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Ribozyme

A ribozyme is a ribonucleic acid (RNA) molecule or complex of RNA molecules that functions as a biological catalyst, accelerating specific chemical reactions in a manner analogous to protein-based enzymes.^[1] These catalytic RNAs were first identified in the early 1980s, fundamentally altering the central dogma of molecular biology by revealing that RNA could serve dual roles as both genetic information carrier and active biochemical agent.^[2] The breakthrough came independently from two researchers: In 1982, Thomas R. Cech demonstrated that the intervening sequence (intron) in the ribosomal RNA precursor of the ciliate protozoan Tetrahymena thermophila undergoes self-splicing, excising itself and ligating the flanking exons without requiring protein enzymes, thus establishing the first example of an RNA catalyst.^[3] Shortly thereafter, in 1983, Sidney Altman showed that the RNA subunit of ribonuclease P (RNase P), an enzyme essential for tRNA maturation in cells including Escherichia coli, performs the catalytic cleavage of precursor tRNAs independently of its protein components.^[4] For these discoveries, Cech and Altman were jointly awarded the 1989 Nobel Prize in Chemistry, recognizing the paradigm-shifting insight that RNA possesses enzymatic properties.^[2] Ribozymes encompass a diverse array of structures and functions, ranging from large, intricate molecules to small, compact motifs. Notable examples include the self-splicing group I and group II introns found in organelles and bacteria, which catalyze RNA splicing; the RNase P ribozyme, which processes tRNA precursors; and smaller self-cleaving ribozymes such as the hammerhead, discovered in 1986 within plant satellite RNAs like that of tobacco ringspot virus, and the hepatitis delta virus (HDV) ribozyme, identified in 1988, both of which facilitate precise phosphodiester bond cleavage.^[5] Additionally, the peptidyl transferase center of the ribosome, composed of ribosomal RNA (rRNA), acts as a ribozyme to catalyze peptide bond formation during protein synthesis, underscoring RNA's central role in translation.^[6] The existence of ribozymes provides strong evidence for the RNA world hypothesis, positing that RNA preceded DNA and proteins in early life evolution, serving as both genome and catalyst before the emergence of more efficient protein enzymes.^[7] Beyond fundamental biology, ribozymes have inspired biotechnological applications, including RNA-based therapeutics for gene silencing (e.g., via ribozyme-mediated cleavage of disease-causing RNAs) and tools for synthetic biology, such as in vitro-evolved ribozymes that perform ligation, polymerization, or metabolite sensing.^[8] Ongoing research continues to uncover novel ribozymes through bioinformatics and experimental selection, expanding our understanding of RNA's catalytic potential in diverse organisms and contexts.^[8]

Fundamentals and History

Definition and Properties

A ribozyme is a ribonucleic acid (RNA) molecule, or a molecule containing an RNA moiety, that functions as a biological catalyst by accelerating specific chemical reactions. Like protein enzymes, ribozymes lower the activation energy of these reactions without being altered or consumed in the process, thereby enabling efficient biochemical transformations in cells.^[9] Ribozymes exhibit several distinctive properties that underpin their catalytic capabilities. They typically bind substrates through sequence-specific base-pairing interactions, which provide high fidelity in recognition akin to Watson-Crick hybridization. The active site is formed by a conserved catalytic core comprising specific nucleotide motifs and secondary structures that position reactive groups for catalysis. Many ribozymes, particularly self-cleaving ones, demonstrate the ability to act on themselves, facilitating intramolecular reactions. Additionally, their activity often depends on divalent metal ions, such as Mg²⁺, which neutralize the negative charge of the RNA phosphate backbone to promote proper folding and directly participate in the reaction mechanism by coordinating substrates or activating nucleophiles.^[9]^[10]^[11] In kinetic terms, ribozymes share fundamental similarities with protein enzymes, displaying Michaelis-Menten behavior characterized by parameters such as the turnover number (k_cat) and the Michaelis constant (K_m), which reflect substrate affinity and catalytic efficiency. For instance, self-cleaving ribozymes can achieve rate enhancements of 10³ to 10⁶-fold over uncatalyzed phosphodiester bond cleavage rates, though this is generally less than the 10¹⁰ to 10¹⁵-fold accelerations typical of protein counterparts for analogous reactions. Thermodynamically, ribozyme function relies on the RNA folding into precise secondary (e.g., helices and loops) and tertiary structures to form the active conformation, a process stabilized by ionic interactions that screen electrostatic repulsions; optimal folding and activity are thus highly sensitive to salt concentration and cation type. First identified in the early 1980s, these properties highlight ribozymes' role as versatile catalysts in biological systems.^[9]^[10]^[12]^[13]

