Tetrahymena thermophila and Candida albicans Group I intron-derived ribozymes can catalyze the trans-excision-splicing reaction

Group I intron-derived ribozymes can catalyze a variety of non-native reactions. For the trans-excision-splicing (TES) reaction, an intron-derived ribozyme from the opportunistic pathogen Pneumocystis carinii catalyzes the excision of a predefined region from within an RNA substrate with subsequent ligation of the flanking regions. To establish TES as a general ribozyme-mediated reaction, intron-derived ribozymes from Tetrahymena thermophila and Candida albicans, which are similar to but not the same as that from Pneumocystis, were investigated for their propensity to catalyze the TES reaction. We now report that the Tetrahymena and Candida ribozymes can catalyze the excision of a single nucleotide from within their ribozyme-specific substrates. Under the conditions studied, the Tetrahymena and Candida ribozymes, however, catalyze the TES reaction with lower yields and rates [Tetrahymena (kobs) = 0.14/min and Candida (kobs) = 0.34/min] than the Pneumocystis ribozyme (kobs = 3.2/min). The lower yields are likely partially due to the fact that the Tetrahymena and Candida catalyze additional reactions, separate from TES. The differences in rates are likely partially due to the individual ribozymes ability to effectively bind their 3′ terminal guanosines as intramolecular nucleophiles. Nevertheless, our results demonstrate that group I intron-derived ribozymes are inherently able to catalyze the TES reaction

Encoding information onto the charge and spin state of a paramagnetic atom using MgO tunnelling spintronics

An electrical current that flows across individual atoms or molecules can generate exotic quantum-based behavior, from memristive effects to Coulomb blockade and the promotion of quantum excited states. These fundamental effects typically appear one at a time in model junctions built using atomic tip or lateral techniques. So far, however, a viable industrial pathway for such discrete state devices has been lacking. Here, we demonstrate that a commercialized device platform can serve as this industrial pathway for quantum technologies. We have studied magnetic tunnel junctions with a MgO barrier containing C atoms. The paramagnetic localized electrons due to individual C atoms generate parallel nanotransport paths across the micronic device as deduced from magnetotransport experiments. Coulomb blockade effects linked to tunnelling magnetoresistance peaks can be electrically controlled, leading to a persistent memory effect. Our results position MgO tunneling spintronics as a promising platform to industrially implement quantum technologies

One RNA plays three roles to provide catalytic activity to a group I intron lacking an endogenous internal guide sequence

Catalytic RNA molecules possess simultaneously a genotype and a phenotype. However, a single RNA genotype has the potential to adopt two or perhaps more distinct phenotypes as a result of differential folding and/or catalytic activity. Such multifunctionality would be particularly significant if the phenotypes were functionally inter-related in a common biochemical pathway. Here, this phenomenon is demonstrated by the ability of the Azoarcus group I ribozyme to function when its canonical internal guide sequence (GUG) has been removed from the 5′ end of the molecule, and added back exogenously in trans. The presence of GUG triplets in non-covalent fragments of the ribozyme allow trans-splicing to occur in both a reverse splicing assay and a covalent self-assembly assay in which the internal guide sequence (IGS)-less ribozyme can put itself together from two of its component pieces. Analysis of these reactions indicates that a single RNA fragment can perform up to three distinct roles in a reaction: behaving as a portion of a catalyst, behaving as a substrate, and providing an exogenous IGS. This property of RNA to be multifunctional in a single reaction pathway bolsters the probability that a system of self-replicating molecules could have existed in an RNA world during the origins of life on the Earth

Genetic transformation and genomic resources for next-generation precise genome engineering in vegetable crops

In the frame of modern agriculture facing the predicted increase of population and general environmental changes, the securement of high quality food remains a major challenge to deal with. Vegetable crops include a large number of species, characterized by multiple geographical origins, large genetic variability and diverse reproductive features. Due to their nutritional value, they have an important place in human diet. In recent years, many crop genomes have been sequenced permitting the identification of genes and superior alleles associated with desirable traits. Furthermore, innovative biotechnological approaches allow to take a step forward towards the development of new improved cultivars harboring precise genome modifications. Sequence-based knowledge coupled with advanced biotechnologies is supporting the widespread application of new plant breeding techniques to enhance the success in modification and transfer of useful alleles into target varieties. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 system, zinc-finger nucleases, and transcription activator-like effector nucleases represent the main methods available for plant genome engineering through targeted modifications. Such technologies, however, require efficient transformation protocols as well as extensive genomic resources and accurate knowledge before they can be efficiently exploited in practical breeding programs. In this review, we revise the state of the art in relation to availability of such scientific and technological resources in various groups of vegetables, describe genome editing results obtained so far and discuss the implications for future applications

