RNA ligands that distinguish metabolite-induced conformations in the TPP riboswitch

Exploring the structure, function of thiamine pyrophosphate riboswitch, and designing small molecules for antibacterial activity

During the last decade, riboswitches emerged as new small-molecule sensing RNA in bacteria. Thiamine pyrophosphate (TPP) riboswitch is widely distributed and occurs in plants, bacteria, fungi, and archaea. Extensive biochemical, structural, and genetic studies have been carried out to elucidate the recognition mechanism of TPP riboswitches. However, a comprehensive report summarizing all information on recognition principles and newly designed ligands for TPP riboswitch is scarce in the literature. This review gives a comprehensive understanding of the TPP riboswitch's structure, mechanism, and methods applied to design ligands for the TPP riboswitch. The ligand-bound TPP riboswitch was studied with various experimental and theoretical techniques to elucidate the conformational dynamics. The mutation studies shed light on the significance of pyrimidine sensing helix for the binding of ligands. Further, the structure-activity relationship study and fragment-based approach lead to the development of ligands with Kd values at the sub-micromolar level. However, there is a need to design more potent inhibitors for TPP riboswitch for therapeutic applications. The recent advancements in ligand design highlight the TPP riboswitch as a promising target for developing new antibiotics. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Riboswitches Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.

Trapping Transient RNA Complexes by Chemically Reversible Acylation

RNA-RNA interactions are essential for biology, but they can be difficult to study due to their transient nature. While crosslinking strategies can in principle be used to trap such interactions, virtually all existing strategies for crosslinking are poorly reversible, chemically modifying the RNA and hindering molecular analysis. We describe a soluble crosslinker design (BINARI) that reacts with RNA through acylation. We show that it efficiently crosslinks noncovalent RNA complexes with mimimal sequence bias and establish that the crosslink can be reversed by phosphine reduction of azide trigger groups, thereby liberating the individual RNA components for further analysis. The utility of the new approach is demonstrated by reversible protection against nuclease degradation and trapping transient RNA complexes of E. coli DsrA-rpoS derived bulge-loop interactions, which underlines the potential of BINARI crosslinkers to probe RNA regulatory networks.

In vitro selection of l-DNA aptamers that bind a structured d-RNA molecule

The development of structure-specific RNA binding reagents remains a central challenge in RNA biochemistry and drug discovery. Previously, we showed in vitro selection techniques could be used to evolve l-RNA aptamers that bind tightly to structured d-RNAs. However, whether similar RNA-binding properties can be achieved using aptamers composed of l-DNA, which has several practical advantages compared to l-RNA, remains unknown. Here, we report the discovery and characterization of the first l-DNA aptamers against a structured RNA molecule, precursor microRNA-155, thereby establishing the capacity of DNA and RNA molecules of the opposite handedness to form tight and specific ‘cross-chiral’ interactions with each other. l-DNA aptamers bind pre-miR-155 with low nanomolar affinity and high selectivity despite the inability of l-DNA to interact with native d-RNA via Watson–Crick base pairing. Furthermore, l-DNA aptamers inhibit Dicer-mediated processing of pre-miRNA-155. The sequence and structure of l-DNA aptamers are distinct from previously reported l-RNA aptamers against pre-miR-155, indicating that l-DNA and l-RNA interact with the same RNA sequence through unique modes of recognition. Overall, this work demonstrates that l-DNA may be pursued as an alternative to l-RNA for the generation of RNA-binding aptamers, providing a robust and practical approach for targeting structured RNAs.

An l-RNA Aptamer with Expanded Chemical Functionality that Inhibits MicroRNA Biogenesis

To facilitate isolation of l-aptamers with novel RNA-binding properties, we employed a cationic nucleotide, 5-aminoallyluridine, during the mirror image in vitro selection process. Through this effort, we identified a modified l-RNA aptamer (MlRA) capable of binding oncogenic precursor microRNA 19a (pre-miR-19a) with exceptional affinity, and we showed that cationic modification is absolutely critical for binding. Furthermore, formation of the MlRA-pre-miR-19a complex inhibited Dicer-mediated cleavage of the pre-miR, thus blocking formation of the mature functional microRNA. The MlRA reported here not only represents the first l-aptamer to be evolved by using modified nucleotides but also the first modified aptamer (of any type) to be selected against a structured RNA target. Our results demonstrate that functionalized l-aptamers, which are intrinsically nuclease-resistant, provide an attractive approach for developing robust RNA-binding reagents.