Discovery and Early Research

The discovery of ribozymes began in 1982 when Thomas Cech and his colleagues at the University of Colorado identified self-splicing introns in the ribosomal RNA precursor of the ciliate protozoan Tetrahymena thermophila. In their key experiments, Cech's team conducted in vitro transcription and splicing assays using purified pre-rRNA transcripts, demonstrating that the intervening sequence (IVS) RNA could excise itself and cyclize without requiring protein enzymes, indicating RNA autocatalysis. This finding was initially surprising, as the team had anticipated protein involvement in the splicing process, but fractionation studies revealed the RNA component alone was sufficient for the reaction under physiological conditions like monovalent and divalent cations.^[14] In 1983, Sidney Altman and collaborators at Yale University reported the catalytic role of the RNA subunit in ribonuclease P (RNase P), an enzyme essential for tRNA maturation in bacteria. Through fractionation and reconstitution experiments with Escherichia coli extracts, they isolated the RNA moiety (M1 RNA) and showed it could cleave precursor tRNA substrates in vitro when provided with magnesium ions, independent of the protein subunit, thus establishing it as the catalytic component. Altman's prior work in the 1970s had already suggested RNase P contained an RNA component, but these 1983 assays confirmed its enzymatic activity, paralleling Cech's observations.^[15] The groundbreaking revelations by Cech and Altman culminated in the 1989 Nobel Prize in Chemistry, awarded jointly for their discovery of catalytic properties in RNA.^[1] This recognition highlighted how ribozymes expanded the understanding of RNA's functional versatility, shifting the paradigm from viewing RNA solely as a passive messenger in the central dogma of molecular biology to recognizing it as an active biocatalyst capable of both storing genetic information and accelerating chemical reactions.^[1] Early research thus laid the foundation for exploring RNA's dual roles, influencing subsequent studies on its evolutionary and biochemical significance.^[16]