Modulating RNA structure and catalysis: lessons from small cleaving ribozymes

RNA is a key molecule in life, and comprehending its structure/function relationships is a crucial step towards a more complete understanding of molecular biology. Even though most of the information required for their correct folding is contained in their primary sequences, we are as yet unable to accurately predict both the folding pathways and active tertiary structures of RNA species. Ribozymes are interesting molecules to study when addressing these questions because any modifications in their structures are often reflected in their catalytic properties. The recent progress in the study of the structures, the folding pathways and the modulation of the small ribozymes derived from natural, self-cleaving, RNA motifs have significantly contributed to today’s knowledge in the field

Design, synthesis, and analysis of conformationally constrained nucleic acids

In this review I discuss straightforward and general methods to modify nucleic acid structure with disulfide cross-links. A motivating factor in developing this chemistry was the notion that disulfide bonds would be excellent tools to probe the structure, dynamics, thermodynamics, folding, and function of DNA and RNA, much in the way that cystine cross-links have been used to study proteins. The chemistry described has been used to synthesize disulfide cross-linked hairpins and duplexes, higher order structures like triplexes, nonground-state conformations, and tRNAs. Since the cross-links form quantitatively by mild air oxidation and do not perturb either secondary or tertiary structure, this modification should prove quite useful for the study of nucleic acids. © 1998 John Wiley & Sons, Inc. Biopoly 48: 83–96, 1998Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/37876/1/8_ftp.pd

Divalent Metal Ions Tune the Self-Splicing Reaction of the Yeast Mitochondrial Group II Intron Sc.ai5γ

Group II introns are large ribozymes, consisting of six functionally distinct domains that assemble in the presence of Mg2+ to the active structure catalyzing a variety of reactions. The first step of intron splicing is well characterized by a Michaelis–Menten-type cleavage reaction using a two-piece group II intron: the substrate RNA, the 5′-exon covalently linked to domains 1, 2, and 3, is cleaved upon addition of domain 5 acting as a catalyst. Here we investigate the effect of Ca2+, Mn2+, Ni2+, Zn2+, Cd2+, Pb2+, and [Co(NH3)6]3+ on the first step of splicing of the Saccharomyces cerevisiae mitochondrial group II intron Sc.ai5γ. We find that this group II intron is very sensitive to the presence of divalent metal ions other than Mg2+. For example, the presence of only 5% Ca2+ relative to Mg2+ results in a decrease in the maximal turnover rate k cat by 50%. Ca2+ thereby has a twofold effect: this metal ion interferes initially with folding, but then also competes directly with Mg2+ in the folded state, the latter being indicative of at least one specific Ca2+ binding pocket interfering directly with catalysis. Similar results are obtained with Mn2+, Cd2+, and [Co(NH3)6]3+. Ni2+ is a much more powerful inhibitor and the presence of either Zn2+ or Pb2+ leads to rapid degradation of the RNA. These results show a surprising sensitivity of such a large multidomain RNA on trace amounts of cations other than Mg2+ and raises the question of biological relevance at least in the case of Ca2+

Exploration des nanocanaux de transport de dispositifs spintroniques pour l’encodage de l'information et la récolte énergétique

Ever since spintronics revolutionized information storage, it has found cross-disciplinary applications in sensing, energy harvesting, the Internet of things, neuromorphic computing, and many more. To design and develop novel functionalities in spintronic devices, it is crucial to understand the nano-transport paths that occur across these devices. In this thesis, the spintronic nano-transport channels across inorganic (MgO) and organic (CoPc) magnetic tunnel junctions are explored. We demonstrate new experimental techniques using synchrotron X-rays to understand the role of oxygen defects in the MgO barrier in the operation of an MTJ. Here, multifunctional spintronic devices for encoding information and energy harvesting are highlighted. Backed by theory and experiment, we establish how the quantum excited state of a CoPc molecular spin chain can be used to encode information in a solid-state device. Following this, we design a spintronic nano engine using Co paramagnetic centres, and record room temperature power output, thereby bridging molecular spintronics and quantum thermodynamics.Depuis que la spintronique a révolutionné le stockage de l'information, elle a trouvé des applications interdisciplinaires dans la détection, la collecte d'énergie, l'Internet des objets, l'informatique neuromorphique, et bien d'autres encore. Pour concevoir et développer de nouvelles fonctionnalités dans les dispositifs spintroniques, il est crucial de comprendre les nanocanaux de transport au travers de ceux-ci. Dans cette thèse, les canaux de nanotransport spintronique à travers des jonctions magnétiques inorganiques (MgO) et organiques (CoPc) sont explorés. Nous faisons la démonstration de nouvelles techniques expérimentales utilisant les rayons X synchrotron pour comprendre le rôle des défauts de l'oxygène dans la barrière de MgO dans le fonctionnement d'un MTJ. Ici, des dispositifs spintroniques multifonctionnels pour le codage de l'information et la collecte d'énergie sont mis en évidence. En s'appuyant sur la théorie et l'expérience, nous demonstrons que l’etat quantique excite d’une chaine de spin moleculaire peut etre utilisee pour encoder de l’information un dispositif à l'état solide.Enfin, nous concevons un nano-moteur spintronique utilisant des centres paramagnétiques Co qui développe une forte puissances électrique à température ambiante, ce qui réalise un pont entre la spintronique moléculaire et la thermodynamique quantique

