First crystallization experiments

Ivana Nikšić-Franjić is, from Oct. 3rd to 7th, 2022, at the Institute for Molecular Biosciences of the University of Graz (group of prof. Karl Gruber) performing first set of over 2000 crystallization experiments within the frame of calixDNA project. Ivana is searching for initial crystallization conditions of the macromolecular [SBB4/d(GTATATATAC)2] complex. This research visit is realized by courtesy of prof. Karl Gruber, scientific advisor of the calixDNA project, which is deeply acknowledged. This Ivana’s visit to Graz is a major step forward for the calixDNA project, as it marks the kick-off of the activities in the domain of macromolecular crystallography which is envisaged to be a cornerstone of the entire project. Fingers crossed.

5th online calixDNA team meeting

On 13th of July, 2022, from 11:00 to 12:20 CET, the fifth meeting of the calixDNA research team was held, in presence of A. Višnjevac, I. Piantanida, O. Reinaud, B. Kojić-Prodić, K. Gruber, I. Nikšić-Franjić, D. Pavlović Saftić, M. Wallet and M. Legras. M. Wallet and M. Legras presented the results obtained during their internship at the calixDNA project, which started on April 23rd, 2022, and will continue until the end of July 2022, which was followed by the vivid discussion and many questions to the presenters. Research stay of I.Nikšić-Franjić at the research group of prof. K. Gruber was confirmed for the late September/early October, during which she will set up the first round of crystallization experiments of the genZ SBB4 – DNA oligomere complexes. Research visits of A. Višnjevac and I. Nikšić Franjić to the Paris lab, where they will continue the synthesis of the gram quantities of the most promissing SBB derivatives, was also mentioned and confirmed.

The presentation is available here.

calixDNA positively reviewed

Board of Directors of the Croatian Science Foundation, at its 27th session held on June 17th, 2022, based on the evaluations and recommendations of the evaluators, made a decision (Class: 120-02/22-02/13, Registration number: 63-02/ 01-22-33) on the acceptance of the 1st periodic report of calixDNA project (Feb. 1st, 2021 – Jan. 31st, 2022). Final grade B (Good progress) has been assigned to the report with the remark that “the project has achieved most of the goals for the given period, and the reasons for not achieving some goals are justified”. Consequently, the board has decided to continue financing the project.

calixDNA@HRT1 show “Prometej”

calixDNA project was presented to the widest audience in Croatia by the well known science&technology dedicated TV show “Prometej” which was broadcasted on 4th od June, 2022 at 2:30 PM at HRT1. The cameras of the HRT entered the Laboratory of Chemical and Biological Crystallograhy and Laboratory for biomolecular interactions and spectroscopy at the Ruđer Bošković Institute to get an insight into the research process within the calixDNA project. The project was presented by its head, dr. sc. Aleksandar Višnjevac, and particular research activities by dr. sc. Ivana Nikšić-Franjić, Malorie Wallet and Marine Legrass, team members.

Dr. Ivana Nikšić-Franjić explaining the calixDNA project for Croatian Television

New interns @calixDNA

calixDNA team is joined, from April 23rd, 2022, by Marine Legras and Malorie Wallet, students of the second year of chemistry at the ENSICAEN (Ecole Nationale Superieure de Caen). During their internship at the Ruđer Bošković Institute, they will be working on the recognition and binding studies of the gen1 supramolecular biomimetic binders, as well as on the series of crystallization experiments pertaining to the structural studies of the genZ SBB- mononulceotide tweezer like complexes, and metal complexes of some of the genZ SBBs. Both Malorie and Marine will stay with us for a period of three months.

Marine Legras
Malorie Wallet

NJC coverpage for calixDNA team

Upon invitation by the editorial board of New Journal of Chemistry, our artwork illustrating recently published paper Impact of positive charge and ring-size on the interactions of calixarenes with DNA, RNA and nucleotides, will appear on the frontpage of this journal (NJC, Issue 15, online 11/04/2022). The illustration was prepared by authors I. Piantanida and A. Višnjevac and designed by Toni Lijić. Toni Lijić is a M.Sc in general chemistry and digital designer with a growing portfolio in natural sciences related illustrations. His signature stands also on the banner of calixDNA.org. For more on Toni’s work, please follow this link.

Coverpage of New Journal of Chemistry, 2022, Issue 15 by I.Piantanida, A. Višnjevac and T. Lijić

New publication accepted

Our article entitled Impact of positive charge and ring-size on interactions of calixarenes with DNA, RNA and nucleotides by Ivona Krošl, Ena Otković, Ivana Nikšić-Franjić, Benoit Colasson, Olivia Reinaud, Aleksandar Višnjevac and Ivo Piantanida, has been accepted for publication in New Journal of Chemistry. The publication summarizes part of the work accomplished during the first product period, on the recognition and binding study of the selected SBVs towards variety of polynucleotide chains and some mononucleotides.

ABSTRACT

Comparison of various calix[6]arene and calix[4]arene derivatives revealed that only analogues bearing permanent positive charge non-covalently bind to ds-DNA and ds-RNA, by insertion into DNA minor groove or RNA major groove. Also, these cationic analogues revealed strong and highly selective charge-dependent stabilization of AT-DNA against thermal denaturation, calix[6]arene trication being for an order of magnitude more efficient than its calix[4]arene dicationic analogue. At variance to DNA/RNA selectivity for only cationic calixarenes, both, neutral and cationic calixarenes bind nucleoside monophosphates with similar efficiency, by forming tweezer-like supramolecular complexes, with nucleobases inserted between aromatic pendant arms grafted to calixarene rims. Such nucleotide-calixarene complexes were monitored by emission change of calixarene as a function of nucleobase insertion, at variance to DNA/RNA complexes in which calixarene is inserted into polynucleotide groove, which does not change calixarene emission – stressing importance of the ligand insertion within calix-basket for the fluorimetric sensing.

MSc/BSc thesis @calixDNA

We are, again, looking for motivated students interested in joining our international calixDNA team in frame of their BSc/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 a position in the field of the recognition and binding studies of our supramolecular biomimetic binders (SBBs) to the oligonucleotide chains. Experimental work will be organized at the Ruđer Bošković Institute in Zagreb, Bijenička c. 54.

The project is ongoing, hence your experimental work can start immediately. 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.

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.