Department of Biopolymer Chemistry

 


 

Head:
Assoc. Prof. Marcin K. Chmielewski, PhD, DSc 

 

 


Staff:
Jolanta Brzezińska,PhD;

Agnieszka Witkowska, PhD Eng;

Martyna Barciszewska,MSc Eng.;

Dominika Krygier,MSc Eng.;

 


PhD students:
Tomasz Kaczyński, MSc Eng.;  

 

 


 

Rys.1

 


Rys.2


Rys.3


 

 

 

 

 

 

 

Key words:
nucleoside, nucleotide, oligodeoxynucleotides, oligoribonucleotide, nucleic acid, DNA, RNA, peptides, protecting groups, thermolabile protecting group, cyclization, chemical synthesis, triphosphates, microarrays, nanostructure, fluorescent labels

 

Research offer:
We offer cooperation within research projects with the use of modern equipment, allowing for synthesis and analysis of biopolymers and their bioconjugates:

  • Synthesis of oligonucleotides RNA / DNA

          - Synthesis of oligomers on a solid support, at a scale of 0.1; 0.2 and 1 µmol;

          - Incorporation of different modifications in both 5 'and 3' end of oligomers (including fluorescent dye).

  • System for liquid chromatography UHPLC (version semipreparative) with DAD detector and Charged Areosol Detection (CAD)

          - The system is designed for the assay of compounds without chromophore and all the non-volatile

             compounds;

          - Possibility to purify large quantities of compounds (up to 10 mg at one-time dispensing of the sample).

  • The UFLC liquid chromatography, with an automatic sample changer, temperature control of samples and columns, PDA and fluorescent detectors

           - The system is intended for separation and quantification of mixtures of nucleic acids, nucleosides, amino

              acids, peptides etc.

  • System for capillary electrophoresis, equipped with UV-VIS

         - Analysis of the level of RNA / DNA of a particular length, in the biological material, with the ability to

            determine the level of degradation; analysis of RNA/DNA using modified nucleotides; analysis of the

            structure of particular RNA molecules.

  • System for fluorescent profile analysis:
          - High sensitivity spectrophotometer allowing for registration of emission and excitation spectra;
  • High sensitivity spectrophotometer allowing for registration of emission and excitation spectra;
    - Spectrofluorometer enabling detection and determination of trace amounts of substances having
            luminescent properties in the analyzed samples.


          - Spectrofluorometer enabling detection and determination of trace amounts of substances having

             luminescent properties in the analyzed samples.

 

Equipment:
Synthesizer DNA/RNA, UFLC Performance Liquid Chromatograph (ultra-high-speed analysis and ultra-high separation) with a fluorescence detector,  Liquid Chromatograph (semi-preparative version) with Charged Aerosol Detection (CAD), Set of Capillary Electrophoresis, Fluorescence Spectrophotometer,  Microwave Reactor

 

Scientific profile:

  1. Our research include the development of techniques for detection of DNA/RNA ( e.g. in cells), using new types of fluorescent hybridization probes via fluorophore-quencher system.
  2. Investigation of the controllable, solid surfaces covered with organofunctional silanes, for immobilization of DNA/RNA molecules (also branched oligomers). Proper placement of nucleic acids on the surface is the key for building a RNA nanostructure with precise architecture and function (e.g. therapeutic or diagnostic application). In most cases, this could be achieved with the support of diver protecting groups, for example using the methodology of Thermolabile Protecting Groups where groups can be removed (also in physiological environment) only through exposure to temperature rise.
  3. Thermolytic, mutually compatible protection system, based on 2-pyridinyl structure (orthogonal protecting system for biomolecule synthesis: peptides/carbohydrates etc.)
  4. The development of the methodology for temporary modifications of biologically active compounds, that must be at the same time very stable and readily liberated (an apparent contradiction), creating an opportunity for changing their properties. 2-pyridinyl groups change the solubility of biomolecules, like RNAs, facilitating cellular uptake and its delivery to the active side. Removal of the protecting group, via temperature changes (e.g. laser irradiation or microwave), enables the recovery of RNA properties in a particular cell site.

