Jack Szostak

Jack Szostak
Nobel Laureate
Howard Hughes Medical Institute | HHMI

About

453
Publications
67,489
Reads
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51,368
Citations
Citations since 2017
98 Research Items
14090 Citations
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201720182019202020212022202305001,0001,5002,0002,500
201720182019202020212022202305001,0001,5002,0002,500
201720182019202020212022202305001,0001,5002,0002,500
Introduction
Skills and Expertise

Publications

Publications (453)
Preprint
Full-text available
Nonenzymatic template-directed RNA primer extension with 2-aminoimidazole activated nucleotides begins with the generation of an imidazolium-bridged dinucleotide intermediate that binds to the template adjacent to the primer. Crystal structures have illuminated the overall conformation of the primer/template/bridged-dinucleotide complex, but critic...
Preprint
Full-text available
The virtual circular genome (VCG) model was proposed as a means of going beyond template copying to indefinite cycles of nonenzymatic RNA replication during the origin of life. In the VCG model the protocellular genome is a collection of short oligonucleotides that map to both strands of a virtual circular sequence. Replication is driven by templat...
Preprint
Full-text available
Semipermeable membranes are a key feature of all living organisms. While specialized membrane transporters in cells can import otherwise impermeable nutrients, the earliest cells would have lacked a mechanism to import nutrients rapidly under nutrient-rich circumstances. Using both experiments and simulations, we find that a process akin to passive...
Article
Full-text available
In all known genetic polymers, molecular recognition via hydrogen bonding between complementary subunits underpins their ability to encode and transmit information, to form sequence-defined duplexes, and to fold into catalytically active forms. Reversible covalent interactions between complementary subunits provide a different way to encode informa...
Article
Full-text available
Hybridization and strand displacement kinetics determine the evolution of the base paired configurations of mixtures of oligonucleotides over time. Although much attention has been focused on the thermodynamics of DNA and RNA base pairing in the scientific literature, much less work has been done on the time dependence of interactions involving mul...
Article
Full-text available
The first ribozymes are thought to have emerged at a time when RNA replication proceeded via nonenzymatic template copying processes. However, functional RNAs have stable folded structures, and such structures are much more difficult to copy than short unstructured RNAs. How can these conflicting requirements be reconciled? Also, how can the inhibi...
Article
Nonenzymatic RNA replication is thought to have been an essential step on the path to the emergence of the first ribozymes during the origin of life. However, current nonenzymatic RNA replication models are limited by the extent and fidelity of primer extension chemistry, and the difficulty of copying the strands of the product duplex. Here we disc...
Article
Full-text available
Significance The replication of RNA without the aid of evolved enzymes may have enabled the inheritance of useful molecular functions during the origin of life. Template-directed RNA copying is a posited step in RNA replication. Key steps on the path to copying of RNA templates have been studied in isolation, including chemical nucleotide activatio...
Article
Full-text available
Significance The emergence of a primordial ribosome from the RNA world would have required access to aminoacylated RNA substrates. The spontaneous generation of such substrates without enzymes is inefficient, and it remains unclear how they could be selected for in a prebiotic milieu. In our study, we identify a possible role for aminoacylated RNA...
Article
Full-text available
The identification of nonenzymatic pathways for nucleic acid replication is a key challenge in understanding the origin of life. We have previously shown that nonenzymatic RNA primer extension using 2-aminoimidazole (2AI) activated nucleotides occurs primarily through an imidazolium-bridged dinucleotide intermediate. The reactive nature and preorga...
Preprint
Full-text available
The identification of nonenzymatic pathways for nucleic acid replication is a key challenge in understanding the origin of life. We have previously shown that nonenzymatic RNA primer extension using 2-aminoimidazole (2AI) activated nucleotides occurs primarily through an imidazolium-bridged dinucleotide intermediate. The reactive nature and preorga...
Preprint
Aminoacylated tRNAs, which harbor a covalent linkage between amino acids and RNA, are a universally conserved feature of life. Because they are essential substrates for ribosomal translation, aminoacylated oligonucleotides must have been present in the RNA World prior to the evolution of the ribosome. One possibility we are exploring is that the am...
Preprint
Full-text available
Nonenzymatic template-directed RNA copying using chemically activated nucleotides is thought to have played a key role in the emergence of genetic information on the early Earth. A longstanding question concerns the number and nature of different environments that might have been necessary to enable all of the steps from nucleotide synthesis to RNA...
