 sourceNot checked — no full text of the source

Glyceraldehyde is then added, resulting in formation of the various pentose amino-oxazolines, including the arabinose compound.

“Glyceraldehyde is then added, resulting in formation of the various pentose amino-oxazolines, including the arabinose compound.”

• cites Powner et al. 2009 sourceNot checked — no full text of the source

It is possible that the locale for life's origins was not racemic, although the global chemical environment contained nearly equal amounts of each pair of stereoisomers.

“It is possible that the locale for life's origins was not racemic, although the global chemical environment contained nearly equal amounts of each pair of stereoisomers.”

• AssumptionRests on an assumption: The global chemical environment contained nearly equal amounts of each pair of stereoisomers.

Polynucleotides based on the pyranosyl analog of ribose (p-RNA) form Watson-Crick-paired double helices that are more stable than RNA.

“polynucleotides based on the pyranosyl analog of ribose (p-RNA) form Watson-Crick-paired double helices that are more stable than RNA”

• cites Pitsch et al. 1993 sourceNot checked — no full text of the source
• cites Pitsch et al. 1995 sourceNot checked — no full text of the source
• cites Pitsch et al. 2003 sourceNot checked — no full text of the source

Complementary oligomers of GNA form antiparallel double helices with surprisingly high duplex stabilities.

“Complementary oligomers of GNA form antiparallel, double helices with surprisingly high duplex stabilities.”

• cites Zhang et al. 2005 sourceNot checked — no full text of the source

Enantiomeric cross-inhibition is certainly a serious problem if life arose in a racemic environment.

“However, enantiomeric cross-inhibition is certainly a serious problem if life arose in a racemic environment.”

p-RNA does not interact with normal RNA to form base-paired double helices.

“However, p-RNA does not interact with normal RNA to form base-paired double helices.”

TNA provides an example of a pairing system based on a sugar that could be formed more readily than ribose.

“This provides an example of a pairing system based on a sugar that could be formed more readily than ribose.”

The proportion of copies of an RNA that are error free is determined by the fidelity of the component condensation reactions required to produce a complete copy.

“The proportion of copies of an RNA that are error free is determined by the fidelity of the component condensation reactions that are required to produce a complete copy.”

Because oligonucleotides can have a long residence time on the template, a slow rate of ligation is not necessarily a problem, so long as the reaction can go to completion.

“Because oligonucleotides can have a long residence time on the template, a slow rate of ligation is not necessarily a problem, so long as the reaction can go to completion.”

Subsequent activation of the 3'-phosphate allows ligation and formation of a 3',5'-phosphodiester.

“Subsequent activation of the 3 ′ -phosphate allows for ligation and formation of a 3 ′ ,5 ′ -phosphodiester.”

Because the ligation reaction is slow, the final yield is determined by competition with hydrolysis of the activated phosphate.

“Because the ligation reaction is slow, the final yield is determined by competition with hydrolysis of the activated phosphate.”

As fidelity improves, a larger genome can be maintained.

“As fidelity improves, a larger genome can be maintained.”

The identity of the leaving group on the 5'-phosphate of the downstream nucleotide has a large effect on the rate of the reaction between the primer and the adjacent monomer.

“the identity of the leaving group on the 5 ′ -phosphate of the downstream nucleotide has a large effect on the rate of the reaction between the primer and the adjacent monomer”

• cites Wu and Orgel 1992bNot matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

An N-alkyl-imidazole can leave as a neutral species that does not require protonation.

“an N-alkyl-imidazole as an activating agent because it can leave as a neutral species that does not require protonation.”

The error threshold is expressed as n < |ln s| / |ln q|.

“n < |ln s| / |ln q|.”

The 3'-hydroxyl of the primer must be deprotonated during nucleophilic attack on the phosphate of the incoming monomer.

“the 3 ′ -hydroxyl of the primer must be deprotonated during nucleophilic attack on the phosphate of the incoming monomer.”

In template-directed ligation of DNA oligonucleotides mediated by cyanogen bromide, when random hexamers were annealed to a defined template, most ligation products had perfect complementarity to the template.

“when random hexamers were annealed to a defined template, most of the ligation products had perfect complementarity to the template.”

• cites James and Ellington 1997 sourceNot checked — no full text of the source

For a self-replicating RNA formed by template-directed condensation of activated mononucleotides, a total of 2n-2 condensation reactions are required to produce a complete copy.