Biophysical Foundations

Structural Features

Ribozymes exhibit characteristic secondary structures primarily formed through Watson-Crick base pairing, resulting in double-helical stems, internal and terminal loops, and unpaired bulges that contribute to overall folding and stability. These elements create a scaffold where stems provide rigidity via A-form helices, while loops and bulges introduce flexibility and sites for tertiary interactions.^[17] For instance, in small self-cleaving ribozymes, secondary structures often consist of three helical domains connected at a central junction, as seen in the hammerhead ribozyme. Tertiary structures of ribozymes are stabilized by motifs that pack helices and single-stranded regions into compact architectures, including pseudoknots, coaxial helical stacking, and A-minor motifs.^[18] Pseudoknots arise when a single-stranded loop base-pairs with a distant complementary sequence, forming an additional helix that interlocks with existing stems, as observed in variants of the hammerhead ribozyme (PDB: 8YDC).^[19] Coaxial stacking aligns adjacent helices end-to-end for extended rigid domains, while A-minor interactions involve adenine bases inserting into the minor grooves of helices to mediate long-range contacts, exemplified in the P4-P6 domain of group I introns (PDB: 1GID).^[20] Crystal structures, such as that of the hatchet ribozyme (PDB: 6JQ6), reveal pseudosymmetric dimeric scaffolds with these motifs enabling tight packing essential for function.^[17] Divalent ions, particularly Mg²⁺, play a critical role in ribozyme tertiary folding and active site formation through coordination to phosphate backbones and nucleobases.^[21] In many ribozymes, Mg²⁺ ions occupy positions in the active site, often in a two-metal-ion mechanism where they neutralize negative charges and position substrates for catalysis, as detailed in structures of the hammerhead and group I introns.^[22] Environmental factors like pH and temperature influence stability; optimal folding typically occurs at neutral pH (around 7-8) and moderate temperatures (e.g., 37-50°C), where deviations can disrupt base pairing or ion binding, leading to misfolding.^[23] For example, elevated temperatures denature thermolabile small ribozymes, while low pH protonates key residues, impairing Mg²⁺ coordination. Structural diversity among ribozymes reflects their functional specialization, with small ribozymes (e.g., hammerhead, ~50 nucleotides) adopting compact, single-domain folds dominated by local interactions, whereas large ribozymes like group I introns (~400 nucleotides) feature modular architectures with multiple domains assembled via peripheral elements.^[24] This modularity in group I introns allows hierarchical folding, starting from conserved core helices and progressing to docking of peripheral domains (PDB: 1U6B).^[25] In contrast, the compact nature of small ribozymes enables rapid folding but limits complexity compared to the expansive, multi-subunit-like organization of larger ones.^[26]

Catalytic Mechanisms

Ribozymes accelerate chemical reactions through several general strategies that mimic enzymatic catalysis, primarily involving the manipulation of phosphate group transfers. These mechanisms rely on the RNA backbone and nucleobases to facilitate nucleophilic attacks and stabilize transition states, often in conjunction with divalent metal ions. General acid-base catalysis is achieved via nucleobases such as guanine or adenine, which donate or accept protons to activate nucleophiles or stabilize leaving groups; for instance, the N1 of guanine can act as a general acid by protonating the departing 5'-oxygen during phosphodiester bond cleavage.^[27]^[28] Metal ion-mediated Lewis acid catalysis further enhances reactivity, where ions like Mg²⁺ coordinate to non-bridging phosphate oxygens, neutralizing negative charges and polarizing the phosphorus center to promote bond breakage. Substrate positioning is another critical strategy, wherein RNA's tertiary structure orients reactive groups into optimal geometries, such as aligning a 2'-hydroxyl nucleophile for an inline attack on the adjacent phosphorus atom. The kinetics of ribozyme catalysis generally follow the Michaelis-Menten model, describing the rate of reaction as dependent on enzyme (ribozyme) and substrate concentrations:

v = \frac{k_{\text{cat}} [E][S]}{K_m + [S]}

where v is the initial velocity, k_{\text{cat}} is the turnover number, [E] and [S] are the concentrations of ribozyme and substrate, and K_m reflects substrate affinity. For natural ribozymes, typical k_{\text{cat}} values range from 1 to 100 min⁻¹, indicating moderate catalytic efficiency compared to uncatalyzed rates, with enhancements up to 10¹⁰-fold for phosphodiester cleavage. In activation mechanisms, such as phosphodiester bond cleavage, the 2'-OH group acts as a nucleophile in an S_N2-like inline attack on the phosphorus, forming a trigonal bipyramidal transition state that leads to a 2',3'-cyclic phosphate intermediate and a 5'-OH leaving group. Transition state stabilization occurs through electrostatic interactions, including hydrogen bonding from nearby nucleobases or metal ions that delocalize negative charge on the oxygens.^[27] Despite these capabilities, ribozyme catalysis exhibits limitations inherent to RNA's chemical composition, resulting in slower rates than protein enzymes. RNA possesses fewer diverse functional groups—primarily the 2'-OH, nucleobase nitrogens, and phosphate oxygens—limiting its ability to form extensive hydrogen bond networks or hydrophobic pockets for precise substrate discrimination and transition state binding.^[29] This constraint often necessitates reliance on metal ions for charge neutralization, and overall rate enhancements rarely exceed 10⁷-fold for small-molecule reactions, far below the 10¹²- to 10¹⁷-fold typical of proteins. Active site loops and helices provide the structural motifs that support these mechanisms by organizing catalytic residues.