 

Current research activity

  • The study of nucleic acid nanostructures
  • The search of new, efficient fluorescent labels
  • A new protecting system in chemical synthesis of nucleic acids and peptides/ carbohydrates and their bioconjugates
  • The application of thermolability in enzymatic processes
  • Synthesis of triphosphate, compounds with significant biological activity

 

Most important research achievements:

  • Evolution of new thermal protecting groups of the hydroxyl, phosphate and carboxyl function.
  • New methods for construction of DNA microarrays on solid-support modified epoxy and azidosilanes.
  • The "click-clack" approach for increasing the durability of the thermal protecting group of the phosphate center, and its application in oxidation and synthesis of polyphosphates
  • A new method for branched oligonucleotide synthesis, and their application in construction of nanodevices.
  • The “chemical switch” approach for modulating the stability of 2-Pyridinyl Thermolabile Protecting Groups (2-Py TPGs), by changing the electronic properties of the substituents on the pyridinyl ring and pH of the environment.
  • Development of new modified support for effective nucleic acids synthesis.

 

Currently implemented research projects:

Development of chemical methods for the synthesis of biologically active triphosphate using thermolabile protecting group (UMO-2012/07/ B/ ST5/03035)

 

Selected publications:

J. Brzezinska, A. Witkowska , S. Bałabańska, M.K. Chmielewski 2-Pyridinyl-N-(2,4-difluorobenzyl)aminoethyl Group As Thermocontrolled Implement for Protection of Carboxylic Acids Organic Letters 18, 3230–3233 (2016)

M. Barciszewska, A. Sucha, S. Bałabańska, M.K Chmielewski Gel electrophoresis in a polyvinylalcohol coated fused silica capillary for purity assessment of modified and secondary-structured oligo- and polyribonucleotides Scientific Reports 6, 19437 (2016)

T.P. Kaczyński, T. Manszewski , M.K. Chmielewski Stereoselective P-Cyclisation and ­Diastereoisomeric Purification of 5-Phenyl-3-(pyridin-2-yl)-1,3,2-oxazaphospholidine Formed from a Thermolabile Protecting Group The Journal of Organic Chemistry 14, 2522–2527 (2016)

Kujawski, K. Czaja, K, E. Jodłowska, K. Dettlaff, M. Politańska, R. Kujawski, T. Ratajczak, M.K. Chmielewski, M.K. Bernard Structural and spectroscopic properties of econazole and sulconazole - Experimental and theoretical studies Journal of Molecular Structure 1119, 250–258 (2016)

A. Witkowska, D. Krygier, J. Brzezińska, M.K. Chmielewski Modulating the Stability of 2-Piridinyl Thermolabile Hydroxyl Protecting Groups via the „Chemical Switch Approach The Journal of Organic Chemistry 80(24), 12129-12136 (2015)

S. Janczak, A. Olejniczak, S. Balabanska, M. K. Chmielewski, M. Lupu, C. Viñas, Z. J. Lesnikowski The boron clusters as a platform for new materials: synthesis of functionalized o-carborane (C2B10H12) derivatives incorporating DNA fragments Chemistry - A European Journal 21, 15118-15122 (2015)

M. K.Chmielewski, E. Tykarska; W. T. Markiewicz, W. R. Rypniewski Engineering N-(2-pyridyl)aminoethyl alcohols as potential precursor of thermolabile protection groups
New J. Chem. 36, 603-612 (2012).

M. K. Chmielewski Novel thermolabile protecting group with higher stability in ambient temperature Tetrahedron Letters 53, 666-669 (2012).

B. Uszczyńska, T. Ratajczak, E. Frydrych, H. Maciejewski, M. Figlerowicz, W.T. Markiewicz, M. K.Chmielewski The application of click chemistry to the production of DNA microarrays Lab Chip 12, 1151-1156 (2012).

T. Ratajczak, M. K. Chmielewski Oxidation of H-Phosphonates with Iodine by Intramolecular Support of a 2-Pyridyl Thermolabile Protecting Group J. Org. Chem. 77, 7866-7872 (2012).

M. K. Chmielewski Protecting of a thermolabile protecting group: "Click-clack" approach. Organic Letters 11, 3742-3745 (2009).