“For a self-replicating RNA that is formed by the template-directed condensation of activated mononucleotides, a total of 2n -2 condensation reactions are required to produce a complete copy.”

The 2'-hydroxyl is regenerated by slow hydrolytic loss of the acetyl group.

“the 2 ′ -hydroxyl is regenerated by slow hydrolytic loss of the acetyl group.”

Continuous addition of EDC could in principle lead to continuing primer extension.

“the continuous addition of EDC could in principle lead to continuing primer extension”

The very slow rate at which the last nucleotide of a template is copied relative to internal sites suggested that other factors influenced the reaction.

“the very slow rate at which the last nucleotide of a template is copied relative to internal sites (Wu and Orgel 1992a), suggested that other factors influenced the reaction.”

• cites Wu and Orgel 1992aNot matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Template copying fidelity can be improved by the use of nucleotide analogs.

“Template copying fidelity can be improved by the use of nucleotide analogs.”

The reaction of the primer with an activated nucleotide is catalyzed by a downstream, activated nucleotide that is base-paired to the template at the primer +2 position.

“the reaction of the primer with an activated nucleotide is catalyzed by a downstream, activated nucleotide that is base-paired to the template at the primer +2 position.”

• cites Wu and Orgel 1992bNot matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

This study suggests that oligonucleotide ligation could play a significant role in nonenzymatic RNA-templated synthesis, if more efficient ligation chemistry could be defined.

“This study suggests that oligonucleotide ligation could play a significant role in nonenzymatic RNA-templated synthesis, if more efficient ligation chemistry could be defined.”

For s > 1 and q > 0.9, the error threshold simplifies to n < ln s / (1-q).

“For s > 1 and q > 0.9, this equation simplifies to n < ln s / (1q).”

Primer extension following a mismatch was generally very slow, depending on the specific mismatch.

“primer extension following a mismatch was generally very slow, depending on the specific mismatch.”

The probability of obtaining a completely error-free copy is q^n, the product of the fidelity of the component condensation reactions.

“The probability of obtaining a completely error-free copy is given by q n , which is the product of the fidelity of the component condensation reactions.”

The intermediate is a 5',5'-imidazolium-bridged dinucleotide, generated by attack of the nucleophilic nitrogen of an unprotonated phosphoroimidazolide on the phosphate of a protonated imidazolide.

“Nuclear magnetic resonance experiments identified this intermediate as a 5 ′ ,5 ′ -imidazolium-bridged dinucleotide, generated by an attack of the nucleophilic nitrogen of an unprotonated phosphoroimidazolide on the phosphate of a protonated imidazolide”

If an advantageous individual is to outgrow its competitors, q^n must exceed the superiority s of that individual.

“If an advantageous individual is to outgrow its competitors, q n must exceed the superiority, s, of that individual.”

If the first genomes encoded a small but relatively efficient ribozyme for which roughly 25 nucleotides must be specified, a fidelity of about 0.98 would be required to enable inheritance of the corresponding information.

“If one assumes that the first genomes encoded a small but relatively efficient ribozyme, for which the identity of roughly 25 nucleotides must be specified, then a fidelity of ∼0.98 would be required to enable inheritance of the corresponding information.”

• AssumptionThe authors state this as an assumption: The first genomes encoded a small but relatively efficient ribozyme for which the identity of roughly 25 nucleotides must be specified.

If full-length copies can serve as templates for the next round of copying as soon as they are completed, there will be enrichment for accurate copies during exponential amplification.

“If full-length copies can serve as templates for the next round of copying as soon as they are completed, then there will be enrichment for accurate copies during the course of exponential amplification.”

Such a hybrid process would avoid some difficulties inherent to template copying solely by ligation of oligonucleotide substrates, such as gaps or overhangs.

“Such a hybrid process would avoid some of the difficulties inherent to template copying solely by ligation of oligonucleotide substrates, such as the formation of gaps or overhangs.”

For an advantageous RNA to outgrow its competitors, its net rate of production must exceed the mean rate of production of all other RNAs in the population.

“For an advantageous RNA to outgrow its competitors, its net rate of production must exceed the mean rate of production of all other RNAs in the population.”

A leaving group that departs as an anion with low pKa could provide a much faster reaction rate at elevated pH.

“Therefore, a leaving group that departs as an anion (with low pK a ) could provide a much faster reaction rate at elevated pH.”

The L1 structure shows a bound metal ion in the active site, coordinated by three nonbridging phosphate oxygens, one of which belongs to the newly formed phosphodiester linkage.

