Self-association of short DNA loops through minor groove C:G:G:C tetrads

In addition to the better known guanine-quadruplex,four-stranded nucleic acid structures can be formed by tetrads resulting from the association of Watson–Crick base pairs. When such association occurs through the minor groove side of the base pairs, the resulting structure presents distinctive features, clearly different from quadruplex structures containing planar G-tetrads. Although we have found this unusual DNA motif in a number of cyclic oligonucleotides, this is the first time that this DNA motif is found in linear oligonucleotides in solution, demonstrating that cyclization is not required to stabilize minor groove tetrads in solution. In this article, we have determined the solution structure of two linear octamers of sequence d(TGCTTCGT) and d(TCGTTGCT), and their cyclic analogue d, utilizing 2D NMR spectroscopy and restrained molecular dynamics. These three molecules self-associate forming symmetric dimers stabilized by a novel kind of minor groove C:G:G:C tetrad, in which the pattern of hydrogen bonds differs from previously reported ones. We hypothesize that these quadruplex structures can be formed by many different DNA sequences, but its observation in linear oligonucleotides is usually hampered by competing Watson–Crick duplexes.Peer reviewe

The surveys: nexus between industry and academia

[EN] Analysis and improvement processes are key aspects in any quality management system and they have to be applied on the quality management systems that have all degrees currently taught at Spanish Universities. In this way, surveys can be an important tool. For this reason, the Faculty of Chemistry of the Universitat de Barcelona prepared a survey for chemical and pharmaceutical companies to identify the type of training that is required for students. The survey has questions related to the laboratory operations, chemical processes, calculation methods, management systems of quality, environment and safety, general management information, etc. The items are related to the formation given to the students in the Faculty. The scores obtained (minimum 1, maximum 4) are between 2 and 3 in all the items, both the required knowledge as to the skills demonstrated by students. This means a good agreement between the formation achieved by the students and the expectations of the industries. However, these results also show that the training ofstudents can still be improved.Fernandez, J.; Cruells, M.; Escaja, N.; Garrido, JA.; Giménez, J.; Llauradó, M.; Roca, A.... (2015). The surveys: nexus between industry and academia. En 1ST INTERNATIONAL CONFERENCE ON HIGHER EDUCATION ADVANCES (HEAD' 15). Editorial Universitat Politècnica de València. 662-667. https://doi.org/10.4995/HEAd15.2015.37066266

Les competències transversals i les auditories als laboratoris de pràctiques de la Facultat de Química: desenvolupament i anàlisi

S’ha treballat la formació competencial dels estudiants mitjançant la realització d’auditories del sistema de gestió de la qualitat dels laboratoris de practiques de la Facultat de Química. Per fer aquesta tasca, s’ha seleccionat com auditors a 102 estudiants de l’assignatura “Qualitat i Prevenció” del Grau de Química, els quals, després d’una breu formació, han actuat com auditors en 49 auditories, la qual cosa ha implicat també la participació de 99 estudiants i 49 professors com a interlocutors en els laboratoris auditats. En total han estat auditats 49 torns de pràctiques relacionats amb els diferents tipus d’assignatures pràctiques impartides per tots els departaments de la Facultat i corresponents als tres graus que s’imparteixen (Química, Enginyeria Química i Enginyeria de Materials), havent estat auditats pràcticament tots els laboratoris docents de la Facultat. Seguint els objectius del projecte, els estudiants han pogut treballar competències transversals relacionades amb l’ètica, la capacitat d’expressió oral i escrita, la capacitat de diàleg, la capacitat de lideratge, l’anàlisi i la interpretació de dades, la gestió de la qualitat, el treball respectuós amb el medi ambient, la seguretat, etc. Per tant, aquest projecte ha sigut una eina important en la seva formació. D’altra banda, dels resultats dels informes d’auditoria realitzats pels estudiants, s’han posat de manifest una sèrie de mancances i problemes als laboratoris que estan sent analitzats per tal de millorar la qualitat de les pràctiques. Finalment, s’han realitzat enquestes de satisfacció a tots els grups implicats (estudiants auditors, estudiants auditats, professors auditats) i els resultats de les mateixes han posat de manifest un alt grau de satisfacció amb la feina feta i la manera de fer-la.PMI

The surveys to the companies: a tool for the improvement of degrees

In scientific and technical degrees, the opinion of the final employers on the given subjects is really important. For this reason, the Quality Committee (CQ) of the Faculty of Chemistry of the University of Barcelona prepared a survey for chemical, engineering and pharmaceutical companies asking about the academic training required by the companies. The survey consists of nine sections including items related to laboratory operations, chemical processes, calculation methods, management systems (quality, environment and safety) or general management information. In addition, at the end of each section, a question inquires the companies about the competences shown by students in the items of the section. The results were compared with that of a similar survey carried out in 2007. The scores obtained, between 2 and 3, for all the items (score: 1, not important; 2, unimportant; 3, important; 4, very important), show that companies accept the training given to our students and the competences achieved by them. However, according to their opinion, it is possible to improve this training, especially in the subjects related to management (time, information, environment, quality, safety, etc.). Therefore, surveys are a good tool for the evaluation of the training achieved in our degrees and, consequently, for improving degrees and the teaching task, according the Quality Management System implemented in the Faculty of Chemistry