Reporter Gene-Based Screening for TPP Riboswitch Activators

With the rise of multidrug resistant bacteria and a growing number of nosocomial infections, there has been an increased interest in finding new antibacterial drugs and drug targets. Riboswitches represent attractive new antibacterial drug targets, because they not only inherently recognize a specific metabolite or ion with their RNA aptamer domain, but also often regulate essential metabolic pathways. Here, we describe a reporter gene-based screen to identify compounds that activate the thiamine pyrophosphate (TPP) riboswitch in bacteria. This assay can be easily adapted for different riboswitch classes and thus has the potential to target many essential metabolic pathways and a broad spectrum of bacterial pathogens.

The emerging role of long non-coding RNAs in cutaneous melanoma

Malignant melanoma is a highly aggressive form of skin cancer, the incidence of which is rising rapidly. Although MAPK-targeting therapies and immune checkpoint blockade are emerging as attractive therapeutic approaches, their utility is limited to only a subset of patients who often acquire resistance. A better understanding of the aetiologies and genetic underpinnings of melanoma is therefore critical for the development of adjuvant or alternative therapeutic strategies aimed at increasing the proportion of responders and improving treatment efficacy. A key step in identifying novel therapeutic targets may be the shift in focus from the protein-coding components to the non-coding portion of the genome. The latter, representing about 98% of the genome, serves as a template for the transcription of many thousands of long non-coding RNAs (lncRNAs). Intriguingly, lncRNA loci are frequently mutated or altered in a variety of cancers, including melanoma, and there is growing evidence that lncRNAs can function as cancer-causing oncogenes or tumour suppressors. In this review, we summarize recent data highlighting the importance of lncRNAs in the biology of melanoma and their potential utility as biomarkers and therapeutic targets.

Riboswitches: From living biosensors to novel targets of antibiotics

Riboswitches are generally located in 5'-UTR region of mRNAs and specifically bind small ligands. Following ligand binding, gene expression is controlled mostly by transcription termination, translation inhibition or mRNA degradation processes. More than 30 classes of known riboswitches have been identified by now. Most riboswitches consist of an aptamer domain and an expression platform. The aptamer domain of each class of riboswitch is a conserved structure and stabilizes specific structures of the expression platforms through binding to specific compounds. In this review, we are highlighting most aspects of riboswitch research including the novel riboswitch discoveries, routine methods for discovering and investigating riboswitches along with newly discovered classes and mechanistic principles of riboswitch-mediated gene expression control. Moreover, we will give an overview about the potential of riboswitches as therapeutic targets for antibiotic design and also their utilization as biosensors for molecular detection.

Small and Long Non-Coding RNAs: Novel Targets in Perspective Cancer Therapy

Non-coding RNA refers to a large group of endogenous RNA molecules that have no protein coding capacity, while having specialized cellular and molecular functions. They possess wide range of functions such as the regulation of gene transcription and translation, post-transcriptional modification, epigenetic landscape establishment, protein scaffolding and cofactors recruitments. They are further divided into small non-coding RNAs with size < 200nt (e.g. miRNA, piRNA) and long non-coding RNAs with size >= 200nt (e.g. lincRNA, NAT). Increasing evidences suggest that both non-coding RNAs groups play important roles in cancer development, progression and pathology. Clinically, non-coding RNAs aberrations show high diagnostic and prognostic values. With improved understanding of the nature and roles of non-coding RNAs, it is believed that we can develop therapeutic treatment against cancer via the modulation of these RNA molecules. Advances in nucleic acid drug technology and computational simulation prompt the development of agents to intervene the malignant effects of non-coding RNAs. In this review, we will discuss the role of non-coding RNAs in cancer, and evaluate the potential of non-coding RNA-based cancer therapies.