Article
The template-directed synthesis of RNA played an important role in the transition from prebiotic chemistry to the beginnings of RNA based life, but the mechanism of RNA copying chemistry is incompletely understood. We measured the kinetics of template copying with a set of primers with modified 3′-nucleotides and determined the crystal structures o...
Article
The template-directed synthesis of RNA played an important role in the transition from prebiotic chemistry to the beginnings of RNA based life, but the mechanism of RNA copying chemistry is incompletely understood. We measured the kinetics of template copying with a set of primers with modified 3′-nucleotides and determined the crystal structures o...
Article
Full-text available
Substitution of exocyclic oxygen with sulfur was shown to substantially influence the properties of RNA/DNA bases, which are crucial for prebiotic chemistry and photodynamic therapies. Upon UV irradiation, thionucleobases were shown to efficiently populate triplet excited states and can be involved in characteristic photochemistry or generation of...
Article
Full-text available
Nonenzymatic copying of RNA templates with activated nucleotides is a useful model for studying the emergence of heredity at the origin of life. Previous experiments with defined-sequence templates have pointed to the poor fidelity of primer extension as a major problem. Here we examine the origin of mismatches during primer extension on random tem...
Article
Full-text available
Recent advances in prebiotic chemistry are beginning to outline plausible pathways for the synthesis of the canonical ribonucleotides and their assembly into oligoribonucleotides. However, these reaction pathways suggest that many noncanonical nucleotides are likely to have been generated alongside the standard ribonucleotides. Thus, the oligomeriz...
Article
Full-text available
Advances in origins of life research and prebiotic chemistry suggest that life as we know it may have emerged from an earlier RNA World. However, it has been difficult to reconcile the conditions used in laboratory experiments with real-world geochemical environments that may have existed on the early Earth and hosted the origin(s) of life. This ch...
Article
Full-text available
Aminoacylated tRNAs are the substrates for ribosomal protein synthesis in all branches of life, implying an ancient origin for aminoacylation chemistry. In the 1970s, Orgel and colleagues reported potentially prebiotic routes to aminoacylated nucleotides and their RNA-templated condensation to form amino acid-bridged dinucleotides. However, it is u...
Article
Full-text available
UV light has been invoked as a source of energy for driving prebiotic chemistry, but such high energy photons are also known to cause damage to biomolecules and their precursors. One potential mechanism for increasing the lifetime of UV-photounstable molecules is to invoke a protection or shielding mechanism. UV shielding could either occur by the...
Preprint
Full-text available
Nonenzymatic copying of RNA templates with activated nucleotides is a useful model for studying the emergence of heredity at the origin of life. Previous experiments with defined-sequence templates have pointed to the poor fidelity of primer extension as a major problem. Here we examine the origin of mismatches during primer extension on random tem...
Article
Full-text available
The prebiotic synthesis of ribonucleotides is likely to have been accompanied by the synthesis of non-canonical nucleotides including the threo-nucleotide building blocks of TNA. Here, we examine the ability of activated threo-nucleotides to participate in nonenzymatic template-directed polymerization. We find that primer extension by multiple sequ...
Preprint
Aminoacylated tRNAs are the substrates for ribosomal protein synthesis in all branches of life, implying an ancient origin for aminoacylation chemistry. In the 1970s, Orgel and colleagues reported potentially prebiotic routes to aminoacylated nucleotides and their RNA templated condensation to form amino acid bridged dinucleotides. However, it is u...
Preprint
Full-text available
The prebiotic synthesis of ribonucleotides is likely to have been accompanied by the synthesis of noncanonical nucleotides including the threo-nucleotide building blocks of TNA. Here we examine the ability of activated threo-nucleotides to participate in nonenzymatic template-directed polymerization. We find that primer extension by multiple sequen...
Article
Genetic biopolymers utilize defined sequences and monomer-specific molecular recognition to store and transfer information. Synthetic polymers that mimic these attributes using reversible covalent chemistry for base-pairing pose unique synthetic challenges. Here, we describe a solid-phase synthesis methodology for the efficient construction of ethy...
Article
Full-text available
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...
Article
The RNA world hypothesis describes a scenario where early life forms relied on RNA to govern both inheritance and catalyze useful chemical reactions. Prior to the emergence of enzymes capable of replicating the RNA genome, a nonenzymatic replication process would have been necessary to initiate Darwinian Evolution. However, the one-pot nonenzymatic...
