Directed evolution of nucleic acid enzymes

DNAzymes Targeting theiclGene Inhibit ICL Expression and DecreaseMycobacterium tuberculosisSurvival in Macrophages

Latent infection with Mycobacterium tuberculosis presents a big obstacle for tuberculosis therapy. In this study, we investigated the effects of sequence-specific DNAzymes targeting the mRNA of isocitrate lyase (ICL), an enzyme playing a pivotal role in the metabolism of M. tuberculosis in the latent state, on the expression of ICL and survival of M. tuberculosis. In vitro studies showed that four of five designed DNAzymes, DZ1, DZ3, DZ4, and DZ5 could cleave icl mRNA efficiently and specifically. Treatment of virulent M. tuberculosis with 5microM DZ4 plus a subinhibitory concentration of isoniazid (INH) decreased ICL expression and the survival of M. tuberculosis in macrophages but had no obvious influence on the growth of M. tuberculosis in vitro. This study demonstrates that using INH to soften the cell wall of M. tuberculosis and help the entry of biomolecules is an efficient method of improving the uptake of DNAzymes. Silencing the icl gene by DNAzyme is a promising method to combat latent infection of tuberculosis.

Laboratory-directed protein evolution

Systematic approaches to directed evolution of proteins have been documented since the 1970s. The ability to recruit new protein functions arises from the considerable substrate ambiguity of many proteins. The substrate ambiguity of a protein can be interpreted as the evolutionary potential that allows a protein to acquire new specificities through mutation or to regain function via mutations that differ from the original protein sequence. All organisms have evolutionarily exploited this substrate ambiguity. When exploited in a laboratory under controlled mutagenesis and selection, it enables a protein to "evolve" in desired directions. One of the most effective strategies in directed protein evolution is to gradually accumulate mutations, either sequentially or by recombination, while applying selective pressure. This is typically achieved by the generation of libraries of mutants followed by efficient screening of these libraries for targeted functions and subsequent repetition of the process using improved mutants from the previous screening. Here we review some of the successful strategies in creating protein diversity and the more recent progress in directed protein evolution in a wide range of scientific disciplines and its impacts in chemical, pharmaceutical, and agricultural sciences.

Stimuli-Responsive Disassembly of Nanoparticle Aggregates for Light-Up Colorimetric Sensing

Controlled assembly of nanomaterials has been the focus of much research. In contrast, controlled disassembly has not received much attention, even though both processes have been shown to be important in biology. By using a Pb2+-dependent RNA-cleaving DNAzyme, we demonstrate here control of the disassembly of gold nanoparticle aggregates in response to Pb2+. In the process, we show that nanoparticle alignment plays an important role in the disassembly process, with the tail-to-tail configuration being the most optimal, probably because of the large steric hindrance of other configurations. The rate of disassembly is significantly accelerated by using small pieces of DNA to invade the cleaved substrate of the DNAzyme. Investigation of such a controlled disassembly process allows the transformation of previously designed "light-down" colorimetric Pb2+ sensors into "light-up" sensors.

Zn2+-dependent deoxyribozymes that form natural and unnatural RNA linkages

We report Zn(2+)-dependent deoxyribozymes that ligate RNA. The DNA enzymes were identified by in vitro selection and ligate RNA with k(obs) up to 0.5 min(-)(1) at 1 mM Zn(2+) and 23 degrees C, pH 7.9, which is substantially faster than our previously reported Mg(2+)-dependent deoxyribozymes. Each new Zn(2+)-dependent deoxyribozyme mediates the reaction of a specific nucleophile on one RNA substrate with a 2',3'-cyclic phosphate on a second RNA substrate. Some of the Zn(2+)-dependent deoxyribozymes create native 3'-5' RNA linkages (with k(obs) up to 0.02 min(-)(1)), whereas all of our previous Mg(2+)-dependent deoxyribozymes that use a 2',3'-cyclic phosphate create non-native 2'-5' RNA linkages. On this basis, Zn(2+)-dependent deoxyribozymes have promise for synthesis of native 3'-5'-linked RNA using 2',3'-cyclic phosphate RNA substrates, although these particular Zn(2+)-dependent deoxyribozymes are likely not useful for this practical application. Some of the new Zn(2+)-dependent deoxyribozymes instead create non-native 2'-5' linkages, just like their Mg(2+) counterparts. Unexpectedly, other Zn(2+)-dependent deoxyribozymes synthesize one of three unnatural linkages that are formed upon the reaction of an RNA nucleophile other than a 5'-hydroxyl group. Two of these unnatural linkages are the 3'-2' and 2'-2' linear junctions created when the 2'-hydroxyl of the 5'-terminal guanosine of one RNA substrate attacks the 2',3'-cyclic phosphate of the second RNA substrate. The third unnatural linkage is a branched RNA that results from attack of a specific internal 2'-hydroxyl of one RNA substrate at the 2',3'-cyclic phosphate. When compared with the consistent creation of 2'-5' linkages by Mg(2+)-dependent ligation, formation of this variety of RNA ligation products by Zn(2+)-dependent deoxyribozymes highlights the versatility of transition metals such as Zn(2+) for mediating nucleic acid catalysis.