Linking aptamer-ligand binding and expression platform folding in riboswitches: prospects for mechanistic modeling and design

The power of riboswitches in regulation of bacterial metabolism derives from coupling of two characteristics: recognition and folding. Riboswitches contain aptamers, which function as biosensors. Upon detection of the signaling molecule, the riboswitch transduces the signal into a genetic decision. The genetic decision is coupled to refolding of the expression platform, which is distinct from, although overlapping with, the aptamer. Early biophysical studies of riboswitches focused on recognition of the ligand by the aptamer-an important consideration for drug design. A mechanistic understanding of ligand-induced riboswitch RNA folding can further enhance riboswitch ligand design, and inform efforts to tune and engineer riboswitches with novel properties. X-ray structures of aptamer/ligand complexes point to mechanisms through which the ligand brings together distal strand segments to form a P1 helix. Transcriptional riboswitches must detect the ligand and form this P1 helix within the timescale of transcription. Depending on the cell's metabolic state and cellular environmental conditions, the folding and genetic outcome may therefore be affected by kinetics of ligand binding, RNA folding, and transcriptional pausing, among other factors. Although some studies of isolated riboswitch aptamers found homogeneous, prefolded conformations, experimental, and theoretical studies point to functional and structural heterogeneity for nascent transcripts. Recently it has been shown that some riboswitch segments, containing the aptamer and partial expression platforms, can form binding-competent conformers that incorporate an incomplete aptamer secondary structure. Consideration of the free energy landscape for riboswitch RNA folding suggests models for how these conformers may act as transition states-facilitating rapid, ligand-mediated aptamer folding.

(Dis)similar Analogues of Riboswitch Metabolites as Antibacterial Lead Compounds

The rise of antimicrobial resistance in human pathogenic bacteria has increased the necessity for the discovery of novel, yet unexplored antibacterial drug targets. Riboswitches, which are embedded in untranslated regions of bacterial messenger RNA (mRNA), represent such an interesting target structure. These RNA elements regulate gene expression upon binding to natural metabolites, second messengers, and inorganic ions, such as fluoride with high affinity and in a highly discriminative manner. Recently, efforts have been directed toward the identification of artificial riboswitch activators by establishing high-throughput screening assays, fragment-based screening, and structure-guided ligand design approaches. Emphasis in this review is placed on the special requirements and synthesis of new potential antibiotic drugs that target riboswitches in which dissimilarity is an important aspect in the design of potential lead compounds.

Epithelial-mesenchymal transition and cancer stem cells, mediated by a long non-coding RNA, HOTAIR, are involved in cell malignant transformation induced by cigarette smoke extract

The incidence of lung diseases, including cancer, caused by cigarette smoke is increasing, but the molecular mechanisms of gene regulation induced by cigarette smoke remain unclear. This report describes a long noncoding RNA (lncRNA) that is induced by cigarette smoke extract (CSE) and experiments utilizing lncRNAs to integrate inflammation with the epithelial-mesenchymal transition (EMT) in human bronchial epithelial (HBE) cells. The present study shows that, induced by CSE, IL-6, a pro-inflammatory cytokine, leads to activation of STAT3, a transcription activator. A ChIP assay determined that the interaction of STAT3 with the promoter regions of HOX transcript antisense RNA (HOTAIR) increased levels of HOTAIR. Blocking of IL-6 with anti-IL-6 antibody, decreasing STAT3, and inhibiting STAT3 activation reduced HOTAIR expression. Moreover, for HBE cells cultured in the presence of HOTAIR siRNA for 24h, the CSE-induced EMT, formation of cancer stem cells (CSCs), and malignant transformation were reversed. Thus, IL-6, acting on STAT3 signaling, which up-regulates HOTAIR in an autocrine manner, contributes to the EMT and to CSCs induced by CSE. These data define a link between inflammation and EMT, processes involved in the malignant transformation of cells caused by CSE. This link, mediated through lncRNAs, establishes a mechanism for CSE-induced lung carcinogenesis.

