Ena Otković defended her MSc thesis

Ena Otković

On Sep. 22nd, 2021, the first MSc student at the calixDNA project, Ms Ena Otković, from the University of Zagreb, Faculty of Sciences, successfully defended her thesis of the title STUDY OF CATIONIC CALIXARENES INTERACTIONS WITH NUCLEOTIDES, DNA AND RNA, accomplished under the supervision of dr. sc. Ivo Piantanida. The thesis was defended before the evaluation committee, president of which was prof. Snežana Miljanić, members were profs. Željka Soldin and Marko Močibob, while prof. Adriana Kenđel was appointed first replacement. Thesis is written in Croatian, with an abstract available in English, and is deposited in Central Chemical Library, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia and in Repository of the Faculty of Science, University of Zagreb. Full text in Croatian is also available on the calixDNA website.

4th calixDNA team meeting

The calixDNA project team had today its 4th online meeting from 2:00 PM to 3:30 PM, in presence of A. Višnjevac, O. Reinaud, B. Colasson, I. Piantanida, I. Krošl, I. Nikšić-Franjić and C. Thouzé. The central point on the agenda was the final internship report of Corentin Thouzé, who will terminate his internship at the calixDNA project on Aug. 13th, 2021, as planned. Corentin has wrapped up and presented, in a form of a 35 min long PPT presentation, the results obtained so far on the research of the binding of two calixarene derivatives and their corresponding Cu(II) complexes (supramolecular biomimetic binders, SBBs) to various mono- and polynucleotides. The research involved UV/Vis, fluorometric and CD spectroscopies, as well as thermal denaturation monitoring, which, combined, provided a detailed insight into the chemical behaviour of the studied SBBs in presence of variety of polynucleotide chains, as well as in presence of their building blocks – mononucleotides. The results were put in context of the previously obtained ones, on the series of four closely related SBBs, which are the basis of the MSc thesis of Ena Otković, and of the first calixDNA original scientific paper to be submitted shortly to the special issue of Molecules – an open access journal. The presentation incited a vivid scientific discussion, which, in many aspects, contributed to better understanding of the presented results. One of the conclusions was that Corentin shall continue the research on Ena’s SBBs, by studying binding ability of their copper(II) complexes to polynucleotide chains.

We have briefly discussed the paper in preparation (vide supra) and current project management issues. French team members will, over the two weeks to come, review the manuscript and send their comments and suggestions, so that the paper will be ready for submission in August 2021. A. Višnjevac will, if the circumstances remain favorable to international visit exchange, visit the Lab at the University of Paris, during November/December 2021, in frame of the joint team efforts to speed up the synthesis of the zero generation SBBs, needed for the envisaged recognition, binding and structural studies during the second project year.

Thouzé: First progress report

Cu(II) complex of AB118 with an intra-cavity bound molecule of MeCN. Molecular structure obtained by single crystal X-ray diffraction data

Today, at 10:30 AM, Corentin Thouzé, student at the ENSICAEN, Caen, France, and currently intern at the calixDNA project, has presented the results of the recognition and binding studies of the genZ SBB specimen coded AB118 with the series of polynucleotide chains as well as on some mononucleotides. Corentin was employing UV-Vis and CD spectroscopy, fluorimetric titrations, as well as thermal denaturation experiments, in order to establish the stability of the AB118 SBB, and its potential [and potential of its in-situ prepared Cu (I), Cu(II) and Zn (II) complexes] to recognize specific portions of the various nucleic acid chains. The presentation included highly intriguing comparison of the Corentin’s results with those previously obtained by E. Otković (both Corentin and Ena were directly mentored by I. Krošl) on four related ligands from the generation zero SBBs. In line with these physico-chemical experiments, which are in the focus of Corentin’s and Ena’s research activities, the complementary computational studies are being perfromed by I. Nikšić-Franjić in order to identify specific portions of the SBB molecules responsible for the fluorimetric signals obtained. Finally, structural studies led by A. Višnjevac are there to complete the picture. Single crystal structure of the Cu(II) complex of the AB118 is solved, which gave a valuable insight into the size and conformational features of this compound. The presented results shall guide the design of the experiments to follow, which was also the subject of a discussion that followed Corentin’s presentation. The members of the local (Croatian) part of the calixDNA team were present: A. Višnjevac, I. Piantanida, I. Nikšić-Franjić, I. Krošl and E. Otković. The meeting ended at 12:00.

3rd meeting of the calixDNA project team

The growing and ever younger calixDNA team had today at 2:00 PM its third team meeting with the participation of team members A. Višnjevac, O. Reinaud, I. Piantanida, B. Colasson, I. Nikšić-Franjić, E. Otković and C. Thouzé, as well as external collaborators I. Krošl and N. Nyssen. A. Višnjevac informed team members on the current issues pertaining to the project management, as well as on the results in the domain of the structural investigation of the genZ supramolecular biomimetic binders. New team members I. Nikšić-Franjić (postdoc) and C. Thouzé (student, intern) introduced themselves briefly and reported on their ongoing work within the project. I. Piantanida gave a summary report on the results of the recognition and binding studies obtained on three genZ SBBs that are currently under investigation in frame of the MSc thesis of E. Otković, and in the frame of the internship of C. Thouzé (both directly supervised by I. Krošl). The report was followed by a short discussion. A problem of the provision of small but essential quantities of the compounds (genZ SBBs) needed to wrap up the ongoing research was mentioned, and possible solutions discussed. B. Colasson will come up with possible temporary solutions of this problem by the end of June which may provide an efficient time bridge until the arrival of the PhD student who will be working at the SBB synthesis (presumably last quarter of 2021). The meeting ended at 2:45 PM.

