Design and optimization of effector-activated ribozyme ligases

Breaking up is easy to do (if you're a DNA enzyme that cleaves RNA)

In this issue of Chemistry & Biology, Cruz et al. use in vitro selection to select deoxyribozymes that collectively cleave almost any RNA dinucleotide junction. More remarkable is the finding that the new enzymes are related to the 8-17 deoxyribozyme that cleaves AG dinucleotide junctions.

Sensing complex regulatory networks by conformationally controlled hairpin ribozymes

The hairpin ribozyme catalyses RNA cleavage by a mechanism utilizing its conformational flexibility during the docking of two independently folded internal loop domains A and B. Based on this mechanism, we designed hairpin ribozyme variants that can be induced or repressed by external effector oligonucleotides influencing the docking process. We incorporated a third domain C to assimilate alternate stable RNA motifs such as a pseudo-half-knot or an internal stem-loop structure. Small sequence changes in domain C allowed targeted switching of ribozyme activity: the same effector oligonucleotide can either serve as an inducer or repressor. The ribozymes were applied to trp leader mRNA, the RNA sequence tightly bound by l-tryptophan-activated trp-RNA-binding attenuation protein (TRAP). When domain C is complementary to this mRNA, ribozyme activity can be altered by annealing trp leader mRNA, then specifically reverted by its TRAP/tryptophan-mediated sequestration. This approach allows to precisely sense the activity status of a protein controlled by its metabolite molecule.

A three-fluorophore FRET assay for high-throughput screening of small-molecule inhibitors of ribosome assembly

In one of the first steps of prokaryotic ribosome assembly, the ribosomal protein S15 binds to a three-way junction in the central domain of the 16S rRNA. Binding causes a conformational change that is required for subsequent binding events. Using a novel fluorescence resonance energy transfer assay with three fluorophores, two on the RNA and one on the S15 protein, small-molecule libraries can be screened for potential inhibitors of this initial step in ribosome assembly. The employment of three fluorophores allows both the conformational change of the RNA and the binding of S15 to be monitored in a single assay.

A novel strategy for selection of allosteric ribozymes yields RiboReporter sensors for caffeine and aspartame

We have utilized in vitro selection technology to develop allosteric ribozyme sensors that are specific for the small molecule analytes caffeine or aspartame. Caffeine- or aspartame-responsive ribozymes were converted into fluorescence-based RiboReporter trade mark sensor systems that were able to detect caffeine or aspartame in solution over a concentration range from 0.5 to 5 mM. With read-times as short as 5 min, these caffeine- or aspartame-dependent ribozymes function as highly specific and facile molecular sensors. Interestingly, successful isolation of allosteric ribozymes for the analytes described here was enabled by a novel selection strategy that incorporated elements of both modular design and activity-based selection methods typically used for generation of catalytic nucleic acids.

Zeptomole detection of a viral nucleic acid using a target-activated ribozyme

We describe a strategy for the ultra-sensitive detection of nucleic acids using "half" ribozymes that are devoid of catalytic activity unless completed by a trans-acting target nucleic acid. The half-ribozyme concept was initially demonstrated using a construct derived from a multiple turnover Class I ligase. Iterative RNA selection was carried out to evolve this half-ribozyme into one activated by a conserved sequence present in the hepatitis C virus (HCV) genome. Following sequence optimization of substrate RNAs, this HCV-activated half-ribozyme displayed a maximal turnover rate of 69 min(-1) (pH 8.3) and was induced in rate by approximately 2.6 x 10(9)-fold by the HCV target. It detected the HCV target oligonucleotide in the zeptomole range (6700 molecules), a sensitivity of detection roughly 2.6 x 10(6)-fold greater than that previously demonstrated by oligonucleotide-activated ribozymes, and one that is sufficient for molecular diagnostic applications.