Preprint
Our manuscript describes a hypothesis for the replication of primordial RNA genomes by entirely nonenzymatic processes. Our proposal circumvents long standing problems such as the difficulty of copying long templates by nonenzymatic chemistry, the need for defined primers, and the so-called ‘last base addition problem’. Our hypothesis leads to surp...
Article
Full-text available
Our current understanding of the chemistry of the primordial genetic material is fragmentary at best. The chemical replication of oligonucleotides long enough to perform catalytic functions is particularly problematic because of the low efficiency of nonenzymatic template copying. Here we show that this problem can be circumvented by assembling a f...
Article
Full-text available
The nonenzymatic replication of ribonucleic acid (RNA) may have enabled the propagation of genetic information during the origin of life. RNA copying can be initiated in the laboratory with chemically activated nucleotides, but continued copying requires a source of chemical energy for in situ nucleotide activation. Recent work has illuminated a po...
Article
The desire to create cell-like models for fundamental science and applications has spurred extensive effort towards creating giant unilamellar vesicles (GUVs). However, a route to selectively self-assemble GUVs in bulk has remained elusive. In bulk solution, membrane-forming molecules such as phospholipids, single-tailed surfactants, and block copo...
Article
Full-text available
Non‐enzymatic RNA Copying: Enhanced non‐enzymatic ligation allows the rapid copying of long RNA template and short RNA splinted templates, thus suggesting a potential route to the assembly of artificial systems capable of evolution. Abstract The non‐enzymatic replication of the primordial genetic material is thought to have enabled the evolution o...
Article
Full-text available
The non‐enzymatic replication of the primordial genetic material is thought to have enabled the evolution of early forms of RNA‐based life. However, the replication of oligonucleotides long enough to encode catalytic functions is problematic due to the low efficiency of template copying with mononucleotides. Here we show that template‐directed liga...
Article
Full-text available
Life emerging in an RNA world is expected to propagate RNA as hereditary information, requiring some form of primitive replication without enzymes. Non-enzymatic template-directed RNA primer extension is a model of the copying step in this posited form of replication. The sequence space accessed by primer extension dictates potential pathways to se...
Preprint
Full-text available
The nonenzymatic replication of ribonucleic acid (RNA) oligonucleotides may have enabled the propagation of genetic in-formation during the origin of life. RNA copying can be initiated in the laboratory with chemically activated nucleotides, but continued copying requires a source of chemical energy for in situ nucleotide activation. Recent work ha...
Article
Full-text available
Many proteins that are needed for progression through S-phase are produced from transcripts that peak in the S-phase, linking temporal expression of those proteins to the time that they are required in cell cycle. Here, we explore the potential roles of long non-coding RNAs in cell cycle progression. We use a sensitive click-chemistry approach to i...
Article
Full-text available
A previously proposed synthesis of pyrimidine ribonucleotides makes use of ultraviolet (UV) light to convert β-d-ribocytidine-2',3'-cyclic phosphate to β-d-ribouridine-2',3'-cyclic phosphate, while simultaneously selectively degrading synthetic byproducts. Past studies of the photochemical reactions of pyrimidines have employed mercury arc lamps, c...
Article
Full-text available
All known polymerases copy genetic material by catalyzing phosphodiester bond formation. This highly conserved activity proceeds by a common mechanism, such that incorporated nucleoside analogs terminate chain elongation if the resulting primer strand lacks a terminal hydroxyl group. Even conservatively substituted 3′-amino nucleotides generally ac...
Preprint
The desire to create cell-like models for fundamental science and applications has spurred extensive effort towards creating giant unilamellar vesicles (GUVs). However, membrane-forming molecules such as phospholipids, single-tailed surfactants, and block copolymers typically self-assemble into multilamellar, onion-like structures. So although self...
Article
Full-text available
Significance Current models for the origin of life include an earlier period when prebiotic chemistry dictated the nonenzymatic copying of RNA polymers, followed by a period of ribozyme-catalyzed reactions using nucleoside-5′-triphosphate (NTP) substrates. Our study addresses the transition from nonenzymatic to ribozyme-catalyzed RNA template copyi...
Preprint
Full-text available
Advances in origins of life research and prebiotic chemistry suggest that life as we know it may have emerged from an earlier RNA World. However, it has been difficult to reconcile the conditions used in laboratory experiments with real-world geochemical environments that may have existed on the early Earth and hosted the origin(s) of life. This ch...