“The L1 structure (Fig. 6A) shows a bound metal ion in the active site, coordinated by three nonbridging phosphate oxygens, one of which belongs to the newly formed phosphodiester linkage.”

• cites Robertson and Scott 2007 sourceNot checked — no full text of the source

Bartel and colleagues converted the class I ligase to a bona fide RNA polymerase that operates on a separate RNA template.

“Bartel and colleagues performed further in vitro evolution experiments to convert the class I ligase to a bona fide RNA polymerase that operates on a separate RNA template”

• cites Johnston et al. 2001 sourceNot checked — no full text of the source

The improved fidelity appears to be the underlying source for the improvements in the maximum length of extension and the rate of polymerization.

“This improved fidelity appears to be the underlying source for the improvements in the maximum length of extension and the rate of polymerization.”

Use of the 2AI leaving group combined with activated downstream trinucleotides enabled efficient copying of mixed-sequence templates containing up to seven nucleotides.

“the use of the 2AI leaving group combined with activated downstream trinucleotides enabled the efficient copying of mixed-sequence templates containing up to seven nucleotides.”

These structures point to a universal catalytic strategy very similar to that used by modern protein-based RNA polymerases.

“These structures point to a universal catalytic strategy, very similar to that used by modern protein-based RNA polymerases.”

Strand reannealing is very fast relative to the time scale of nonenzymatic template copying.

“strand reannealing is very fast relative to the time scale of nonenzymatic template copying.”

Recent advances in the prebiotic chemistry of pyrimidine nucleotides suggest that a mixture of U and 2-thio-U might be obtained through the synthesis of 2-thio-C, followed by spontaneous deamination.

“Recent advances in the prebiotic chemistry of pyrimidine nucleotides suggest that a mixture of U and 2-thio-U might be obtained through the synthesis of 2-thio-C, followed by spontaneous deamination”

• cites Xu et al. 2017Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Because the product of template copying is a double-stranded RNA, there must be some means of either strand separation or strand displacement synthesis.

“Because the product of template copying is a double-stranded RNA, there must be some means of either strand separation or strand displacement synthesis.”

From a population of replicating RNAs, particular RNAs would have gained in relative abundance if they enjoyed a selective advantage because of a higher net rate of production.

“particular RNAs would have gained in relative abundance if they enjoyed a selective advantage because of a higher net rate of production.”

• AssumptionThe authors state this as an assumption: The RNA-first view assumes that a supply of activated nucleotides was available through some set of abiotic processes.
• AssumptionThe authors state this as an assumption: The RNA-first view assumes that a means existed to convert activated nucleotides to an ensemble of random sequence polynucleotides, a subset of which could undergo nonenzymatic replication.

Achieving a reannealing time of hours by dilution would require strand concentrations in the picomolar range, which likely would be too low to maintain RNA replication within a protocell.

“achieving a reannealing time of hours would require strand concentrations in the picomolar range, which likely would be too low to maintain RNA replication within a protocell.”

Phase-separated droplets containing only RNA form when the RNAs contain certain triplet repeats, which enable the formation of a highly branched interconnected network.

“These droplets form when the RNAs contain certain triplet repeats, which enable the formation of a highly branched interconnected network.”

• cites Jain and Vale 2017Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Addition of citrate enabled the copying of an RNA homopolymer template inside fatty acid vesicles.

“Addition of citrate enabled the copying of an RNA homopolymer template inside fatty acid vesicles.”

Work involving ribozymes developed through in vitro evolution makes clear that an RNA replicase ribozyme could have existed.

“The possibility that an RNA replicase ribozyme could have existed has been made abundantly clear by work involving ribozymes that have been developed through in vitro evolution”

• cites Bartel and Szostak 1993 sourceNot checked — no full text of the source
• cites Ekland et al. 1995 sourceNot checked — no full text of the source
• cites Johnston et al. 2001 sourceNot checked — no full text of the source

The inheritance of RNA-based genetic information requires cycles of both plus- and minus-strand synthesis.

“The inheritance of RNA-based genetic information requires cycles of both plus-and minus-strand synthesis.”

This ribozyme variant displays significantly improved fidelity, particularly with respect to discrimination against G•U wobble pairs.

“this ribozyme variant displays significantly improved fidelity, particularly with respect to discrimination against G•U wobble pairs.”

• cites Zaher and Unrau 2007 sourceNot checked — no full text of the source

With ongoing selective pressure, chemical replication would become supplanted by a biochemical replication process.