Engineered catalytic RNA and DNA : new biochemical tools for drug discovery and design

Since the fundamental discovery that RNA catalyzes critical biological reactions, the conceptual and practical utility of nucleic acid catalysts as molecular therapeutic and diagnostic agents continually develops. RNA and DNA catalysts are particularly attractive tools for drug discovery and design due to their relative ease of synthesis and tractable rational design features. Such catalysts can intervene in cellular or viral gene expression by effectively destroying virtually any target RNA, repairing messenger RNAs derived from mutant genes, or directly disrupting target genes. Consequently, catalytic nucleic acids are apt tools for dissecting gene function and for effecting gene pharmacogenomic strategies. It is in this capacity that RNA and DNA catalysts have been most widely utilized to affect gene expression of medically relevant targets associated with various disease states, where a number of such catalysts are presently being evaluated in clinical trials. Additionally, biotechnological prospects for catalytic nucleic acids are seemingly unlimited. Controllable nucleic acid catalysts, termed allosteric ribozymes or deoxyribozymes, form the basis of effector or ligand-dependent molecular switches and sensors. Allosteric nucleic acid catalysts promise to be useful tools for detecting and scrutinizing the function of specified components of the metabolome, proteome, transcriptome, and genome. The remarkable versatility of nucleic acid catalysis is thus the fountainhead for wide-ranging applications of ribozymes and deoxyribozymes in biomedical and biotechnological research.

Primordial genetics: phenotype of the ribocyte

The idea that the ancestors of modern cells were RNA cells (ribocytes) can be investigated by asking whether all essential cellular functions might be performed by RNAs. This requires isolating suitable molecules by selection-amplification when the predicted molecules are presently extinct. In fact, RNAs with many properties required during a period in which RNA was the major macromolecular agent in cells (an RNA world) have been selected in modern experiments. There is, accordingly, reason to inquire how such a ribocyte might appear, based on the properties of the RNAs that composed it. Combining the intrinsic qualities of RNA with the fundamental characteristics of selection from randomized sequence pools, one predicts ribocytes with a cell cycle measured (roughly) in weeks. Such cells likely had a rapidly varying genome, composed of many small genetic and catalytic elements made of tens of ribonucleotides. There are substantial arguments that, at the mid-RNA era, a subset of these nucleotides are reproducibly available and resemble the modern four. Such cells are predicted to evolve rapidly. Instead of modifying preexisting genes, ribocytes frequently draw new functions from an internal pool containing zeptomoles (<1 attomole) of predominantly inactive random sequences.

Exponential growth by cross-catalytic cleavage of deoxyribozymogens

We have designed an autocatalytic cycle based on the highly efficient 10-23 RNA-cleaving deoxyribozyme that is capable of exponential amplification of catalysis. In this system, complementary 10-23 variants were inactivated by circularization, creating deoxyribozymogens. Upon linearization, the enzymes can act on their complements, creating a cascade in which linearized species accumulate exponentially. Seeding the system with a pool of linear catalysts resulted not only in amplification of function but in sequence selection and represents an in vitro selection experiment conducted in the absence of any protein enzymes.

New highly sensitive and selective catalytic DNA biosensors for metal ions

While remarkable progress has been made in developing sensors for metal ions such as Ca(II) and Zn(II), designing and synthesizing sensitive and selective metal ion sensors remains a significant challenge. Perhaps the biggest challenge is the design and synthesis of a sensor capable of specific and strong metal binding. Since our knowledge about the construction of metal-binding sites in general is limited, searching for sensors in a combinatorial way is of significant value. Therefore, we have been able to use a combinatorial method called in vitro selection to obtain catalytic DNA that can bind a metal ion of choice strongly and specifically. The metal ion selectivity of the catalytic DNA was further improved using a 'negative selection' strategy where catalytic DNA that are selective for competing metal ions are discarded in the in vitro selection processes. By labeling the resulting catalytic DNA with a fluorophore/quencher pair, we have made a new class of metal ion fluorescent sensors that are the first examples of catalytic DNA biosensors for metal ions. The sensors combine the high selectivity of catalytic DNA with the high sensitivity of fluorescent detection, and can be applied to the quantitative detection of metal ions over a wide concentration range and with high selectivity. The use of DNA sensors in detection and quantification of lead ions in environmental samples such as water from Lake Michigan has been demonstrated. DNA is stable, cost-effective, environmentally benign, and easily adaptable to optical fiber and microarray technology for device manufacture. Thus, the DNA sensors explained here hold great promise for on-site and real-time monitoring of metal ions in the fields of environmental monitoring, developmental biology, clinical toxicology, wastewater treatment, and industrial process monitoring.

Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made from RNA

Switches and sensors play important roles in our everyday lives. The chemical properties of RNA make it amenable for use as a switch or sensor, both artificially and in nature. This review focuses on recent advances in artificial RNA switches and sensors. Researchers have been applying classical biochemical principles such as allostery in elegant ways that are influencing the development of biosensors and other applications. Particular attention is given here to allosteric ribozymes (aptazymes) that are regulated by small organic molecules, by proteins, or by oligonucleotides. Also discussed are ribozymes whose activities are controlled by various nonallosteric strategies.

Ribozymes: recent advances in the development of RNA tools

The discovery 20 years ago that some RNA molecules, called ribozymes, are able to catalyze chemical reactions was a breakthrough in biology. Over the last two decades numerous natural RNA motifs endowed with catalytic activity have been described. They all fit within a few well-defined types that respond to a specific RNA structure. The prototype catalytic domain of each one has been engineered to generate trans-acting ribozymes that catalyze the site-specific cleavage of other RNA molecules. On the 20th anniversary of ribozyme discovery we briefly summarize the main features of the different natural catalytic RNAs. We also describe progress towards developing strategies to ensure an efficient ribozyme-based technology, dedicating special attention to the ones aimed to achieve a new generation of therapeutic agents.

Simultaneous detection of diverse analytes with an aptazyme ligase array

Allosteric ribozymes (aptazymes) can transduce the noncovalent recognition of analytes into the catalytic generation of readily observable signals. Aptazymes are easily engineered, can detect diverse classes of biologically relevant molecules, and have high signal-to-noise ratios. These features make aptazymes useful candidates for incorporation into biosensor arrays. Allosteric ribozyme ligases that can recognize a variety of analytes ranging from small organics to proteins have been generated. Upon incorporation into an array format, multiple different aptazyme ligases were able to simultaneously detect their cognate analytes with high specificity. Analyte concentrations could be accurately measured into the nanomolar range. The fact that analytes induced the formation of new covalent bonds in aptazyme ligases (as opposed to noncovalent bonds in antibodies) potentiated stringent washing of the array, leading to improved signal-to-noise ratios and limits of detection.

In search of an RNA replicase ribozyme

The theory that an RNA world played a pivotal role in life's evolutionary past has prompted investigations into the scope of RNA catalysis. These efforts have attempted to demonstrate the plausibility of an RNA-based genetic system, which would require RNA molecules that catalyze their own replication. The mechanistic features of modern protein polymerases have been used to guide the laboratory evolution of catalytic RNAs (ribozymes) that exhibit polymerase-like activity. Ribozymes have been developed that recognize a primer-template complex in a general way and catalyze the template-directed polymerization of mononucleotides. These experiments demonstrate that RNA replicase behavior is likely within the catalytic repertoire of RNA, although many obstacles remain to be overcome in order to demonstrate that RNA can catalyze its own replication in a manner that could have sustained a genetic system on the early Earth.

Group I aptazymes as genetic regulatory switches

BACKGROUND

Allosteric ribozymes (aptazymes) that have extraordinary activation parameters have been generated in vitro by design and selection. For example, hammerhead and ligase ribozymes that are activated by small organic effectors and protein effectors have been selected from random sequence pools appended to extant ribozymes. Many ribozymes, especially self-splicing introns, are known control gene regulation or viral replication in vivo. We attempted to generate Group I self-splicing introns that were activated by a small organic effector, theophylline, and to show that such Group I aptazymes could mediate theophylline-dependent splicing in vivo.

RESULTS

By appending aptamers to the Group I self-splicing intron, we have generated a Group I aptazyme whose in vivo splicing is controlled by exogenously added small molecules. Substantial differences in gene regulation could be observed with compounds that differed by as little as a single methyl group. The effector-specificity of the Group I aptazyme could be rationally engineered for new effector molecules.