Exploration des nanocanaux de transport de dispositifs spintroniques pour l’encodage de l'information et la récolte énergétique

Depuis que la spintronique a révolutionné le stockage de l'information, elle a trouvé des applications interdisciplinaires dans la détection, la collecte d'énergie, l'Internet des objets, l'informatique neuromorphique, et bien d'autres encore. Pour concevoir et développer de nouvelles fonctionnalités dans les dispositifs spintroniques, il est crucial de comprendre les nanocanaux de transport au travers de ceux-ci. Dans cette thèse, les canaux de nanotransport spintronique à travers des jonctions magnétiques inorganiques (MgO) et organiques (CoPc) sont explorés. Nous faisons la démonstration de nouvelles techniques expérimentales utilisant les rayons X synchrotron pour comprendre le rôle des défauts de l'oxygène dans la barrière de MgO dans le fonctionnement d'un MTJ. Ici, des dispositifs spintroniques multifonctionnels pour le codage de l'information et la collecte d'énergie sont mis en évidence. En s'appuyant sur la théorie et l'expérience, nous demonstrons que l’etat quantique excite d’une chaine de spin moleculaire peut etre utilisee pour encoder de l’information un dispositif à l'état solide. Enfin, nous concevons un nano-moteur spintronique utilisant des centres paramagnétiques Co qui développe une forte puissances électrique à température ambiante, ce qui réalise un pont entre la spintronique moléculaire et la thermodynamique quantique.Ever since spintronics revolutionized information storage, it has found cross-disciplinary applications in sensing, energy harvesting, the Internet of things, neuromorphic computing, and many more. To design and develop novel functionalities in spintronic devices, it is crucial to understand the nano-transport paths that occurs across these devices. In this thesis, the spintronic nano-transport channels across inorganic (MgO) and organic (CoPc) magnetic tunnel junctions are explored. We demonstrate new experimental techniques using synchrotron X-rays to understand the role of oxygen defects in MgO barrier in the operation of an MTJ. Here, multifunctional spintronic devices for encoding information and energy harvesting are highlighted. Backed by theory and experiment, we establish how the quantum excited state of a CoPc molecular spin chain can be used to encode information in a solid-state device. Following this, we design a spintronic nanoengine using Co paramagnetic centers, and record room temperature power output, thereby bridging molecular spintronics and quantum thermodynamics

Exploration des nanocanaux de transport de dispositifs spintroniques pour l’encodage de l'information et la récolte énergétique

Ever since spintronics revolutionized information storage, it has found cross-disciplinary applications in sensing, energy harvesting, the Internet of things, neuromorphic computing, and many more. To design and develop novel functionalities in spintronic devices, it is crucial to understand the nano-transport paths that occurs across these devices. In this thesis, the spintronic nano-transport channels across inorganic (MgO) and organic (CoPc) magnetic tunnel junctions are explored. We demonstrate new experimental techniques using synchrotron X-rays to understand the role of oxygen defects in MgO barrier in the operation of an MTJ. Here, multifunctional spintronic devices for encoding information and energy harvesting are highlighted. Backed by theory and experiment, we establish how the quantum excited state of a CoPc molecular spin chain can be used to encode information in a solid-state device. Following this, we design a spintronic nanoengine using Co paramagnetic centers, and record room temperature power output, thereby bridging molecular spintronics and quantum thermodynamics.Depuis que la spintronique a révolutionné le stockage de l'information, elle a trouvé des applications interdisciplinaires dans la détection, la collecte d'énergie, l'Internet des objets, l'informatique neuromorphique, et bien d'autres encore. Pour concevoir et développer de nouvelles fonctionnalités dans les dispositifs spintroniques, il est crucial de comprendre les nanocanaux de transport au travers de ceux-ci. Dans cette thèse, les canaux de nanotransport spintronique à travers des jonctions magnétiques inorganiques (MgO) et organiques (CoPc) sont explorés. Nous faisons la démonstration de nouvelles techniques expérimentales utilisant les rayons X synchrotron pour comprendre le rôle des défauts de l'oxygène dans la barrière de MgO dans le fonctionnement d'un MTJ. Ici, des dispositifs spintroniques multifonctionnels pour le codage de l'information et la collecte d'énergie sont mis en évidence. En s'appuyant sur la théorie et l'expérience, nous demonstrons que l’etat quantique excite d’une chaine de spin moleculaire peut etre utilisee pour encoder de l’information un dispositif à l'état solide. Enfin, nous concevons un nano-moteur spintronique utilisant des centres paramagnétiques Co qui développe une forte puissances électrique à température ambiante, ce qui réalise un pont entre la spintronique moléculaire et la thermodynamique quantique