“With ongoing selective pressure, this chemical replication process would become supplanted by a biochemical replication process.”

The polymerization of activated nucleotides proceeds via nucleophilic attack by the 3'-hydroxyl of a template-bound oligonucleotide at the α-phosphorus of an adjacent template-bound nucleotide derivative.

“The polymerization of activated nucleotides proceeds via nucleophilic attack by the 3 ′ -hydroxyl of a template-bound oligonucleotide at the α-phosphorus of an adjacent template-bound nucleotide derivative.”

They added 76 random sequence nucleotides to the 3' end of the class I ligase that were evolved to form an accessory domain assisting polymerization of template-bound NTPs.

“To the 3 ′ end of the class I ligase, they added 76 random sequence nucleotides that were evolved to form an accessory domain that assists in the polymerization of template-bound NTPs.”

• cites Johnston et al. 2001 sourceNot checked — no full text of the source

The class I ribozyme was shown to catalyze a polymerization reaction in which the 5'-triphosphate-bearing oligonucleotide is replaced by one or more nucleoside 5'-triphosphates (NTPs).

“the class I ribozyme was shown to catalyze a polymerization reaction in which the 5 ′ -triphosphate-bearing oligonucleotide is replaced by one or more nucleoside 5 ′ -triphosphates (NTPs)”

• cites Ekland and Bartel 1996 sourceNot checked — no full text of the source

The fact that an RNA polymerase ribozyme also can function as a reverse transcriptase suggests that a bridge may have existed between RNA and DNA as a selective adaptation of the RNA world.

“The fact that an RNA polymerase ribozyme also can function as a reverse transcriptase suggests that a bridge may have existed between RNA and DNA as a selective adaptation of the RNA world.”

Reverse transcriptase activity likely was necessary for the transition from RNA to DNA genomes during the early history of life on Earth.

“Reverse transcriptase activity likely was necessary for the transition from RNA to DNA genomes during the early history of life on Earth.”

It continues to show a good average fidelity of 0.97.

“It continues to show a good average fidelity of 0.97.”

• cites Wochner et al. 2011 sourceNot checked — no full text of the source

High membrane permeability is likely necessary for protocell growth.

“High membrane permeability is likely to be necessary for protocell growth but is not a demanding physical requirement.”

• AssumptionRests on an assumption: Fatty acid-based membranes show high permeability to ions, including divalent cations, as well as to larger polar and charged molecules, such as nucleotides.

High membrane permeability can limit the ability of a protocell to evolve metabolic functions because metabolites synthesized within the protocell could leak out and be lost to the environment or captured by competing protocells.

“However, high permeability can also limit the ability of a protocell to evolve metabolic functions because any metabolites synthesized within the protocell could leak out and be lost to the environment or captured by competing protocells.”

• AssumptionRests on an assumption: Fatty acid-based membranes show high permeability to ions, including divalent cations, as well as to larger polar and charged molecules, such as nucleotides.

The most advanced form of the polymerase cannot replicate long RNA sequences because attempts to do so are thwarted by the emergence of shorter amplicons that are copied more efficiently.

“The most advanced form of the polymerase cannot replicate long RNA sequences because attempts to do so are thwarted by the emergence of shorter amplicons that are copied more efficiently.”

The class I polymerase was improved so that it can synthesize long RNA products, in some cases exceeding 100 nucleotides in length.

“the activity of the class I polymerase was greatly improved so that it can synthesize long RNA products, in some cases exceeding 100 nucleotides in length”

• cites Wochner et al. 2011 sourceNot checked — no full text of the source

RNA polymerase enzymes solve the problems of metal ion catalysis by binding and precisely positioning the metal ion for catalysis.

“RNA polymerase enzymes solve these problems by binding and precisely positioning the metal ion for catalysis (Zhang et al. 1999;Cramer et al. 2001;Robertson and Scott 2007;Shechner et al. 2009).”

• cites Zhang et al. 1999 sourceNot checked — no full text of the source
• cites Cramer et al. 2001 sourceNot checked — no full text of the source
• cites Robertson and Scott 2007 sourceNot checked — no full text of the source

• AssumptionRests on an assumption: Divalent metal cations are essential for efficient RNA copying.

A variant small subunit rRNA that lacks modifications can still be efficiently assembled into ribosomes.

“Ichihashi and colleagues were able to evolve a variant small subunit rRNA that lacks modifications and can still be efficiently assembled into ribosomes (Murase et al. 2018).”

• cites Murase et al. 2018Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.