CONCLUSION

Group I aptazymes may find applications as genetic regulatory switches for generating conditional knockouts at the level of mRNA or for developing economically viable gene therapies.

A biosensor for theophylline based on fluorescence detection of ligand-induced hammerhead ribozyme cleavage

Recently, Breaker and coworkers engineered hammerhead ribozymes that rearrange from a catalytically inactive to an active conformation upon allosteric binding of a specific ligand. To monitor cleavage activity in real time, we have coupled a donor-acceptor fluorophore pair to the termini of the substrate RNA of such a hammerhead ribozyme, modified to cleave in trans in the presence of the bronchodilator theophylline. In the intact substrate, the fluorophores interact by fluorescence resonance energy transfer (FRET). The specific FRET signal breaks down as the effector ligand binds, the substrate is cleaved, and the products dissociate, with a rate constant dependent on the concentration of the ligand. Our biosensor cleaves substrate at 0.46 min(-1) in 1 mM theophylline and 0.04 min(-1) without effector, and discriminates against caffeine, a structural relative of theophylline. We have measured the theophylline-dependence profile of this biosensor, showing that concentrations as low as 1 microM can be distinguished from background. To probe the mechanism of allosteric regulation, a single nucleotide in the communication domain between the catalytic and ligand-binding domains was mutated to destabilize the inactive conformation of the ribozyme. As predicted, this mutant shows the same activity (0.3 min(-1)) in the presence and absence of theophylline. Additionally, time-resolved FRET measurements on the biosensor ribozyme in complex with a noncleavable substrate analog reveal no significant changes in fluorophore distance distribution upon binding of effector.

Monitoring post-translational modification of proteins with allosteric ribozymes

An allosteric hammerhead ribozyme activated specifically by the unphosphorylated form of the protein kinase ERK2 was created through a rational design strategy that relies on molecular recognition of ERK2 to decrease the formation of an alternate, inactive ribozyme conformer. Neither closely related mitogen-activated protein kinases (MAPKs) nor the phosphorylated form of ERK2 induced ribozyme activity. The ribozyme quantitatively detected ERK2 added to mammalian cell lysates and also functioned quantitatively in a multiplexed solution-phase assay. This same strategy was used to construct a second ribozyme selectively activated by the phosphorylated (active) form of ERK2. This approach is generally applicable to the development of ribozymes capable of monitoring post-translational modification of specific proteins.

Controlling protein activity with ligand-regulated RNA aptamers

Controlling the activity of a protein is necessary for defining its function in vivo. RNA aptamers are capable of inhibiting proteins with high affinity and specificity, but this effect is not readily reversible. We describe a general method for discovering aptamers that bind and inhibit their target protein, but addition of a specific small molecule disrupts the protein-RNA complex. A SELEX protocol was used to raise RNA aptamers to the DNA repair enzyme, formamidopyrimidine glycosylase (Fpg), and neomycin was employed in each round to dissociate Fpg-bound RNAs. We identified an RNA molecule able to completely inhibit Fpg at 100 nM concentration. Importantly, Fpg activity is recovered by the addition of neomycin. We envision these ligand-regulated aptamers (LIRAs) as valuable tools in the study of biological phenomena in which the timing of molecular events is critical.

A ribozyme that ligates RNA to protein

We have used a combination of in vitro selection and rational design to generate ribozymes that form a stable phosphoamide bond between the 5' terminus of an RNA and a specific polypeptide. This reaction differs from that of previously identified ribozymes, although the product is analogous to the enzyme-nucleotidyl intermediates isolated during the reactions of certain proteinaceous enzymes, such as guanyltransferase, DNA ligase, and RNA ligase. Comparative sequence analysis of the isolated ribozymes revealed that they share a compact secondary structure containing six stems arranged in a four-helix junction and branched pseudoknot. An optimized version of the ribozyme reacts with substrate-fusion proteins, allowing it to be used to attach RNA tags to proteins both in vitro and within bacterial cells, suggesting a simple way to tag a specific protein with amplifiable information.