Natural Roles

Biological Activities

Natural ribozymes catalyze a diverse array of chemical reactions critical to cellular physiology, with the predominant activities centered on phosphodiester bond cleavage and ligation, as well as peptide bond formation. Cleavage reactions typically involve site-specific hydrolysis of RNA backbones, enabling precise RNA fragmentation, while ligation facilitates the joining of RNA segments through phosphodiester bond formation. Peptide bond formation, a distinct non-phosphoryl transfer activity, underpins protein synthesis by linking amino acids. These reaction types highlight the versatility of RNA in mediating key biochemical transformations without protein involvement.^[8] In cellular contexts, ribozyme activities are integral to RNA processing, where cleavage and ligation support splicing and maturation to produce functional transcripts. During translation, the peptidyl transferase activity drives the elongation of polypeptide chains within the ribosome. In viroid replication, self-cleavage processes multimeric RNA forms generated by rolling-circle mechanisms, ensuring the production of mature infectious units. These roles underscore ribozymes' contributions to gene expression, protein production, and pathogen propagation.90170-5)^[30]^[31]^[32] The physiological efficiency of natural ribozymes in vivo frequently relies on cofactors such as GTP, which energizes certain ligation steps, or proteins that stabilize structures and enhance turnover rates. Many ribozymes exhibit multi-turnover kinetics, processing multiple substrates sequentially, as seen in tRNA maturation pathways, whereas others perform single-turnover reactions, such as intron self-excision, limiting them to one catalytic event per molecule. This cofactor dependence and kinetic variability optimize ribozyme function within complex cellular environments.^[8] Ribozymes demonstrate remarkable evolutionary conservation, occurring ubiquitously across all domains of life—including bacteria, archaea, and eukaryotes—which points to their primordial emergence and enduring functional importance.^[8]

