Aminoglycoside complexation with a DNA.RNA hybrid duplex: the thermodynamics of recognition and inhibition of RNA processing enzymes

Spectroscopic and calorimetric techniques were employed to characterize and contrast the binding of the aminoglycoside paromomycin to three octamer nucleic acid duplexes of identical sequence but different strand composition (a DNA.RNA hybrid duplex and the corresponding DNA.DNA and RNA.RNA duplexes). In addition, the impact of paromomycin binding on both RNase H- and RNase A-mediated cleavage of the RNA strand in the DNA.RNA duplex was also determined. Our results reveal the following significant features: (i) Paromomycin binding enhances the thermal stabilities of the RNA.RNA and DNA.RNA duplexes to similar extents, with this thermal enhancement being substantially greater in magnitude than that of the DNA.DNA duplex. (ii) Paromomycin binding to the DNA.RNA hybrid duplex induces CD changes consistent with a shift from an A-like to a more canonical A-conformation. (iii) Paromomycin binding to all three octamer duplexes is linked to the uptake of a similar number of protons, with the magnitude of this number being dependent on pH. (iv) The affinity of paromomycin for the three host duplexes follows the hierarchy, RNA.RNA > DNA.RNA > DNA.DNA. (v) The observed affinity of paromomycin for the RNA.RNA and DNA.RNA duplexes decreases with increasing pH. (vi) The binding of paromomycin to the DNA.RNA hybrid duplex inhibits both RNase H- and RNase A-mediated cleavage of the RNA strand. We discuss the implications of our combined results with regard to the specific targeting of DNA.RNA hybrid duplex domains and potential antiretroviral applications.     

Histidine affinity chromatography-based methodology for the simultaneous isolation of Escherichia coli small and ribosomal RNA

Research on RNA has led to many important biological discoveries and the improvement of therapeutic technologies. In particular, there is a great focus on small RNA and ribosomal RNA owing to their key functions in the cell, which make them excellent therapeutic targets. Although the study of these RNA classes is progressing, some limitations have been found regarding the use of suitable techniques that are able to produce and isolate biologically competent and chemically stable RNA. To address this, we have developed a novel histidine affinity chromatography-based isolation methodology for small and ribosomal RNA molecules. The new procedure involves three main steps: (1) cell lysis with guanidinium buffer, (2) RNA primary isolation with ammonium sulfate precipitation and (3) histidine affinity chromatography to specifically purify small RNA and ribosomal RNA from other Escherichia coli impurities (genomic DNA and proteins). The RNA quality assessment revealed that both RNA species were obtained with a high recovery, integrity and purity. The potential of this method to achieve a reproducible RNA isolation with appropriate quality has been demonstrated and it should have broad application in the structural, biophysical and biomedical investigation of systems involving RNA components.     

Applications of synthetic oligoribonucleotide analogues in studies of RNA structure and function

The study of RNA structure and function has been considerably aided by the development of methods for the chemical synthesis of oligoribonucleotides into which have been incorporated modified nucleosides carrying site-specific alterations. Such modifications are designed to eliminate or alter individual functional groups in the RNA which potentially can take part in hydrogen-bonding or other non-covalent interactions. Comparison of the properties of the modified RNA with unmodified RNA models allows conclusions to be drawn concerning the importance or otherwise of specific functional groups within the RNA. The methods have been applied to studies of RNA structure, RNA catalysis, and interactions of RNA with proteins.     