High-throughput electrophoretic mobility shift assays for quantitative analysis of molecular binding reactions

We describe a platform for high-throughput electrophoretic mobility shift assays (EMSAs) for identification and characterization of molecular binding reactions. A photopatterned free-standing polyacrylamide gel array comprised of 8 mm-scale polyacrylamide gel strips acts as a chassis for 96 concurrent EMSAs. The high-throughput EMSAs was employed to assess binding of the Vc2 cyclic-di-GMP riboswitch to its ligand. In optimizing the riboswitch EMSAs on the free-standing polyacrylamide gel array, three design considerations were made: minimizing sample injection dispersion, mitigating evaporation from the open free-standing polyacrylamide gel structures during electrophoresis, and controlling unit-to-unit variation across the large-format free-standing polyacrylamide gel array. Optimized electrophoretic mobility shift conditions allowed for 10% difference in mobility shift baseline resolution within 3 min. The powerful 96-plex EMSAs increased the throughput to ∼10 data/min, notably more efficient than either conventional slab EMSAs (∼0.01 data/min) or even microchannel based microfluidic EMSAs (∼0.3 data/min). The free-standing polyacrylamide gel EMSAs yielded reliable quantification of molecular binding and associated mobility shifts for a riboswitch-ligand interaction, thus demonstrating a screening assay platform suitable for riboswitches and potentially a wide range of RNA and other macromolecular targets.

Novel TPP-riboswitch activators bypass metabolic enzyme dependency

Riboswitches are conserved regions within mRNA molecules that bind specific metabolites and regulate gene expression. TPP-riboswitches, which respond to thiamine pyrophosphate (TPP), are involved in the regulation of thiamine metabolism in numerous bacteria. As these regulatory RNAs are often modulating essential biosynthesis pathways they have become increasingly interesting as promising antibacterial targets. Here, we describe thiamine analogs containing a central 1,2,3-triazole group to induce repression of thiM-riboswitch dependent gene expression in different E. coli strains. Additionally, we show that compound activation is dependent on proteins involved in the metabolic pathways of thiamine uptake and synthesis. The most promising molecule, triazolethiamine (TT), shows concentration dependent reporter gene repression that is dependent on the presence of thiamine kinase ThiK, whereas the effect of pyrithiamine (PT), a known TPP-riboswitch modulator, is ThiK independent. We further show that this dependence can be bypassed by triazolethiamine-derivatives that bear phosphate-mimicking moieties. As triazolethiamine reveals superior activity compared to pyrithiamine, it represents a very promising starting point for developing novel antibacterial compounds that target TPP-riboswitches. Riboswitch-targeting compounds engage diverse endogenous mechanisms to attain in vivo activity. These findings are of importance for the understanding of compounds that require metabolic activation to achieve effective riboswitch modulation and they enable the design of novel compound generations that are independent of endogenous activation mechanisms.

Mechanically interlocked DNA nanostructures for functional devices

CONSPECTUS: Self-assembled functional DNA oligonucleotide based architectures represent highly promising candidates for the creation of nanoscale devices. The field of DNA nanotechnology has emerged to a high level of maturity and currently constitutes one of the most dynamic, creative, and exciting modern research areas. The transformation from structural DNA nanotechnology to functional DNA architectures is already taking place with tremendous pace. Particularly the advent of DNA origami technology has propelled DNA nanotechnology forward. DNA origami provided a versatile method for precisely aligning structural and functional DNA modules in two and three dimensions, thereby serving as a means for constructing scaffolds and chassis required for the precise orchestration of multiple functional DNA architectures. Key modules of these will contain interlocked nanomechanical components made of DNA. The mechanical interlocking allows for performing highly specific and controlled motion, by reducing the dimensionality of diffusion-controlled processes without restrictions in motional flexibility. Examples for nanoscale interlocked DNA architectures illustrate how elementary functional units of future nanomachines can be designed and realized, and show what role interlocked DNA architectures may play in this endeavor. Functional supramolecular systems, in general, and nanomachinery, in particular, self-organize into architectures that reflect different levels of complexity with respect to their function, their arrangement in the second and third dimension, their suitability for different purposes, and their functional interplay. Toward this goal, DNA nanotechnology and especially the DNA origami technology provide opportunities for nanomechanics, nanorobotics, and nanomachines. In this Account, we address approaches that apply to the construction of interlocked DNA nanostructures, drawing largely form our own contributions to interlocked architectures based on double-stranded (ds) circular geometries, and describe progress, opportunities, and challenges in rotaxanes and pseudorotaxanes made of dsDNA. Operating nanomechanical devices in a reliable and repetitive fashion requires methods for switching movable parts in DNA nanostructures from one state to another. An important issue is the orthogonality of switches that allow for operating different parts in parallel under spatiotemporal control. A variety of switching methods have been applied to switch individual components in interlocked DNA nanostructures like rotaxanes and catenanes. They are based on toehold, light, pseudocomplementary peptide nucleic acids (pcPNAs), and others. The key issues discussed here illustrate our perspective on the future prospects of interlocked DNA-based devices and the challenges that lay ahead.

