Reversible 5′-end biotinylation and affinity purification of synthetic RNA

A reversible biotinylation phosphoramidite was synthesized and incorporated onto the 5′-end of an oligoribonucleotide on a solid phase synthesizer. After cleavage and deprotection, the crude synthetic oligomer mixture was incubated with NeutrAvidin^® coated microspheres, and the failure sequences removed by washing with a buffer followed by treating the microspheres with tetrabutylammonium fluoride to give a high quality unmodified full-length oligoribonucleotide.     

Extension of multivariate regression trees to interval data. Application to electricity load profiling

Summary  Several data can be presented as interval curves where intervals reflect a within variability. In particular, this representation is well adapted for load profiles, which depict the electricity consumption of a class of customers. Electricity load profiling consists in assigning a daily load curve to a customer based on their characteristics such as energy requirement. Within the load profiling scope, this paper investigates the extension of multivariate regression trees to the case of interval dependent (or response) variables. The tree method aims at setting up simultaneously load profiles and their assignment rules based on independent variables. The extension of multivariate regression trees to interval responses is detailed and a global approach is defined. It consists in a first stage of a dimension reduction of the interval response variables. Thereafter, the extension of the tree method is applied to the first principal interval components. Outputs are the classes of the interval curves where each class is characterized both by an interval load profile (e.g. the class prototype) and an assignment rule based on the independent variables.     

Evolutionary rate variation and RNA secondary structure prediction

Predicting RNA secondary structure using evolutionary history can be carried out by using an alignment of related RNA sequences with conserved structure. Accurately determining evolutionary substitution rates for base pairs and single stranded nucleotides is a concern for methods based on this type of approach. Determining these rates can be hard to do reliably without a large and accurate initial alignment, which ideally also has structural annotation. Hence, one must often apply rates extracted from other RNA families with trusted alignments and structures. Here, we investigate this problem by applying rates derived from tRNA and rRNA to the prediction of the much more rapidly evolving 5'-region of HIV-1. We find that the HIV-1 prediction is in agreement with experimental data, even though the relative evolutionary rate between A and G is significantly increased, both in stem and loop regions. In addition we obtained an alignment of the 5' HIV-1 region that is more consistent with the structure than that currently in the database. We added randomized noise to the original values of the rates to investigate the stability of predictions to rate matrix deviations. We find that changes within a fairly large range still produce reliable predictions and conclude that using rates from a limited set of RNA sequences is valid over a broader range of sequences.     

Evaluation of the sputtering rate variation in SIMS ultra‐shallow depth profiling using multiple short‐period delta layers

We have developed multiple short‐period delta layers as a reference material for SIMS ultra‐shallow depth profiling. Boron nitride delta layers and silicon spacer layers were sputter‐deposited alternately, with a silicon spacer thickness of 1–5 nm. These delta‐doped layers were used to measure the sputtering rate change in the initial stage of oxygen ion bombardment. A significant variation of sputtering rate was observed in the initial 3 nm or less. The sputtering rate in the initial 3 nm was estimated to be about four times larger than the steady‐state value for 1000 eV oxygen ions. Copyright © 2003 John Wiley & Sons, Ltd.     

Targeting of Single‐Stranded Oligonucleotides through Metal‐Induced Cyclization of Short Complementary Strands

A new strategy to cyclize short synthetic oligonucleotides on DNA or RNA target strands is described. The approach is based on metal‐templated cyclization of short synthetic oligonucleotides conjugated with two chelating 2,2′ : 6′,2′′‐terpyridine (Tpy) moieties at their 3′‐ and 5′‐ends. Cyclization after metal addition (Zn²⁺, Fe²⁺) was demonstrated by means of thermal‐denaturation experiments, MALDI‐Q‐TOF‐MS, and gel electrophoresis (PAGE). 1D‐ and 2D‐NMR Experiments were performed to analyze the association of complementary strands after metal‐mediated cyclization. Our protocol allows the efficient circularization of synthetic oligonucleotides. Thereby, the hybridization on a complementary strand was more efficient with an RNA target strand and a 2′‐O‐methylated circularized oligomer.     