In Vitro Selection of High Temperature Zn2+-Dependent DNAzymes

In vitro selection of Zn(2+)-dependent RNA-cleaving DNAzymes with activity at 90 degrees C has yielded a diverse spool of selected sequences. The RNA cleavage efficiency was found in all cases to be specific for Zn(2+) over Pb(2+), Ca(2+), Cd(2+), Co(2+), Hg(2+), and Mg(2+). The Zn(2+)-dependent activity assay of the most active sequence showed that the DNAzyme possesses an apparent Zn(2+)-binding dissociation constant of 234 muM and that its activity increases with increasing temperatures from 50-90 degrees C. A fit of the Arrhenius plot data gave E(a) = 15.3 kcal mol(-1). Surprisingly, the selected Zn(2+)-dependent DNAzymes showed only a modest (approximately 3-fold) activity enhancement over the background rate of cleavage of random sequences containing a single embedded ribonucleotide within an otherwise DNA oligonucleotide. The result is attributable to the ability of DNA to sustain cleavage activity at high temperature with minimal secondary structure when Zn(2+) is present. Since this effect is highly specific for Zn(2+), this metal ion may play a special role in molecular evolution of nucleic acids at high temperature.

New ligase-derived RNA polymerase ribozymes

The search is underway for a catalytic RNA molecule capable of self-replication. Finding such a ribozyme would lend crucial support to the RNA World hypothesis, which holds that very early life-forms relied on RNA for both replicating and storing genetic information. We previously reported an RNA polymerase isolated from a pool of variants of an existing RNA ligase ribozyme. Here we report eight additional ligase-derived polymerase ribozymes isolated from this pool. Because each of them is a new potential starting point for further in vitro evolution and engineering, together they substantially enrich the set of candidates from which an RNA replicase ribozyme might eventually emerge.

The RNA World on Ice: A New Scenario for the Emergence of RNA Information

The RNA world hypothesis refers to a hypothetical era prior to coded peptide synthesis, where RNA was the major structural, genetic, and catalytic agent. Though it is a widely accepted scenario, a number of vexing difficulties remain. In this review we focus on a missing link of the RNA world hypothesis-primitive miniribozymes, in particular ligases, and discuss the role of these molecules in the evolution of RNA size and complexity. We argue that prebiotic conditions associated with freezing, rather than "warm and wet" conditions, could have been of key importance in the early RNA world.

The promise and peril of continuous in vitro evolution

Experimental evolution methods can be used to address and illuminate issues central to the understanding of evolutionary theory. One of the most powerful of these methods involves the in vitro evolution of nucleic acid enzymes, taking advantage of the direct relationship between the genotype of a nucleic acid sequence and the phenotype of its associated catalytic function. This review and commentary focuses on the past, present, and future potential of systems for the continuous in vitro evolution of nucleic acid enzymes as tools for modeling evolutionary processes in biology. It offers a candid appraisal of both the strengths and the limitations of these systems.