Preprint
Full-text available
Life emerging in an RNA world is expected to propagate RNA as hereditary information, requiring some form of primitive replication without enzymes. Nonenzymatic template-directed RNA primer extension is a model of the polymerisation step in this posited form of replication. The sequence space accessed by primer extension dictates potential pathways...
Preprint
Full-text available
The bacteria Kocuria rhizophila inhibits surveillance of translation toxins by Caenorhabditis elegans . Genetic analysis of Kocuria rhizophila identified a C50 carotenoid that mediates this inhibition of C. elegans defense pathways. Carotenoid extracts restore this anti-immunity activity to carotenoid mutants. Corynebacterium glutamicum inhibits C....
Article
The abiotic synthesis of ribonucleotides is thought to have been an essential step towards the emergence of the RNA world. However, it is likely that the prebiotic synthesis of ribonucleotides was accompanied by the simultaneous synthesis of arabinonucleotides, 2′-deoxyribonucleotides, and other variations on the canonical nucleotides. In order to...
Article
Full-text available
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 displaceme...
Article
Achieving multiple cycles of RNA replication within a model protocell would be a critical step towards demonstrating a path from prebiotic chemistry to cellular biology. Any model for early life based on an ‘RNA world’ must account for RNA strand cleavage and hydrolysis, which would degrade primitive genetic information and lead to an accumulation...
Preprint
The abiotic synthesis of ribonucleotides is thought to have been an essential step towards the emergence of the RNA world. However, it is likely that the prebiotic synthesis of ribonucleotides was accompanied by the simultaneous synthesis of arabinonucleotides, 2'-deoxyribonucleotides, and other variations on the canonical nucleotides. In order to...
Preprint
Non-enzymatic RNA self-replication is integral to the 'RNA World' hypothesis. Despite considerable progress in non-enzymatic template copying, true replication remains challenging due to the difficulty of separating the strands of the product duplex. Here, we report a prebiotically plausible solution to this problem in which short invader oligonucl...
Article
Full-text available
Genetic polymers that could plausibly govern life in the universe might inhabit a broad swath of chemical space. A subset of these genetic systems can exchange information with RNA and DNA and could therefore form the basis for model protocells in the laboratory. N3'→P5' phosphoramidate (NP) DNA is defined by a conservative linkage substitution and...
Preprint
Achieving multiple cycles of RNA replication within a model protocell would be a critical step towards demonstrating a path from prebiotic chemistry to cellular biology. Any model for early life based on an 'RNA world' must account for RNA strand cleavage and hydrolysis, which would degrade primitive genetic information and lead to an accumulation...
Preprint
The non-enzymatic replication of the primordial genetic material is thought to have enabled the evolution of the first ribozymes, leading to early forms of RNA-based life. However, the reported rate of chemical RNA ligation is extremely slow. Here we show that the rate of ligation can be greatly enhanced by employing a 3ʹ-amino group at the 3ʹ-end...
Article
Primitive life must have possessed the essential features of modern cellular life, but without highly evolved proteins to perform dynamic functions such as nutrient transport and membrane remodeling. Here, we consider the membrane properties of protocells — minimal cells with hereditary material, capable of growth and division — and how these prope...
Article
Efforts to develop self-replicating nucleic acids have led to insights into the origin of life, and have also suggested potential pathways to the design of artificial life forms based on non-natural nucleic acids. The template-directed nonenzymatic polymerization of activated ribonucleotide monomers is generally slow because of the relatively weak...
Article
Efficiently copying mixed-sequence oligonucleotide templates nonenzymatically is a long-standing problem both with re-spect to the origin of life, and with regard to bottom up efforts to synthesize artificial living systems. Here we report an effi-cient and sequence-general nonenzymatic process in which RNA templates direct the synthesis of a compl...
Article
The ability of the biopolymers RNA and DNA to store and transfer information is essential to life. Herein, we demonstrate template-directed replication in a set of dimer duplexes that use reversible covalent bonds to form base pairing interactions. Binary sequence information was encoded as a sequence of aniline and benzaldehyde subunits linked tog...
Article
The emergence of a chemical pathway for the replication of RNA oligonucleotides was a critical step in the origin of life. An important laboratory model for the study of nonenzymatic template copying, which would be a key part of any such pathway, involves the reaction of ribonucleoside‐5′‐phosphorimidazolides with an RNA primer/template complex. T...
