EuChemS2022 Chemistry Congress: Oral communication accepted

The abstract entitled Impact of positive charge and ring-size on interactions of calixarenes with DNA, RNA and nucleotides by Ivana Nikšić-Franjić, Aleksandar Višnjevac and Ivo Piantanida has been accepted for an oral presentation at the EuChemS2022 Chemistry Congress. Presenting author is dr. Ivana Nikšić-Franjić, postdoc fellow at the calixDNA.

I. Nikšić-Franjić

ABSTRACT

Calixarenes were traditionally studied as supramolecular receptors for various low molecular mass cationic or anionic species, but only marginally investigated for their biological effects or applications [1]. However, systematic study revealed that cationic calixarenes can be applied as innovative DNA-transfection agents [2]. We have developed three generations of calix[6]arene-based (funnel), as well as two generations of resorcinarene-based (bowl) supramolecular systems featuring two, three or four methylimidazole-containing coordination arms grafted at the large rim, suitable to bind to variety of nucleid acid sequences [3,4].

In this work we focused on calixarenes with short, triazole-attached positively charged substituents (2 and 4) and their neutral analogues (1 and 3, Fig. 1.). Their ability to recognize specific sequences of various DNA chains was studied by thermal denaturation experiments, fluorimetric titrations, circular dichroism experiments and molecular dynamics simulations. Comparison of neutral and cationic calix[6]arene and calix[4]arene derivatives revealed that only cationic analogues non-covalently bind to ds-DNA and ds-RNA, by insertion into DNA minor groove or RNA major groove. Also, cationic analogues revealed strong and highly selective charge-dependent stabilization of AT-DNA against thermal denaturation, 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 do not change calixarene emission – stressing importance of the ligand insertion within calix-basket for the fluorimetric sensing.

Financial support from Croatian Science Foundation (IP-2020-02-3786 & IP-2018-01-5475) is gratefully acknowledged.

Figure 1. Molecular structures of studied cationic calixarenes 2 (as a chloride salt), 4 (as a nitrate salt) and their non-charged analogues 1 and 3.

[1] Baldini L.; Casnati A.; Sansone F., Eur. J. Org. Chem., 2020, 31, 5056-5069.

[2] Bagnacani V.; Franceschi V.; Bassi M.; Lomazzi M.; Donofrio G.; Sansone F.; Casnati A.; Ungaro R., Nat. Commun.,2013, 4, 1721-1727.

[3] Rebilly J.-N.; Colasson B.; Bistri O.; Over D.; Reinaud O., Chem. Soc. Rev., 2015, 44, 467-489.

[4] Višnjevac A.; Gout J.; Ingert N.; Bistri O.; Reinaud O., Org. Lett. 2010, 12, 2044-2047.

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.

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.