Examples of Natural Ribozymes

Natural ribozymes encompass a diverse array of catalytic RNAs found across all domains of life, performing essential roles in RNA processing and regulation. Small self-cleaving ribozymes represent one major class, typically comprising compact structures of 50–200 nucleotides that catalyze site-specific phosphodiester bond cleavage to facilitate RNA maturation or replication. These include the hammerhead ribozyme, first identified in plant viroids and satellite RNAs, which adopts a three-way helical junction structure and enables the processing of multimeric transcripts during rolling-circle replication in eukaryotes such as plants, amphibians, and schistosomes.^[33] The hairpin ribozyme, occurring in satellite RNAs of plant viruses like tobacco ringspot virus, features a complex secondary structure with four helical domains and two internal loops, supporting self-cleavage to generate unit-length RNAs for viral propagation.^[33] Similarly, the VS ribozyme from the Varkud satellite RNA in Neurospora crassa mitochondria exhibits a multi-domain architecture with six helical segments, where it cleaves to resolve RNA dimers during mitochondrial RNA maintenance.^[33] The glmS ribozyme, linked to a riboswitch in Gram-positive bacteria like Bacillus subtilis, forms a double pseudoknot structure and is activated by glucosamine-6-phosphate to cleave the mRNA, thereby autoregulating the synthesis of this metabolite.^[33] Larger splicing ribozymes, often exceeding 200 nucleotides, mediate intron removal in precursor RNAs through more intricate folding patterns. Group I introns, exemplified by the Tetrahymena thermophila pre-rRNA intron, possess a conserved core with 10 helical domains and an internal guide sequence, enabling self-splicing that excises the intron and ligates exons in organellar genes across fungi, protists, plants, bacteria, and phages. Group II introns, prevalent in bacterial and organellar genomes such as those of yeast mitochondria, feature six domains including a lariat-forming branch point, and catalyze self-splicing to process pre-mRNAs, tRNAs, and rRNAs while also exhibiting mobility as retroelements. RNase P, a ubiquitous ribonucleoprotein complex, contains a catalytic RNA subunit (350–500 nucleotides in eukaryotes) with helical elements like P4 and P10–P12 that processes the 5' leader sequence from tRNA precursors, essential for tRNA maturation in all prokaryotes and eukaryotes. The ribosomal peptidyl transferase center, embedded within the 23S rRNA of the large ribosomal subunit, constitutes a universal ribozyme that catalyzes peptide bond formation during protein synthesis across all life forms. This A-site region, formed by conserved rRNA helices such as H80 and H89, positions aminoacyl- and peptidyl-tRNAs to drive the core transpeptidation reaction, underscoring RNA's ancient catalytic primacy in translation. Additional classes of natural ribozymes include the HDV ribozyme from hepatitis delta virus, a compact 85-nucleotide motif with a double pseudoknot that undergoes self-cleavage to process viral antigenomic RNAs during replication in human hepatocytes. More recently discovered via bioinformatics, the twister ribozyme features a four-stem pseudoknot structure in diverse bacteria, archaea, and eukaryotes, where it performs self-cleavage potentially to regulate mRNA stability or process non-coding RNAs, though its precise biological roles remain under investigation. Recent studies (as of 2024) have identified minimal twister sister-like ribozymes in the human genome and validated twister activity in mammalian species such as the bottlenose dolphin, further confirming their presence across eukaryotes.^[34] ^[35] ^[36] The twin ribozyme, identified in bacterial genomes, adopts a pseudoknotted fold with two active sites and catalyzes self-cleavage in intergenic regions, likely contributing to RNA turnover or regulatory circuits, with functions still being elucidated.^[37]

Evolutionary Importance

In the Origin of Life

The RNA world hypothesis posits that in the early stages of life's origin on Earth, RNA served as both the primary genetic material and the principal catalyst for biochemical reactions, predating the emergence of DNA and proteins. This concept suggests that self-replicating RNA molecules could have driven the initial Darwinian evolution by storing information and performing enzymatic functions, including replication. Evidence for this versatility comes from laboratory-evolved ribozymes capable of catalyzing RNA polymerization, demonstrating RNA's potential to replicate itself without protein assistance.^[38]^[39]^[40] Central to this hypothesis are self-replicating RNA systems that would enable the propagation of genetic variants through natural selection. Experiments by Jack Szostak's group have shown that ribozymes can catalyze the template-directed polymerization of RNA, producing longer strands from activated nucleotide monomers under conditions mimicking prebiotic environments, thus supporting the feasibility of RNA-based replication. These findings indicate that such systems could have initiated evolutionary processes by allowing RNA molecules to copy and mutate, leading to increasing complexity.^[41]^[42]^[43] Recent advances as of 2024-2025 have further bolstered the hypothesis. For instance, researchers at the Salk Institute developed an RNA polymerase ribozyme capable of evolving improved replication fidelity through directed evolution, addressing key barriers to sustained RNA replication. Additionally, studies have demonstrated RNA-catalyzed nucleotide synthesis and polymerization under prebiotic conditions, enhancing the plausibility of an RNA-based origin.^[44]^[45] The prebiotic plausibility of ribozymes hinges on their stability in primordial conditions, such as fluctuating temperatures and mineral-rich waters, where RNA's phosphodiester backbone could withstand hydrolysis to some extent when protected by adsorption to surfaces like clays. Ribozymes may also have played a role in metabolic origins by catalyzing the synthesis of cofactors, such as flavin mononucleotide, which are remnants of early RNA-dependent biochemistry and could have facilitated energy transfer in primitive networks. The discovery of natural ribozymes, like self-splicing introns, further bolsters this by exemplifying RNA's catalytic prowess in modern biology.^[46]^[47] Despite these advances, the RNA world faces significant challenges, including RNA's chemical fragility in prebiotic settings, where hydrolysis and UV radiation would degrade strands rapidly without protective mechanisms. The abiotic synthesis of RNA precursors remains a barrier, as forming nucleotides under plausible early Earth conditions is inefficient and requires specific catalysts not yet fully replicated in labs. Counterarguments favoring protein primacy suggest that peptides may have preceded RNA in enabling complex catalysis, highlighting ongoing debates about the sequence of molecular evolution.^[48]^[49]^[50]