Article
The emergence of a chemical pathway for the replication of RNA oligonucleotides was a critical step in the origin of life. An important laboratory model for the study of nonenzymatic template copying, which would be a key part of any such pathway, involves the reaction of ribonucleoside‐5′‐phosphorimidazolides with an RNA primer/template complex. T...
Article
Full-text available
Three 2-aminoazoles important for prebiotic chemistry undergo UV-driven photodegradation on timescales of 7–100 hours under solar irradiation.
Article
Before the advent of polymerase enzymes, the copying of genetic material during the origin of life may have involved the nonenzymatic polymerization of RNA monomers that are more reactive than the biological nucleoside triphosphates. Activated RNA monomers such as nucleotide-5′-phosphoro-2-aminoimidazolides spontaneously form an imidazolium-bridged...
Article
Full-text available
Significance The RNA world hypothesis assumes the abiotic synthesis of nucleotides, as well as their participation in nonenzymatic RNA replication. Whereas prebiotic syntheses of the canonical purine nucleotides remain inefficient, a prebiotically plausible route to the 8-oxo-purines has been reported. Although these noncanonical purine nucleotides...
Article
Full-text available
The study of nonenzymatic template-directed RNA copying is the experimental basis for the search for chemistry and reaction conditions consistent with prebiotic RNA replication. The most effective model systems for RNA copying have so far required a high concentration of Mg2+. Recently, Fe2+, which was abundant on the prebiotic anoxic Earth was sho...
Article
The general notion of an "RNA world" is that, in the early development of life on the Earth, genetic continuity was assured by the replication of RNA, and RNA molecules were the chief agents of catalytic function. Assuming that all of the components of RNA were available in some prebiotic locale, these components could have assembled into activated...
Article
Non‐enzymatic RNA replication may have been one of the processes involved in the appearance of life on Earth. Attempts to recreate this process in a laboratory setting have not been successful thus far, highlighting a critical need for finding prebiotic conditions that increase the rate and the yield. Here, we present a highly parallel assay for te...
Article
Non‐enzymatic RNA replication may have been one of the processes involved in the appearance of life on Earth. Attempts to recreate this process in a laboratory setting have not been successful thus far, highlighting a critical need for finding prebiotic conditions that increase the rate and the yield. Here, we present a highly parallel assay for te...
Article
tRNAs are subject to numerous modifications, including methylation. Mutations in the human N7-methylguanosine (m7G) methyltransferase complex METTL1/WDR4 cause primordial dwarfism and brain malformation, yet the molecular and cellular function in mammals is not well understood. We developed m7G methylated tRNA immunoprecipitation sequencing (MeRIP-...
Data
Table S1: Data collection statistics. Table S2: Structure refinement statistics.
Article
The chemical replication of RNA inside fatty acid vesicles is a plausible step in the emergence of cellular life. On the primitive earth, simple protocells with the ability to import nucleotides and short oligomers from their environment could potentially have replicated and retained larger genomic RNA oligonucleotides within a spatially defined co...
Preprint
Full-text available
The importance of genome replication has inspired detailed crystallographic studies of enzymatic DNA/RNA polymerization. In contrast, the mechanism of nonenzymatic polymerization is less well understood, despite its critical role in the origin of life. Here we report the direct observation of nonenzymatic RNA primer extension through time-resolved...
Article
Full-text available
Liposomes containing single-chain amphiphiles, particularly fatty acids, exhibit distinct properties compared to those containing diacylphospholipids due to the unique chemical properties of these amphiphiles. In particular, fatty acid liposomes enhance dynamic character, due to the relatively high solubility of single-chain amphiphiles. Similarly,...
Article
Nonenzymatic RNA primer extension by activated mononucleotides has long served as a model for the study of prebiotic RNA copying. We have recently shown that the rate of primer extension is greatly enhanced by the formation of an imid-azolium-bridged dinucleotide between the incoming monomer and a second, downstream activated monomer. However, the...
Article
Full-text available
Simple sugars necessary for the synthesis of prebiotic molecules can be generated from UV-driven cyanocuprate photoprocessing under conditions consistent with those expected on the surface of the early Earth.
Article
We report the synthesis of guanosine 5′-(4-methylimidazolyl)-phosphonate (ICG), the third member of a series of nonhydrolyzable nucleoside 5′-phosphoro-2-methylimidazolide (2-MeImpN) analogues designed for mechanistic studies of nonenzymatic RNA primer extension. The addition of a 2-MeImpN monomer to a primer is catalyzed by the presence of a downs...