Protein-dependent ribozymes report molecular interactions in real time

Most approaches to monitoring interactions between biological macromolecules require large amounts of material, rely upon the covalent modification of an interaction partner, or are not amenable to real-time detection. We have developed a generalizable assay system based on interactions between proteins and reporter ribozymes. The assay can be configured in a modular fashion to monitor the presence and concentration of a protein or of molecules that modulate protein function. We report two applications of the assay: screening for a small molecule that disrupts protein binding to its nucleic acid target and screening for protein protein interactions. We screened a structurally diverse library of antibiotics for small molecules that modulate the activity of HIV-1 Rev-responsive ribozymes by binding to Rev. We identified an inhibitor that subsequently inhibited HIV-1 replication in cells. A simple format switch allowed reliable monitoring of domain-specific interactions between the blood-clotting factor thrombin and its protein partners. The rapid identification of interactions between proteins or of compounds that disrupt such interactions should have substantial utility for the drug-discovery process.

Structural characterization of a 2'F-RNA aptamer that binds a HIV-1 SU glycoprotein, gp120

Here we describe the isolation of specific 2'F-substituted RNA ligands for the SU glycoprotein, gp120, of HIV-1 strain HXB2. These aptamers bind the target protein with an affinity of the order of 10(-7) M. Binding was specific to SU glycoprotein and directed to a non-neutralizing epitope that was not shared with the related strain, HIV-1(BaL). The structure of one aptamer was defined by a combination of deletion analysis and enzymatic probing studies, revealing a 42 nt minimal element comprising a three-helix junction that retained the binding affinity of the parental sequence. Interestingly, binding to SU glycoprotein was accompanied by structural changes in the aptamer that stabilized the weakest of the 3 helices.

A general strategy for effector-mediated control of RNA-cleaving ribozymes and DNA enzymes

A novel and general approach is described for generating versions of RNA-cleaving ribozymes (RNA enzymes) and DNAzymes (DNA enzymes), whose catalytic activity can be controlled by the binding of activator molecules. Variants of the RNA-cleaving 10-23 DNAzyme and 8-17 DNAzyme were created, whose catalysis was activated by up to approximately 35-fold by the binding of the effector adenosine. The design of such variants was possible even though the tertiary folding of the two DNAzymes is not known. Variants of the hammerhead ribozyme were constructed, to respond to the effectors ATP and flavin mononucleotide. Whereas in conventional allosteric ribozymes, effector-binding modulates the chemical step of catalysis, here, effectors exercise their effect upon the substrate-binding step, by stabilizing the enzyme-substrate complex. Because such an approach for controlling the activity of DNAzymes/ribozymes requires no prior knowledge of the enzyme's secondary or tertiary folding, this regulatory strategy should be generally applicable to any RNA-cleaving ribozyme or DNAzyme, natural or in vitro selected, provided substrate-recognition is achieved by Watson-Crick base-pairing.

A general approach for the use of oligonucleotide effectors to regulate the catalysis of RNA-cleaving ribozymes and DNAzymes

A general approach is described for controlling the RNA-cleaving activity of nucleic acid enzymes (ribozymes and DNAzymes) via the use of oligonucleotide effectors (regulators). In contrast to the previously developed approaches of allosteric and facilitator-mediated regulation of such enzymes, this approach, called 'expansive' regulation, requires that the regulator bind simultaneously to both enzyme and substrate to form a branched three-way complex. Such three-way enzyme-substrate-regulator complexes are catalytically competent relative to the structurally unstable enzyme-substrate complexes. Using the 8-17 and bipartite DNAzymes and the hammerhead ribozyme as model systems, 20- to 30-fold rate enhancements were achieved in the presence of regulators of engineered variants of the above three enzymes, even under unoptimized conditions. Broadly, using this approach ribozyme and DNAzyme variants that are amenable to regulation by oligonucleotide effectors can be designed even in the absence of any knowledge of the folded structure of the relevant ribozyme or DNAzyme. Expansive regulation therefore represents a new and potentially useful technology for both the regulation of nucleic acid enzymes and the detection of specific RNA transcripts.