In Sexual Reproduction

In Saccharomyces cerevisiae, group I introns play an indirect role in mating-type switching through their evolutionary contribution to the HO endonuclease gene, which is homologous to homing endonucleases encoded by these self-splicing ribozymes. The HO endonuclease initiates unidirectional switching by creating a double-strand break at the MAT locus, triggering gene conversion that copies genetic information from silent cassettes (HML or HMR) to replace the expressed mating-type allele, thereby enabling haploid cells to alternate between a and α types and complete the sexual cycle.^[51]^[52] The mechanisms involve ribozyme-mediated self-splicing of group I introns to express encoded endonucleases, such as VDE (also known as PI-SceI) in related fungal systems like Ascobolus immersus, where the ribozyme activity allows production of the protein that cleaves DNA at specific sites, promoting repair via homologous recombination and allele conversion during meiosis.^[52] This process facilitates precise genetic exchange at mating-type loci, ensuring compatibility and progression through sexual reproduction. Group I intron self-splicing, a core ribozyme function, briefly supports this by excising the intron without protein aid, using guanosine as a cofactor to join exons and release the endonuclease open reading frame.^[53] Broader implications include ribozyme mobility via homing endonuclease activity, which spreads introns unidirectionally during sexual reproduction, altering allele frequencies and contributing to reproductive isolation by favoring specific mating-type configurations across populations.^[54] This parasitic yet beneficial dynamic maintains genetic heterogeneity essential for fungal and protist sexual cycles.^[55]

Engineered Variants

Design and Selection Techniques

In vitro selection, often implemented through the Systematic Evolution of Ligands by EXponential enrichment (SELEX) method, enables the isolation of functional ribozymes from large libraries of random RNA sequences without prior structural knowledge. This process begins with the synthesis of a diverse pool of single-stranded RNA molecules, typically 40–100 nucleotides long, generated via combinatorial chemistry or enzymatic transcription from synthetic DNA templates. The library is then subjected to iterative rounds of selection, where RNAs are exposed to a target substrate or condition that favors catalytic activity, such as ligation or cleavage; active sequences are partitioned from inactive ones, reverse-transcribed to cDNA, amplified by PCR, and transcribed back to RNA for the next round, with stringency increased progressively to enrich for high-affinity variants.^[56]^[57] For aptazymes—ribozymes whose activity is modulated by ligand binding—SELEX variants incorporate ligand-dependent selection steps, yielding constructs like peptide-responsive ligases derived from small RNA scaffolds.^[58] Directed evolution builds on in vitro selection by introducing targeted mutagenesis to explore sequence space and enhance ribozyme performance, such as increasing catalytic rates or specificity. Starting from a lead ribozyme, random or site-directed mutations are introduced via error-prone PCR or chemical synthesis, creating variant libraries that undergo high-throughput screening or selection for improved function; for instance, iterative mutagenesis and selection have produced RNA ligase ribozymes with turnover rates exceeding 100 per hour under physiological conditions. This approach has been pivotal in engineering allosteric ribozymes, where effector molecules trigger conformational changes to activate catalysis, as demonstrated by variants of the hammerhead ribozyme selected for small-molecule responsiveness.^[59]^[60] Computational design complements experimental methods by predicting RNA structures and functions to guide the creation of novel ribozymes, reducing reliance on trial-and-error screening. Algorithms like those in the Rosetta software suite model RNA folding and tertiary interactions using fragment assembly and energy minimization, allowing de novo design of catalytic motifs or optimization of existing scaffolds for desired activities, such as nucleotide synthesis. For example, Rosetta-based protocols have enabled the fixed-backbone redesign of RNA sequences to stabilize active conformations, achieving predicted structures with root-mean-square deviations below 3 Å from experimental models in benchmark tests.^[61]^[62] Recent advances from 2020 to 2025 have integrated these techniques for more sophisticated ribozyme engineering, including autocatalytic systems that mimic primordial synthetases. One breakthrough involves an autocatalytic ribozyme that assembles a chimeric aminoacyl-RNA synthetase through fragment aminoacylation, loop-closing ligation, and self-reinforcing cycles, enabling sustained amino acid attachment to RNA substrates in vitro. Additionally, high-throughput platforms have facilitated the validation of novel hairpin ribozymes, identifying efficient self-cleaving motifs. These developments often start from natural scaffolds like the hammerhead ribozyme to accelerate optimization.^[63]^[64]