Ultraviolet C radiation influences the robustness of RNA integrity measurement

The analytical and clinical validity of analyses of RNA samples destined for clinical diagnosis and therapeutic management is directly impacted by RNA quality. RNA is affected by heat, enzymatic degradation, and Ultraviolet (UV) light. RNA from three eukaryotic cell lines was degraded by heat, RNase, or UV light. RNA integrity values obtained with the benchmark Agilent Bioanalyzer 2100 system were compared with those from the more recent QIAxcel Advanced system. The application of this novel method has allowed us to unravel differences between RNA biophysical and biochemical degradation modes. Agilent RNA integrity number (RIN) and QIAxcel RIS were comparable in heat‐degraded and RNase III‐degraded RNA. Agilent RIN and QIAxcel RIS were comparable at a RIN decision level of 7 in UV‐degraded RNA but not overall. The QIAxcel RIS method was more precise than Agilent RIN for RIN<8, while the inverse was true for RIN≥8. Greater degradation of mRNA and rRNA in UV‐damaged samples hampered the Agilent RIN calculation algorithm. Overall, RIS was more robust than RIN for assessing RNA integrity. The ΔΔCt‐values for heat‐ and UV‐degraded RNA samples showed slightly higher correlation with RIS than with RIN. RNA integrity can be used to categorize RNA samples for suitability for downstream gene expression analyses, independently of the RNA degradation mechanism. The new method QIAxcel is more robust and therefore allows more accurate categorization of compromised RNA samples.     

The oligodeoxynucleotide probes for the site-specific modification of RNA

As the knowledge of the biological functions of RNA expands, the demand for research tools to investigate intracellular RNA is increasing. Oligonucleotides can be rationally designed for the target RNA sequence, and therefore, have become a reliable platform for the development of specific molecules for RNA. The chemical modification of RNA has a strong impact on RNA research; the fluorescent labeling of RNA is useful to monitor RNA production, processing, relocation in the cell, interaction with other intracellular components and degradation, etc. Chemical modification may affect the RNA function through a variety of pathways, and therefore, would be potentially useful for biological research, therapeutic approach and artificial manipulation of the RNA function. This tutorial review starts with an introduction of the biological relevance of modified RNA, and focuses on the recent progress of the oligodeoxynucleotide probes for the covalent modifications of RNA. The prospects of this new technology are also discussed.     

A novel layer-by-layer approach for the fabrication of conducting polymer/RNA multilayer films for controlled release

Poly(anilineboronic acid) (PABA)/ribonucleic acid (RNA) multilayer films were prepared under neutral condition using a layer-by-layer deposition of PABA and RNA. RNA was used both as a polyelectrolyte for multilayer formation as well as dopant for PABA. Photoelastic modulated infrared reflection absorption spectroscopy measurements suggest that PABA interacts covalently with RNA through the formation of a boronate ester, a boron-nitrogen dative bond, as well as electrostatic interactions of anionic phosphates with cationic amines. The deposition procedure was monitored with UV-vis absorption spectroscopy, showing a linear dependence of absorbance with the number of PABA/RNA bilayers deposited. The multilayer films were further characterized using X-ray photoelectron spectroscopy and ellipsometry, which yielded a PABA/RNA bilayer thickness of approximately 10 nm. The PABA/RNA multilayer films are redox-active at neutral pH, consistent with the formation of a self-doped polymer. Electrochemical control of PABA under these conditions allows potential-induced controlled release of RNA from a multilayer at neutral pH, suggesting that this may serve as a novel method for controlled release of RNA under physiological conditions.     

Shape-Selective Targeting on RNA Bulges by Peptidomimetic Metallohelices

RNA bulges represent one of the most common motifs in the RNA secondary structure and serve in a variety of biological functions. Compounds stabilizing RNA bulges are important for probing RNA structure and function and for therapy of some diseases. Here, the ability of a series of enantiomeric pairs of optically pure bimetallic metallohelices with different flexible linkers to target various RNA bulges is investigated. The results show that binding affinities of the metallohelices to bulged RNA differ and strongly depend on the size of the bulge and the base composition of the bulge loop. Notably, the shorter, more compact, and less flexible metallohelices bind to RNA bulges most efficiently and selectively. Interestingly, the ability of the metallohelices to bind to RNA bulges correlates with their previously reported antimicrobial activity, which suggests that the selective recognition of bulged regions in RNA by the metallohelices might also contribute to their biological activity.     