Aptamers for allosteric regulation

Aptamers are useful for allosteric regulation because they are nucleic acid-based structures in which ligand binding induces conformational changes that may alter the function of a connected oligonucleotide at a distant site. Through this approach, a specific input is efficiently converted into an altered output. This property makes these biomolecules ideally suited to function as sensors or switches in biochemical assays or inside living cells. The ability to select oligonucleotide-based recognition elements in vitro in combination with the availability of nucleic acids with enzymatic activity has led to the development of a wide range of engineered allosteric aptasensors and aptazymes. Here, we discuss recent progress in the screening, design and diversity of these conformational switching oligonucleotides. We cover their application in vitro and for regulating gene expression in both prokaryotes and eukaryotes.

A electrogenerated chemiluminescence biosensor for Ramos cancer cell using DNA encapsulated Ru(bpy)₃Cl₂ as signal probe

A label-free sensing technology for detection of Ramos cell was developed based on a signal probe Ru(bpy)3Cl2 (Ru) encapsulated by DNA. Gold electrode or magnetic bead as the sensing surface was firstly modified with long-strand DNA with five repeating units. Then two kinds of short-strand DNA are grafted onto the long-strand DNA to form DNA strands A and B (L-A and L-B) through the hybridization, respectively. The addition of aptamer initiates hybridization of L-A and L-B with the aptamer sequence. As the hybridization proceeds, the four kinds of DNA would finally transform into a three-dimensional network structure and the signal probe Ru was encapsulated by DNA simultaneously. When Ramos cells are introduced to interact with the aptamer, the signal probe is released. In order to confirm the generality of this method the ferrocenecarboxylic acid and luminol selected as a signal probe mode were also tested. The Ru used as a signal probe for electrogenerated chemiluminescence (ECL) detection was detailedly studied. With this ECL biosensor, detection limit as low as 58 cells/mL was achieved for Ramos cell. The biosensor also exhibited excellent sensitivity and selectivity.

Fluorescence-activated cell sorting for aptamer SELEX with cell mixtures

Aptamers that target a specific cell subpopulation within composite mixtures represent invaluable tools in biomedical research and in the development of cell-specific therapeutics. Here we describe a detailed protocol for a modular and generally applicable scheme to select aptamers that target the subpopulations of cells in which you are interested. A fluorescence-activated cell-sorting device is used to simultaneously differentiate and separate those subpopulations of cells having bound and unbound aptamers. There are fewer false positives when using this approach in comparison with other cell-selection approaches in which unspecific binding of nucleic acids to cells with reduced membrane integrity or their unselective uptake by dead cells occurs more often. The protocol provides a state-of-the-art approach for identifying aptamers that selectively target virtually any cell type under investigation. As an example, we provide the step-by-step protocol targeting CD19(+) Burkitt's lymphoma cells, starting from the pre-SELEX (systematic evolution of ligands by exponential amplification) measurements to establish suitable SELEX conditions and ending at completion of the SELEX procedure, which reveals the enriched single-stranded DNA library.

Assembly of dsDNA nanocircles into dimeric and oligomeric aggregates

The assembly of double-stranded (ds) DNA nanocircles both by hybridization with branched oligodeoxynucleotides (ODNs) and by intercalation was analyzed by atomic force microscopy (AFM). Branched ODNs ligated to single-stranded (ss) gap regions of dsDNA nanocircles led to defined, dumbbell-shaped architectures. ODNs containing an aromatic intercalator yielded oligomeric aggregates.