Applications and Recent Developments

Ribozymes have been engineered for gene therapy applications, particularly through hammerhead ribozymes designed to target and cleave specific mRNA transcripts, thereby silencing pathogenic genes. In efforts against HIV, intracellularly expressed single-chain hammerhead ribozymes have demonstrated robust suppression of viral replication by cleaving HIV-1 RNA, with active variants showing up to 90% inhibition in cell culture models. Similarly, trans-cleaving hammerhead ribozymes have been optimized for extracellular delivery to target cancer-related genes, such as those overexpressed in tumors, enabling precise mRNA degradation without intracellular entry requirements. For instance, enhanced hammerhead variants targeting rhodopsin mRNA have exhibited improved kinetic turnover rates, supporting their potential in treating genetic disorders like retinitis pigmentosa, which shares mechanisms with certain cancers. These trans-cleaving designs leverage the modularity of hammerhead ribozymes for conditional gene knockdown in therapeutic contexts. Allosteric ribozymes, inspired by natural metabolite-responsive elements like the glmS ribozyme, have been adapted as biosensors for detecting small molecules in diagnostics. The glmS ribozyme, which undergoes self-cleavage upon binding glucosamine-6-phosphate (GlcN6P), serves as a model for engineering sensors that amplify signals through isothermal assays, achieving colorimetric detection limits as low as 1 μM for GlcN6P. These allosteric constructs integrate with amplification strategies to enhance sensitivity, making them suitable for point-of-care diagnostics where rapid metabolite detection is critical. In synthetic biology, ribozymes facilitate RNA processing circuits that regulate gene expression within cells, such as split ribozyme systems that detect native RNAs and trigger orthogonal gene control. For example, ribozyme-enabled detection of RNA (RENDR) uses cellular transcripts to assemble split hammerhead ribozymes, linking RNA sensing to downstream synthetic outputs with high specificity in mammalian cells. Autocatalytic ribozyme systems have also been incorporated into protocell models to mimic primitive replication, where encapsulation in lipid vesicles supports studies on early life processes. Recent developments from 2020 to 2025 have expanded ribozyme applications through targeted engineering. Engineered hammerhead ribozymes directed against essential gene mRNAs in Escherichia coli have achieved significant growth inhibition, reducing bacterial proliferation by up to 70% and enhancing antibiotic efficacy like tetracycline when combined, marking the first successful targeting of vital prokaryotic transcripts.^[65] RNA-peptide coacervates have been shown to modulate ribozyme activity, with interactions inhibiting hammerhead cleavage rates by 2–3 orders of magnitude inside droplets compared to buffers, while peptide sequence variations tune catalysis for controlled synthetic environments.^[66] Metal-ion tuned structures, particularly Mg²⁺-optimized hammerhead ribozymes, select mechanically stable conformations that improve folding efficiency and catalytic persistence under physiological conditions. Additionally, high-throughput validation of novel hairpin ribozymes has expanded toolkits for RNA engineering.