The catalytic mechanism of hairpin ribozyme studied by hydrostatic pressure

The discovery of ribozymes strengthened the RNA world hypothesis, which assumes that these precursors of modern life both stored information and acted as catalysts. For the first time among extensive studies on ribozymes, we have investigated the influence of hydrostatic pressure on the hairpin ribozyme catalytic activity. High pressures are of interest when studying life under extreme conditions and may help to understand the behavior of macromolecules at the origins of life. Kinetic studies of the hairpin ribozyme self-cleavage were performed under high hydrostatic pressure. The activation volume of the reaction (34 +/- 5 ml/mol) calculated from these experiments is of the same order of magnitude as those of common protein enzymes, and reflects an important compaction of the RNA molecule during catalysis, associated to a water release. Kinetic studies were also carried out under osmotic pressure and confirmed this interpretation and the involvement of water movements (78 +/- 4 water molecules per RNA molecule). Taken together, these results are consistent with structural studies indicating that loops A and B of the ribozyme come into close contact during the formation of the transition state. While validating baro-biochemistry as an efficient tool for investigating dynamics at work during RNA catalysis, these results provide a complementary view of ribozyme catalytic mechanisms.

DNAzyme-mediated silencing of ornithine decarboxylase

The value of reducing the activity of ornithine decarboxylase (ODC), a key enzyme in the biosynthesis of polyamines, is well-appreciated. Polyamines are necessary components for cell growth, and manipulation of polyamine homeostasis may be an effective strategy for the treatment of a number of disorders, including neoplastic diseases. An approach to develop an effective DNAzyme, using the 10-23 model, against ODC is described in these studies. DNAzymes able to cleave the target ODC RNA were identified in vitro and further characterized by the effect each had on ODC protein and activity levels using in vitro translated ODC RNA. ODC protein levels and activity correlated well with the RNA cleavage activity of the DNAzyme. One of the DNAzymes, DZ IV, which exhibited good activity, was optimized for use in cell culture studies. The DNAzyme hybridization arms were altered from equal length arms varying in length (8, 9, 10, or 11 nucleotides) or to unequal length arms (7/11 nucleotides), and kinetic analyses were performed to identify the most catalytically efficient configuration. DZ IV with equal arms nine nucleotides in length proved to be the most catalytically efficient. In HEK 293 cells, DZ IV was able to reduce the amount of translated ODC protein, resulting in approximately 80% reduction in ODC activity-a statistically significant enhancement over the apparent antisense effect of a catalytically inactive DNAzyme. These results indicate that this DNAzyme may be a useful tool to study the function of ODC and may have potential therapeutic uses.

DNA nanodevices

The molecular recognition properties of DNA molecules combined with the distinct mechanical properties of single and double strands of DNA can be utilized for the construction of nanodevices, which can perform ever more tasks with possible applications ranging from nanoconstruction to intelligent drug delivery. With the help of DNA it is possible to construct machinelike devices that are capable of rotational motion, pulling and stretching, or even unidirectional motion. It is possible to devise autonomous nanodevices, to grab and release molecules, and also to perform simple information-processing tasks.

Rational modification of a selection strategy leads to deoxyribozymes that create native 3'-5' RNA linkages

We previously used in vitro selection to identify several classes of deoxyribozymes that mediate RNA ligation by attack of a hydroxyl group at a 5'-triphosphate. In these reactions, the nucleophilic hydroxyl group is located at an internal 2'-position of an RNA substrate, leading to 2',5'-branched RNA. To obtain deoxyribozymes that instead create linear 3'-5'-linked (native) RNA, here we strategically modified the selection approach by embedding the nascent ligation junction within an RNA:DNA duplex region. This approach should favor formation of linear rather than branched RNA because the two RNA termini are spatially constrained by Watson-Crick base pairing during the ligation reaction. Furthermore, because native 3'-5' linkages are more stable in a duplex than isomeric non-native 2'-5' linkages, this strategy is predicted to favor the formation of 3'-5' linkages. All of the new deoxyribozymes indeed create only linear 3'-5' RNA, confirming the effectiveness of the rational design. The new deoxyribozymes ligate RNA with k(obs) values up to 0.5 h(-1) at 37 degrees C and 40 mM Mg2+, pH 9.0, with up to 41% yield at 3 h incubation. They require several specific RNA nucleotides on either side of the ligation junction, which may limit their practical generality. These RNA ligase deoxyribozymes are the first that create native 3'-5' RNA linkages, which to date have been highly elusive via other selection approaches.

