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.

Online kick-off meeting

Members of the calixDNA project team have held on Friday, Dec. 11th, 2020, an online kick-off meeting well ahead the official project start date (Feb. 1st, 2021). The meeting was led by A. Višnjevac, with all team members (Reinaud, Piantanida, Kojić-Prodić and Colasson) participating. Important matters like delivery of the genZ SBBs to be subjected to the binding studies in Piantanida lab, purchase procedures, hiring a postdoc and PhD student etc. were discussed.

calixDNA funded

The Executive board of the Croatian Science Foundation has decided to accept the research project proposal entitled “Biomimetic “funnel” and “bowl” supramolecular systems for the selective recognition of DNA/RNA” or, by its acronyme, “calixDNA” for funding. The proposal was submitted on Feb, 20th, 2020, in frame of the IP-2020-02 call . Research activities are to commence on Feb. 1st, 2021, and to be concluded by Jan. 31st, 2025.