Construction of photoresponsive RNA for photoswitching RNA hybridization

By introducing azobenzenes into RNA using d-threoninol as a scaffold, a photoresponsive RNA was constructed for efficiently photoswitching the formation and dissociation of RNA/RNA duplexes. The difference in melting temperature (T(m)) between the trans and cis forms was so large that efficient photoregulation of RNA hybridization became possible, irrespective of the sequence adjacent to the introduced azobenzene. Compared to the corresponding photoresponsive DNA, the photoregulatory efficiency of azobenzene-modified RNA was even higher due to the drastic destabilization by cis-azobenzene. Structural analysis by NMR and molecular modeling indicated that the planar trans-azobenzene could not stabilize the RNA/RNA duplex with a rigid A-form structure by base pair stacking. However, the large steric hindrance caused by nonplanar cis-azobenzene was quite effective at distorting and destabilizing the duplex structure. We also discuss the effect of methylation of azobenzene at the ortho positions on photoregulation of RNA/RNA duplex formation. This newly constructed photoresponsive RNA has promising applications such as photoswitching of RNA functions.     

A semi-supervised learning approach for RNA secondary structure prediction

RNA secondary structure prediction is a key technology in RNA bioinformatics. Most algorithms for RNA secondary structure prediction use probabilistic models, in which the model parameters are trained with reliable RNA secondary structures. Because of the difficulty of determining RNA secondary structures by experimental procedures, such as NMR or X-ray crystal structural analyses, there are still many RNA sequences that could be useful for training whose secondary structures have not been experimentally determined. In this paper, we introduce a novel semi-supervised learning approach for training parameters in a probabilistic model of RNA secondary structures in which we employ not only RNA sequences with annotated secondary structures but also ones with unknown secondary structures. Our model is based on a hybrid of generative (stochastic context-free grammars) and discriminative models (conditional random fields) that has been successfully applied to natural language processing. Computational experiments indicate that the accuracy of secondary structure prediction is improved by incorporating RNA sequences with unknown secondary structures into training. To our knowledge, this is the first study of a semi-supervised learning approach for RNA secondary structure prediction. This technique will be useful when the number of reliable structures is limited.     

New approach in RNA quantification using arginine-affinity chromatography: potential application in eukaryotic and chemically synthesized RNA

The knowledge of RNA’s role in biological systems and the recent recognition of its potential use as a reliable biotherapeutic tool increase the demand for development and validation of analytical methods for accurate analysis of RNA. Affinity chromatography is a unique technique because of the versatility of applications reliant on the affinity ligand used. Recently, an arginine-based matrix has been effectively applied in the purification of RNA because of the specific recognition mechanism for RNA molecules. This interaction is suggested to be due to the length of arginine side chain and its ability to produce good hydrogen bonding geometries, which promote multi-contact with RNA backbone or RNA bases, based on RNA folding. Thus, this work presents the development and validation of an analytical method with ultraviolet detection for the quantification of RNA using affinity chromatography with arginine amino acid as immobilized ligand. The method was validated according to International and European legislation for bioanalytical methods. The results revealed that the proposed method is suitable for the reliable detection, separation, and quantification of RNA, showing that the method is precise and accurate for concentrations up to 200 ng/μL of RNA. Furthermore, the versatility of the methodology was demonstrated by its applicability in the quantification of RNA from different eukaryotic cells and in crude samples of chemically synthesized RNA. Therefore, the proposed method demonstrates a potential multipurpose applicability in molecular biology RNA-based analysis and RNA therapeutics.

The RNA2-PNA2 hybrid i-motif-a novel RNA-based building block

We report the formation of a hybrid RNA2-PNA2 i-motif comprised of two RNA and two PNA strands based on the sequence specific self assembly of RNA, with potential as a building block for structural RNA nanotechnology.     

Nucleobase‐Modified PNA Suppresses Translation by Forming a Triple Helix with a Hairpin Structure in mRNA In Vitro and in Cells

Compounds that bind specifically to double‐stranded regions of RNA have potential as regulators of structure‐based RNA function; however, sequence‐selective recognition of double‐stranded RNA is challenging. The modification of peptide nucleic acid (PNA) with unnatural nucleobases enables the formation of PNA–RNA triplexes. Herein, we demonstrate that a 9‐mer PNA forms a sequence‐specific PNA–RNA triplex with a dissociation constant of less than 1 nm at physiological pH. The triplex formed within the 5′ untranslated region of an mRNA reduces the protein expression levels both in vitro and in cells. A single triplet mismatch destabilizes the complex, and in this case, no translation suppression is observed. The triplex‐forming PNAs are unique and potent compounds that hold promise as inhibitors of cellular functions that are controlled by double‐stranded RNAs, such as RNA interference, RNA editing, and RNA localization mediated by protein–RNA interactions.     