The effect of the neutral cytidine protonated analogue pseudoisocytidine on the stability of i-motif structures

Incorporation of pseudoisocytidine (psC), a neutral analogue of protonated cytidine, in i-motifs has been studied by spectroscopic methods. Our results show that neutral psC:C base pairs can stabilize i-motifs at neutral pH, but the stabilization only occurs when psC:C base pairs are located at the ends of intercalated C:C stacks. When psC occupies central positions, the resulting i-motifs are only observed at low pH and psC:C or psC:psC hemiprotonated base pairs are formed instead of their neutral analogs. Overall, our results suggest that positively charged base pairs are necessary to stabilize this non-canonical DNA structure.Peer Reviewe

Non-G Base Tetrads

14 pags., 5 figs., 1 tab.-- This article belongs to the Special Issue Frontiers in Nucleic Acid Chemistry—in Memory of Professor Enrique Pedroso for His Outstanding Contributions to Nucleic Acid ChemistryTetrads (or quartets) are arrangements of four nucleobases commonly involved in the stability of four-stranded nucleic acids structures. Four-stranded or quadruplex structures have attracted enormous attention in the last few years, being the most extensively studied guanine quadruplex (G-quadruplex). Consequently, the G-tetrad is the most common and well-known tetrad. However, this is not the only possible arrangement of four nucleobases. A number of tetrads formed by the different nucleobases have been observed in experimental structures. In most cases, these tetrads occur in the context of G-quadruplex structures, either inserted between G-quartets, or as capping elements at the sides of the G-quadruplex core. In other cases, however, non-G tetrads are found in more unusual four stranded structures, such as i-motifs, or different types of peculiar fold-back structures. In this report, we review the diversity of these non-canonical tetrads, and the structural context in which they have been found.This research was funded by Ministerio de Ciencia e Innovación, grant number PID2020- 116620GB-I00. B. M. acknowledges a “Margarita Salas” contract from the Spanish Ministerio de Ciencia e Innovación, and M. G. a European Union Marie Sklodowska Curie Action (799693)

Structure of i-Motif/Duplex Junctions at Neutral pH

5 pags., 4 figs.We report here the three-dimensional structure of an i-motif/duplex junction, determined by NMR methods at neutral pH. By including a minor groove tetrad at one side of the C:C+ stack of a monomeric i-motif, and a stem/loop hairpin at the other side, we have designed stable DNA constructs in which i-DNA and B-DNA regions coexist in a wide range of experimental conditions. This study demonstrates that i- and B-DNA are structurally compatible, giving rise to a distinctive fold with peculiar groove shapes. The effect of different residues at the i-motif/duplex interface has been explored. We also show that these constructs can be adapted to sequences of biological relevance, like that found in the promoter region of the KRAS oncogene.This investigation was supported by research grants from the Spanish “Ministerio de Ciencia e Innovacioń ” (BFU2017- 89707-P, PID2020-116620GB-I00)

Centromeric Alpha-Satellite DNA Adopts Dimeric i-Motif Structures Capped by AT Hoogsteen Base Pairs

International audience© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Human centromeric alpha-satellite DNA is composed of tandem arrays of two types of 171 bp monomers; type A and type B. The differences between these types are concentrated in a 17 bp region of the monomer called the A/B box. Here, we have determined the solution structure of the C-rich strand of the two main variants of the human alpha-satellite A box. We show that, under acidic conditions, the C-rich strands of two A boxes self-recognize and form a head-to-tail dimeric i-motif stabilized by four intercalated hemi-protonated C:C + base pairs. Interestingly, the stack of C:C + base pairs is capped by T:T and Hoogsteen A:T base pairs. The two main variants of the A box adopt a similar three-dimensional structure, although the residues involved in the formation of the i-motif core are different in each case. Together with previous studies showing that the B box (known as the CENP-B box) also forms dimeric i-motif structures, our finding of this non-canonical structure in the A box shows that centromeric alpha satellites in all human chromosomes are able to form i-motifs, which consequently raises the possibility that these structures may play a role in the structural organization of the centromere. Nucleosome organization: All human centromeric alpha-satellites contain sequences that can form dimeric i-motif structures in vitro (see figure). These regions occur every 171 bp and are found at the entrance and exit of the nucleosome. This finding suggests that the i-motif may play a role in the higher order nucleosome organization at the centromere. ; Peer Reviewe