Prebiotic chemistry and the origin of the RNA world

The demonstration that ribosomal peptide synthesis is a ribozyme-catalyzed reaction makes it almost certain that there was once an RNA World. The central problem for origin-of-life studies, therefore, is to understand how a protein-free RNA World became established on the primitive Earth. We first review the literature on the prebiotic synthesis of the nucleotides, the nonenzymatic synthesis and copying of polynucleotides, and the selection of ribozyme catalysts of a kind that might have facilitated polynucleotide replication. This leads to a brief outline of the Molecular Biologists' Dream, an optimistic scenario for the origin of the RNA World. In the second part of the review we point out the many unresolved problems presented by the Molecular Biologists' Dream. This in turn leads to a discussion of genetic systems simpler than RNA that might have "invented" RNA. Finally, we review studies of prebiotic membrane formation.

Natural and engineered nucleic acids as tools to explore biology

RNA and DNA molecules can form complex, three-dimensional folded structures that have surprisingly sophisticated functions, including catalysing chemical reactions and controlling gene expression. Although natural nucleic acids make occasional use of these advanced functions, the true potential for sophisticated function by these biological polymers is far greater. An important challenge for biochemists is to take RNA and DNA beyond their proven use as polymers that form double-helical structures. Molecular engineers are beginning to harness the power of nucleic acids that form more complex three-dimensional structures, and apply them as tools for exploring biological systems and as therapeutics.

Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site

The Tetrahymena intron is an RNA catalyst, or ribozyme. As part of its self-splicing reaction, this ribozyme catalyzes phosphoryl transfer between guanosine and a substrate RNA strand. Here we report the refined crystal structure of an active Tetrahymena ribozyme in the absence of its RNA substrate at 3.8 A resolution. The 3'-terminal guanosine (omegaG), which serves as the attacking group for RNA cleavage, forms a coplanar base triple with the G264-C311 base pair, and this base triple is sandwiched by three other base triples. In addition, a metal ion is present in the active site, contacting or positioned close to the ribose of the omegaG and five phosphates. All of these phosphates have been shown to be important for catalysis. Therefore, we provide a picture of how the ribozyme active site positions both a catalytic metal ion and the nucleophilic guanosine for catalysis prior to binding its RNA substrate.

Reaction discovery enabled by DNA-templated synthesis and in vitro selection

Current approaches to reaction discovery focus on one particular transformation. Typically, researchers choose substrates based on their predicted ability to serve as precursors for the target structure, then evaluate reaction conditions for their ability to effect product formation. This approach is ideal for addressing specific reactivity problems, but its focused nature might leave many areas of chemical reactivity unexplored. Here we report a reaction discovery approach that uses DNA-templated organic synthesis and in vitro selection to simultaneously evaluate many combinations of different substrates for bond-forming reactions in a single solution. Watson-Crick base pairing controls the effective molarities of substrates tethered to DNA strands; bond-forming substrate combinations are then revealed using in vitro selection for bond formation, PCR amplification and DNA microarray analysis. Using this approach, we discovered an efficient and mild carbon-carbon bond-forming reaction that generates an enone from an alkyne and alkene using an inorganic palladium catalyst. Although this approach is restricted to conditions and catalysts that are at least partially compatible with DNA, we expect that its versatility and efficiency will enable the discovery of additional reactions between a wide range of substrates.

DNA-templated organic synthesis and selection of a library of macrocycles

The translation of nucleic acid libraries into corresponding synthetic compounds would enable selection and amplification principles to be applied to man-made molecules. We used multistep DNA-templated organic synthesis to translate libraries of DNA sequences, each containing three "codons," into libraries of sequence-programmed synthetic small-molecule macrocycles. The resulting DNA-macrocycle conjugates were subjected to in vitro selections for protein affinity. The identity of a single macrocycle possessing known target protein affinity was inferred through the sequence of the amplified DNA template surviving the selection. This work represents the translation, selection, and amplification of libraries of nucleic acids encoding synthetic small molecules rather than biological macromolecules.