Potential Achilles heels of SARS-CoV-2 are best displayed by the base order-dependent component of RNA folding energy

The base order-dependent component of folding energy has revealed a highly conserved region in HIV-1 genomes that associates with RNA structure. This corresponds to a packaging signal that is recognized by the nucleocapsid domain of the Gag polyprotein. Long viewed as a potential HIV-1 "Achilles heel," the signal can be targeted by a new antiviral compound. Although SARS-CoV-2 differs in many respects from HIV-1, the same technology displays regions with a high base order-dependent folding energy component, which are also highly conserved. This indicates structural invariance (SI) sustained by natural selection. While the regions are often also protein-encoding (e. g. NSP3, ORF3a), we suggest that their nucleic acid level functions can be considered potential "Achilles heels" for SARS-CoV-2, perhaps susceptible to therapies like those envisaged for AIDS. The ribosomal frameshifting element scored well, but higher SI scores were obtained in other regions, including those encoding NSP13 and the nucleocapsid (N) protein.     

Synthesis of novel analogs of aromatic peptide nucleic acids (APNAs) with modified conformational and electrostatic properties

Aromatic peptide nucleic acid analogs having an N-(2-aminobenzyl)glycine backbone (APNA 1) were previously identified as promising new leads for the design of polyaromatic DNA mimics. Structural modifications of 1, which lock the aromatic backbone into a unique conformation, while maintaining the same space distribution between the nucleobases as in 1, were investigated. The electrostatic potential of the aromatic backbone was also modified in an attempt to improve the solubility of these compounds in aqueous media and to evaluate how the quadrapole of the aromatic backbone may influence the biophysical properties of the APNA oligomers. PNA hexamers containing a single monomer insert of each new APNA monomer were used to explore the hybridization properties of these analogs with poly rA and poly dA. Preliminary results indicated that these modifications do not seriously alter the molecular recognition properties of APNAs towards DNA and RNA.     

Chromatography of plasmid DNA

Liquid chromatography plays a central role in process-scale manufacturing of therapeutic plasmid DNA (pDNA) for gene therapy and DNA vaccination. Apart from its use as a preparative purification step, it is also very useful as an analytical tool to monitor and control pDNA quality during processing and in final formulations. This paper gives an overview of the use of pDNA chromatography. The specificity of pDNA purification and the consequent limitations to the performance of chromatography are described. Strategies currently used to overcome those limitations, as well as other possible solutions are presented. Applications of the different types of chromatography to the purification of therapeutic pDNA are reviewed, and the main advantages and disadvantages behind each technique highlighted.     

Oxygen diffusion in SrCe<Subscript>0.95</Subscript>Yb<Subscript>0.05</Subscript>O<Subscript>3−δ</Subscript>

¹⁸O/¹⁶O isotope exchange depth profiling (IEDP) combined with secondary ion mass spectrometry (SIMS) has been used to measure the oxygen tracer diffusivity of SrCe_0.95Yb_0.05O_3– between 800 °C and 500 °C at a nominal pressure of 200 mbar. The values of D* (oxygen tracer diffusion coefficient) and k (surface exchange coefficient) increase steadily with increasing temperature, and the activation energies are 1.13 eV and 0.96 eV, respectively. Oxygen ion conductivities have been calculated using the Nernst–Einstein equation. The transport number for oxide ions at 769 °C, the highest temperature studied, is only ~0.05. Moreover, SrCe_0.95Yb_0.05O_3– has been studied using impedance spectroscopy under dry O₂, wet O₂ and wet H₂ (N₂/10% H₂) atmospheres, over the range 850–300 °C. Above ~550 °C, SrCe_0.95Yb_0.05O_3– shows higher conductivity in dry O₂ than in wet O₂ or wet H₂; below that temperature the results obtained for the three atmospheres are comparable. Dry O₂ shows the highest activation energy (0.77 eV); the activation energies for wet O₂ and wet H₂ are identical (0.62 eV).Abbreviations HTPC high-temperature proton conductor - IEDP isotope exchange depth profiling - SIMS secondary ion mass spectrometryPresented at the OSSEP Workshop Ionic and Mixed Conductors: Methods and Processes, Aveiro, Portugal, 10–12 April 2003