New member of the calixDNA team

I. Nikšić-Franjić

As from today caliXDNA team is joined by dr. sc. Ivana Nikšić-Franjić, a future postdoc student at our project (with an official kick-off date set for Aug. 1st, 2021). In the meantime, Ivana will join the ongoing research on a voluntary basis, primarily in the domain of computational chemistry, which is an essential addition to our ongling research and a field in which Ivana recently defended her PhD thesis. Ivana will use molecular modeling (docking) methods to determine the thermodynamically stable complex structures and calculate their optical properties.

New internship @calixDNA

C. Thouzé

On April 26th, 2021, calixDNA team is joined by a new student, Corentin Thouzé, who will perform a 16-weeks long internship at our project (until Aug. 13th, 2021). Corentin is a student at the ENSICAEN (Ecole Nationale Superieure de Caen). During his internship at the Ruđer Bošković Institute, he will be working on the recognition and binding studies of the genZ supramolecular biomimetic binders (in particular, calixarene ligand AB118 and its copper(II) complex), as well as on the preliminary determination of the crystallization conditions of several genz SBB ligands and complexes.

2nd project team meeting

CalixDNA project team has had today, scheduled at 11:00 sharp, its second online meeting, with participation of B. Colasson, I. Piantanida, O. Reinaud, and A. Višnjevac (in alphabetical order). Students Ivona Krošl (PhD) and Ena Otković (MS) joined the meeting briefly. Exciting results obtained by experiments of DNA/RNA recognition and binding of our supramolecular biomimetic binders (SBBs), during the first month were extensively discussed. The results were presented by I. Piantanida, and discussion followed. MS student Ena Otković is successfully performing these experiments in frame of her MS thesis, under the supervision of I. Piantanida and direct mentorship of Ivona Krošl. The issue of the timely procurement of calixarene ligands (SBBs) for further recognition/binding studies, as well as for crystallization experiments, was approached. In order to secure the timely delivery of necessary compounds (SBBs), I. Piantanida proposed an establishment of a new collaboration of the project team with the team of synthetic chemists at the Ruđer Bošković Institute with a relevant experience in calixarene synthesis, which was unanimously accepted. The time bridge shall be hence created until the project team is officially joined by a PhD student who will be in charge of the SBB syntheses and shall presumably join the team by the end of 2021. Main focus in this phase, as envisaged by the work plan, will continue to be on recognition and binding studies, of the chosen set of SBBs which were previously delivered from the French partners, including the compound for which recently the single crystal X-ray structure has been determined [Cu(II) complex of the TMPA capped calix[6]arene]. The team working at the recognition and binding studies shall be joined, from April 26th, 2021, by the French intern Correntin Thouze, who will work on the calixDNA project at the Ruđer Bošković Institute in Zagreb, for the duration of three months (until August 2021). The meeting ended at 11:55 h.

Job offer: PostDoc@calixDNA

calixDNA project has launched today a job offer for a postdoctoral fellow who is to join the project team at IRB in Zagreb for a limited duration of 24 months, starting with Aug. 1st, 2021, where he/she will work on a specific problem pertaining to: (i) recognition and binding studies of supramolecular biomimetic calixarene- and resorcinarene-based binders (SBB) to oligonucleotide chains, and (ii) crystallization of biocomplexes SBB-oligonucleotide chains. Engagement in the educational and administrative aspects of the project will also be required. The offer is open until March 12th, 2021, at 10:59 PM, Zagreb time.

For more on the position offered, including the details on how to apply, please follow this link.

First Master student

Ena Otković, second year student of Graduate studies in chemistry at the Faculty of Science, University of Zagreb joined the calixDNA team on Feb. 1st, 2021. Within the calixDNA project, Ena is working on her master’s degree on the study of noncovalent interactions between supramolecular binders of the zero generation (genZ SBBs) and polynucleotide chains, using different spectroscopic techniques.

BSc/MSc thesis at calixDNA

We are looking for motivated students interested in joining our international calixDNA team in frame of their BSc or MSc theses. An ideal candidate would be a student of chemistry or biochemistry, with a strong interest in structural features of the biologically relevant molecules, as well as biological macromolecules. We offer two positions: one in the field of the recognition and binding studies of our supramolecular biomimetic binders (SBBs) to the oligonucleotide chains, and the other pertaining to the crystallization of the water soluble genZ SBBs by use of the macromolecular crystallization techniques. Experimental work will be organized at the Ruđer Bošković Institute in Zagreb, Bijenička c. 54. Crystallization experiments may require short research visits to the Institute of molecular biosciences in Graz, Austria, where the crystallization robot is made available for the calixDNA team members.

The project commences on Feb. 1st, 2021, and so may your experimental work. Please visit calixdna.org for all the details you may be interested in. Should you have any further inquiries, there is a contact form on the website, through which you can reach out. We would be delighted to welcome you on board calixDNA project.