ATP-dependent allosteric DNA enzymes

Effector-activated ribozymes that respond to small organic molecules have previously been generated by appending binding species (aptamers) to ribozymes. In order to determine if deoxyribozymes can similarly be activated by effector molecules, we have appended an anti-adenosine aptamer to a selected deoxyribozyme ligase. The resultant constructs are specifically activated by ATP. Optimization of the joining region resulted in ligases that are activated up to 460-fold by ATP. The selected deoxyribozyme catalyzes ligation largely via a templating mechanism. Effector activation is surprisingly achieved by suppression of the rate of the background, templated ligation reaction in the absence of the effector molecule, probably by misalignment of the oligonucleotide substrates. This novel allosteric mechanism has not previously been observed for nucleic-acid catalysts and is rare even in protein catalysts.

RNA-catalyzed RNA ligation on an external RNA template

Variants of the hc ligase ribozyme, which catalyzes ligation of the 3' end of an RNA substrate to the 5' end of the ribozyme, were utilized to evolve a ribozyme that catalyzes ligation reactions on an external RNA template. The evolved ribozyme catalyzes the joining of an oligonucleotide 3'-hydroxyl to the 5'-triphosphate of an RNA hairpin molecule. The ribozyme can also utilize various substrate sequences, demonstrating a largely sequence-independent mechanism for substrate recognition. The ribozyme also carries out the ligation of two oligonucleotides that are bound at adjacent positions on a complementary template. Finally, it catalyzes addition of mononucleoside 5'-triphosphates onto the 3' end of an oligonucleotide primer in a template-dependent manner. The development of ribozymes that catalyze polymerase-type reactions contributes to the notion that an RNA world could have existed during the early history of life on Earth.

Engineered allosteric ribozymes as biosensor components

RNA and DNA molecules can be engineered to function as molecular switches that trigger catalytic events when a specific target molecule becomes bound. Recent studies on the underlying biochemical properties of these constructs indicate that a significant untapped potential exists for the practical application of allosteric nucleic acids. Engineered molecular switches can be used to report the presence of specific analytes in complex mixtures, making possible the creation of new types of biosensor devices and genetic control elements.

In vitro selection of nucleoprotein enzymes

Natural nucleic acids frequently rely on proteins for stabilization or catalytic activity. In contrast, nucleic acids selected in vitro can catalyze a wide range of reactions even in the absence of proteins. To augment selected nucleic acids with protein functionalities, we have developed a technique for the selection of protein-dependent ribozyme ligases. After randomizing a previously selected ribozyme ligase, L1, we selected variants that required one of two protein cofactors, a tyrosyl transfer RNA (tRNA) synthetase (Cyt18) or hen egg white lysozyme. The resulting nucleoprotein enzymes were activated several thousand fold by their cognate protein effectors, and could specifically recognize the structures of the native proteins. Protein-dependent ribozymes can potentially be adapted to novel assays for detecting target proteins, and the selection method's generality may allow the high-throughput identification of ribozymes capable of recognizing a sizable fraction of a proteome.

Cooperative binding of effectors by an allosteric ribozyme

An allosteric ribozyme that requires two different effectors to induce catalysis was created using modular rational design. This ribozyme construct comprises five conjoined RNA modules that operate in concert as an obligate FMN- and theophylline-dependent molecular switch. When both effectors are present, this 'binary' RNA switch self-cleaves with a rate enhancement of approximately 300-fold over the rate observed in the absence of effectors. Kinetic and structural studies implicate a switching mechanism wherein FMN binding induces formation of the active ribozyme conformation. However, the binding site for FMN is rendered inactive unless theophylline first binds to its corresponding site and reorganizes the RNA structure. This example of cooperative binding between allosteric effectors reveals a level of structural and functional complexity for RNA that is similar to that observed with allosteric proteins.