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This was a very exciting demonstration that RNA could catalyze the chemistry of RNA replication. ... These are the central questions concerning the origin of life ...<|control11|><|separator|>
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Jan 27, 2020 · An RNA polymerase ribozyme was obtained by in vitro evolution that has an unprecedented level of activity in copying complex RNA templates.
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Oct 5, 2015 · We present a current view of the biochemistry of the origin of life, focusing on issues surrounding the emergence of an RNA World in which RNA dominated ...Missing: seminal | Show results with:seminal
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Feb 6, 2021 · But research on ribozymes and riboswitches suggests a potential role for nucleotide-derived cofactors in an RNA world. Ribozymes, that are ...
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Jul 13, 2012 · However, the following objections have been raised to the RNA world hypothesis: (i) RNA is too complex a molecule to have arisen prebiotically; ...
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The RNA world hypothesis: the worst theory of the early evolution of ...
Jul 13, 2012 · The RNA world hypothesis does not necessarily imply that RNA was the first replicating molecule to appear on the Earth (although a new paper by ...Missing: seminal | Show results with:seminal
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Nucleic acid instability challenges RNA world hypothesis
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The yeast mating-type switching endonuclease HO is a ...
In Saccharomyces cerevisiae, HO is the central gene in the mating-type switching process. It was one of the first yeast genes ever discovered, because haploid ...
[47]
Group I Introns and Inteins: Disparate Origins but Convergent ...
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Homing endonucleases from mobile group I introns - PubMed Central
In subsequent years, the YZ endonuclease was renamed the HO endonuclease, and found to belong to the LAGLIDADG protein family. ... group I intron in Chlamydomonas ...
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Evolution of the mating type gene pair and multiple sexes in ... - NIH
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Mar 3, 2014 · Homing endonucleases are highly specific DNA cleaving enzymes that are encoded within genomes of all forms of microbial life including phage and eukaryotic ...
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Inteins, introns, and homing endonucleases: recent revelations ...
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Principles of in vitro selection of ribozymes from random sequence ...
Apr 16, 2025 · In vitro selection selects functional RNA sequences, like ribozymes, from random libraries without prior knowledge of their function. This ...
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The in vitro selection world - ScienceDirect
Aug 15, 2016 · In vitro selection provides the ability to isolate molecules of desired properties and function from large pools (libraries) of random molecules.
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In vitro selection of ribozymes dependent on peptides for activity - NIH
A peptide-dependent ribozyme ligase (aptazyme ligase) has been selected from a random sequence population based on the small L1 ligase.
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Directed Evolution of an RNA Enzyme - Science
An in vitro evolution procedure was used to obtain RNA enzymes with a particular catalytic function.
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Directed evolution of an RNA enzyme - PubMed - NIH
Jul 31, 1992 · An in vitro evolution procedure was used to obtain RNA enzymes with a particular catalytic function.
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RNA-Redesign: a web server for fixed-backbone 3D design of ... - NIH
May 11, 2015 · In addition to outputting 3D models of designed sequences with the lowest Rosetta effective energy, RNA-Redesign also outputs a graphical ...
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[PDF] Modeling Complex RNA Tertiary Folds with Rosetta
Computational modeling of RNA structures is advancing rapidly, with recent developments improving prediction and design of both second- ary and tertiary ...
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Autocatalytic assembly of a chimeric aminoacyl-RNA synthetase ...
Apr 2, 2025 · Here we report an autocatalytic assembly pathway that generates a chimeric, amino acid–bridged aminoacyl-RNA synthetase ribozyme.
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High-throughput experimental validation of novel hairpin ribozymes
Jul 9, 2025 · Here, a high-throughput sequencing-based approach was used to evaluate the co-transcriptional self-cleavage activity of 855 different hairpin ...Missing: microfluidics | Show results with:microfluidics