The chemical biology of aptamers

Aptamers are small single-stranded nucleic acids that fold into a well-defined three-dimensional structure. They show a high affinity and specificity for their target molecules and inhibit their biological functions. Aptamers belong to the nucleic acids family and can be synthesized by chemical or enzymatic procedures, or a combination of the two. They can, therefore, be considered as both chemical and biological substances. This Review summarizes the most convenient approaches to their preparation and new developments in the field of aptamers. The application of aptamers in chemical biology is also discussed.

Theoretical studies on the interaction of modified pyrimidines and purines with purine riboswitch

Recent experimental study [S.D. Gilbert, S.J. Mediatore, R.T. Batey, Modified pyrimidine specifically bind the purine riboswitch, J. Am. Chem. Soc. 128 (2006) 14214-14215] demonstrated that the purine riboswitch could specifically bind some ligands other than purines such as amino-pyrimidines, and the authors proposed that the five-membered ring of purine was not required for recognition. To get insight into the interaction details, we used molecular docking method to investigate the interactions of a mutant form of guanine riboswitch with a series of amino-purines, amino-pyrimidines and imidazole derivatives, and employed molecular simulation method to study the dynamic behavior of the selected complexes. The calculation results reveal that (1) all the amino-purines and amino-pyrimidines bind in a same cavity composed of four nucleobases including U22, U47, U51 and U74, which is consistent with the experimental results, while the two imidazole derivatives adopt other binding modes; (2) the purines are engulfed within three-way junction motifs, but most pyrimidines only form two-way junctions with the riboswitch; (3) the number and position of amino substituents could seriously affect the binding of pyrimidines. As riboswitches are potentially excellent candidates for antibiotic therapeutics, these findings may be useful for understanding the range of compounds that riboswitch can specifically recognize.

In vitro selection of conformational probes for riboswitches

Riboswitches are non-coding RNA elements mainly located in the 5' untranslated regions (UTR) of bacterial genes. They bind to small metabolites and upon binding conformational changes occur that trigger the expression of a certain gene. Riboswitches have been identified that bind to amino acids, purines, and other small metabolites such as thiamine pyrophosphate. Riboswitches contain an aptamer domain which is necessary for interaction with the metabolite and a related expression domain which harbours structural and sequence information required for interference with gene expression. The binding of a metabolite to the aptamer domain induces structural rearrangements that are relayed to the expression domain, thereby interfering with gene expression. To investigate and determine domains of the riboswitches which undergo conformational changes upon metabolite binding we used a dynamic SELEX process and identified RNA aptamers that bind to the metabolite-free variant of the riboswitch but are released upon metabolite addition. By this means, and after determination of the binding region, domains which are necessary for proper function of a full-length riboswitch can be identified.

The UA_handle: a versatile submotif in stable RNA architectures

Stable RNAs are modular and hierarchical 3D architectures taking advantage of recurrent structural motifs to form extensive non-covalent tertiary interactions. Sequence and atomic structure analysis has revealed a novel submotif involving a minimal set of five nucleotides, termed the UA_handle motif (5'XU/AN(n)X3'). It consists of a U:A Watson-Crick: Hoogsteen trans base pair stacked over a classic Watson-Crick base pair, and a bulge of one or more nucleotides that can act as a handle for making different types of long-range interactions. This motif is one of the most versatile building blocks identified in stable RNAs. It enters into the composition of numerous recurrent motifs of greater structural complexity such as the T-loop, the 11-nt receptor, the UAA/GAN and the G-ribo motifs. Several structural principles pertaining to RNA motifs are derived from our analysis. A limited set of basic submotifs can account for the formation of most structural motifs uncovered in ribosomal and stable RNAs. Structural motifs can act as structural scaffoldings and be functionally and topologically equivalent despite sequence and structural differences. The sequence network resulting from the structural relationships shared by these RNA motifs can be used as a proto-language for assisting prediction and rational design of RNA tertiary structures.