Cooperative binding and self-assembling behavior of cationic low molecular-weight dendrons with RNA molecules

Tri(ethylene glycol) derived, low molecular-weight dendrons with various amine end groups were synthesized and characterized for their properties of binding and self-assembling with RNA using the Candida ribozyme as a model RNA molecule. These dendritic compounds form stable complexes and well-defined nanoscale particles with RNA molecules via electrostatic interactions and self-assembly process, while leaving the other terminal of the tri(ethylene glycol) chain accessible for targeting. This suggests that dendrimers of this type hold great promise for specific RNA targeting and RNA delivery.     

Loading of Amino Acids onto RNA in a Putative RNA-Peptide World

RNA is a molecule that can both store genetic information and perform catalytic reactions. This observed dualism places RNA into the limelight of concepts about the origin of life. The RNA world concept argues that life started from self-replicating RNA molecules, which evolved toward increasingly complex structures. Recently, we demonstrated that RNA, with the help of conserved non-canonical nucleosides, which are also putative relics of an early RNA world, had the ability to grow peptides covalently connected to RNA nucleobases, creating RNA-peptide chimeras. It is conceivable that such molecules, which combined the information-coding properties of RNA with the catalytic potential of amino acid side chains, were once the structures from which life emerged. Herein, we report prebiotic chemistry that enabled the loading of both nucleosides and RNAs with amino acids as the first step toward RNA-based peptide synthesis in a putative RNA-peptide world.     

Evaluation of chemical labeling strategies for monitoring HCV RNA using vibrational microscopy

Raman and coherent anti-Stokes Raman scattering (CARS) microscopies have the potential to aid in detailed longitudinal studies of RNA localization. Here, we evaluate the use of carbon-deuterium and benzonitrile functional group labels as contrast agents for vibrational imaging of hepatitis C virus (HCV) replicon RNA. Dynamic light scattering and atomic force microscopy were used to evaluate the structural consequences of altering HCV subgenomic replicon RNA. Modification with benzonitrile labels caused the replicon RNA tertiary structure to partially unfold. Conversely, deuterium-modified replicon RNA was structurally similar to unmodified replicon RNA. Furthermore, the deuterated replicon RNA provided promising vibrational contrast in Raman imaging experiments. The functional effect of modifying subgenomic HCV replicon RNA was evaluated using the luciferase gene as a genetic reporter of translation. Benzonitrile labeling of the replicon RNA prevented translation in cell-based luciferase assays, while the deuterated replicon RNA retained both translation and replication competency. Thus, while the scattering cross-section for benzonitrile labels was higher, only carbon-deuterium labels proved to be non-perturbative to the function of HCV replicon RNA.     

ULTRAVIOLET INACTIVATION OF THE MIDI VARIANT OF QP RNA: CHARACTERIZATION OF TEMPLATE ACTIVITY

Abstract— MDV-1 RNA is a 218 nucleotide variant of bacteriophage Qβ RNA. Qβ replicase catalyzes the formation of a strand complementary to a single-stranded (SS) MDV-I template. Upon phenol extraction, the template and complementary strands become double-stranded (DS). Polyacrylamide gel electrophoresis of the products of this reaction revealed SS RNA, DS RNA, and discrete intermediate bands. UV irradiation of the template caused a decrease in DS RNA production which followed single-hit kinetics with a quantum yield of 1.6 × 10^--³. Concomitant with this diminished DS RNA production were increases in SS RNA and intermediate sized RNA. The latter was shown to consist of a full sized SS template annealed to a partially completed nascent strand. Upon electrophoresis, these partially completed duplexes migrated in the same positions as those found in the analysis of unirradiated template, suggesting that this RNA contains replication obstruction areas in which UV lesions cause an increase in replication inhibition.