Generating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes

Allosteric ribozymes are engineered RNAs that operate as molecular switches whose rates of catalytic activity are modulated by the binding of specific effector molecules. New RNA molecular switches can be created by using "allosteric selection," a molecular engineering process that combines modular rational design and in vitro evolution strategies. In this report, we describe the characterization of 3',5'-cyclic nucleotide monophosphate (cNMP)-dependent hammerhead ribozymes that were created using allosteric selection (Koizumi et al., Nat Struct Biol, 1999, 6:1062-1071). Artificial phylogeny data generated by random mutagenesis and reselection of existing cGMP-, cCMP-, and cAMP-dependent ribozymes indicate that each is comprised of distinct effector-binding and catalytic domains. In addition, patterns of nucleotide covariation and direct mutational analysis both support distinct secondary-structure organizations for the effector-binding domains. Guided by these structural models, we were able to disintegrate each allosteric ribozyme into separate ligand-binding and catalytic modules. Examinations of the independent effector-binding domains reveal that each retains its corresponding cNMP-binding function. These results validate the use of allosteric selection and modular engineering as a means of simultaneously generating new nucleic acid structures that selectively bind ligands. Furthermore, we demonstrate that the binding affinity of an allosteric ribozyme can be improved through random mutagenesis and allosteric selection under conditions that favor tighter binding. This "affinity maturation" effect is expected to be a valuable attribute of allosteric selection as future endeavors seek to apply engineered allosteric ribozymes as biosensor components and as controllable genetic switches.

Immobilized RNA switches for the analysis of complex chemical and biological mixtures

A prototype biosensor array has been assembled from engineered RNA molecular switches that undergo ribozyme-mediated self-cleavage when triggered by specific effectors. Each type of switch is prepared with a 5'-thiotriphosphate moiety that permits immobilization on gold to form individually addressable pixels. The ribozymes comprising each pixel become active only when presented with their corresponding effector, such that each type of switch serves as a specific analyte sensor. An addressed array created with seven different RNA switches was used to report the status of targets in complex mixtures containing metal ion, enzyme cofactor, metabolite, and drug analytes. The RNA switch array also was used to determine the phenotypes of Escherichia coli strains for adenylate cyclase function by detecting naturally produced 3',5'- cyclic adenosine monophosphate (cAMP) in bacterial culture media.

Optimization and optimality of a short ribozyme ligase that joins non-Watson-Crick base pairings

A small ribozyme ligase (L1) selected from a random sequence population appears to utilize non-Watson-Crick base pairs at its ligation junction. Mutational and selection analyses confirmed the presence of these base pairings. Randomization of the L1 core and selection of active ligases yielded highly active variants whose rates were on the order of 1 min(-1). Base-pairing covariations confirmed the general secondary structure of the ligase, and the most active ligases contained a novel pentuple sequence covariation. The optimized L1 ligases may be optimal within their sequence spaces, and minimal ligases that span less than 60 nt in length have been engineered based on these results.

The effect of cytidine on the structure and function of an RNA ligase ribozyme

A cytidine-free ribozyme with RNA ligase activity was obtained by in vitro evolution, starting from a pool of random-sequence RNAs that contained only guanosine, adenosine, and uridine. This ribozyme contains 74 nt and catalyzes formation of a 3',5'-phosphodiester linkage with a catalytic rate of 0.016 min(-1). The RNA adopts a simple secondary structure based on a three-way junction motif, with ligation occurring at the end of a stem region located several nucleotides away from the junction. Cytidine was introduced to the cytidine-free ribozyme in a combinatorial fashion and additional rounds of in vitro evolution were carried out to allow the molecule to adapt to this added component. The resulting cytidine-containing ribozyme formed a 3',5' linkage with a catalytic rate of 0.32 min(-1). The improved rate of the cytidine-containing ribozyme was the result of 12 mutations, including seven added cytidines, that remodeled the internal bulge loops located adjacent to the three-way junction and stabilized the peripheral stem regions.

Allosteric nucleic acid catalysts

Endowing nucleic acid catalysts with allosteric properties provides new prospects for RNA and DNA as controllable therapeutic agents or as sensors of their cognate effector compounds. The ability to engineer RNA catalysts that are allosterically regulated by effector binding has been propelled by the union of modular rational design principles and powerful combinatorial strategies.