Secondary structures and functional requirements for thiM riboswitches from Desulfovibrio vulgaris, Erwinia carotovora and Rhodobacter spheroides

Abstract Bacterial thiM riboswitches contain aptamer domains that bind the metabolite thiamine pyrophosphate (TPP). Binding of TPP to the aptamer domain induces structural rearrangements that are relayed to the expression domain, thereby interfering with gene expression. Here, we report identification of three putative thiM riboswitches from different bacteria and analysis of their secondary structures. Chemical probing revealed that the riboswitches share similar secondary structures in their aptamer domains that can communicate with the highly variant expression domains in a mechanism likely involving sequestration of the Shine-Dalgarno sequence. Remarkably, the aptamer domain of the thiM gene of Desulfovibrio vulgaris binds TPP with similar affinity and selectivity as that of Escherichia coli, although nucleotides previously shown to form direct contacts to the metabolite are mutated. We also designed small RNA hairpins for each riboswitch that bind the RNA only in the absence of the metabolite. Our study shows that aptamer domains in riboswitches with high similarity in their secondary structures can communicate with a broad variety of non-related expression domains by similar mechanisms.

An RNA molecule that specifically inhibits G-protein-coupled receptor kinase 2 in vitro

G-protein-coupled receptors are desensitized by a two-step process. In a first step, G-protein-coupled receptor kinases (GRKs) phosphorylate agonist-activated receptors that subsequently bind to a second class of proteins, the arrestins. GRKs can be classified into three subfamilies, which have been implicated in various diseases. The physiological role(s) of GRKs have been difficult to study as selective inhibitors are not available. We have used SELEX (systematic evolution of ligands by exponential enrichment) to develop RNA aptamers that potently and selectively inhibit GRK2. This process has yielded an aptamer, C13, which bound to GRK2 with a high affinity and inhibited GRK2-catalyzed rhodopsin phosphorylation with an IC50 of 4.1 nM. Phosphorylation of rhodopsin catalyzed by GRK5 was also inhibited, albeit with 20-fold lower potency (IC50 of 79 nM). Furthermore, C13 reveals significant specificity, since almost no inhibitory activity was detectable testing it against a panel of 14 other kinases. The aptamer is two orders of magnitude more potent than the best GRK2 inhibitors described previously and shows high selectivity for the GRK family of protein kinases.

Molecular basis of gene regulation by the THI-box riboswitch

Riboswitches are genetic control elements located mainly within the 5' untranslated regions of messenger RNAs. These RNA elements undergo conformational changes that modulate gene expression upon binding of regulatory signals including vitamins, amino acids, nucleobases and uncharged tRNA. The thiamin pyrophosphate (TPP)-binding riboswitch (THI-box) is found in all three kingdoms of life and can regulate gene expression at the levels of premature termination of transcription, initiation of translation and mRNA splicing. The THI-box is composed of two parallel stacked helices bound by another helix in a three-way junction. We performed an in vivo expression analysis of mutants with substitutions in conserved bases located at the interior and terminal loops of the Escherichia coli thiM THI-box, which is translationally regulated, and observed two different phenotypic classes. One class exhibited high expression during growth in the presence or absence of thiamin, while the second class exhibited low expression regardless of the presence of thiamin. Accessibility of the Shine-Dalgarno region of the RNA following the addition of TPP was monitored by means of an oligonucleotide-dependent RNase H cleavage assay, and binding of 30S ribosomal subunits. These studies showed that high- and low-expression mutant RNAs are locked in the non-repressive and repressive conformations respectively.

Conformational changes in the expression domain of the Escherichia coli thiM riboswitch

The thiM riboswitch contains an aptamer domain that adaptively binds the coenzyme thiamine pyrophosphate (TPP). The binding of TPP to the aptamer domain induces structural rearrangements that are relayed to a second domain, the so-called expression domain, thereby interfering with gene expression. The recently solved crystal structures of the aptamer domains of the thiM riboswitches in complex with TPP revealed how TPP stabilizes secondary and tertiary structures in the RNA ligand complex. To understand the global modes of reorganization between the two domains upon metabolite binding the structure of the entire riboswitch in presence and absence of TPP needs to be determined. Here we report the secondary structure of the entire thiM riboswitch from Escherichia coli in its TPP-free form and its transition into the TPP-bound variant, thereby depicting domains of the riboswitch that serve as communication links between the aptamer and the expression domain. Furthermore, structural probing provides an explanation for the lack of genetic control exerted by a riboswitch variant with mutations in the expression domain that still binds TPP.