Pracownia Biomateriałów

Pracownia zajmuje się następującą problematyką badawczą:

  • Projektowanie, synteza oraz zastosowanie nanocząstek bazujących na RNA w kontroli ekspresji genów
  • Analiza interakcji ligand-białko, szczególnie kompleksu tRNA-białko, in silico oraz in vitro
  • Badanie związków optycznie czynnych w komórkach zwierzęcych
  • Wpływ nukleotydów i ich analogów na podstawowe procesy życiowe komórek eukariotycznych
  • Dokowanie, modelowanie oraz dynamika molekularna
  • Projektowanie oraz biodruk 3D
Rola zewnątrzkomórkowej frakcji ATP w indukcji przemiany epitelialno-mezenchymalnej – badania
z wykorzystaniem analogów nukleotydowych

Kierownik projektu: dr Róża Pawłowska
Typ projektu: Grant NCN, SONATA-13
Numer grantu: 2017/26/D/ST5/01046

Opis projektu



Nanocząstki zbudowane z RNA stosowane do regulacji ekspresji genow w ukladzie modelowym

Kierownik projektu: dr hab. Arkadiusz Chworoś
Typ projektu: Grant NCN, OPUS-10
Numer grantu: 2015/19/B/ST5/03087

Opis projektu



Barwienie membran komorkowych za pomoca oligoelektrolitow fenylenowinylenowych

Kierownik projektu: dr hab. Arkadiusz Chworoś
Typ projektu: Grant NCN, OPUS-3
Numer grantu: 2012/05/B/ST5/00364


Badanie tworzenia kompleksu tRNA/cytochrom C i jego wpływ na apoptozę komórki

Kierownik projektu: dr hab. Arkadiusz Chworoś
Typ projektu: Grant NCN, OPUS-1
Numer grantu: 2011/01/B/NZ3/02090


Badanie odporności agregatów RNA na degradację nukleolityczną

Kierownik projektu: dr hab. Arkadiusz Chworoś
Typ projektu: Grant MNiSW
Numer grantu: N302/643740


Aplikacje powstałe podczas pracy przy dokowaniach oraz modelowaniach molekularnych:

  • AutoDockVinaDB – moduł Python3 służący do budowania bazy danych w oparciu o wyniki dokowania molekularnego za pomocą programów AutoDockVina oraz UCSF Chimera
  • VinaConfig – prosty program Python3 tworzący pliki konfiguracyjne do modułu AutoDockVina
  • Protein-Ligand Merger – program łączący plik powstały po dokowaniu w AutoDockVina z natywnym białkiem

Self-Assembling RNA Nanoparticle for Gene Expression Regulation in a Model System
Dominika Jedrzejczyk, Arkadiusz Chworos
ACS Synthetic Biol. 2019, 8(3):491-497

Theoretical and experimental study on the electronic structure of distyrylnaphthalene-based conjugated oligoelectrolytes
Agnieszka Kowalska-Baron, Remigiusz Zurawinski, Beata Lukasik, Arkadiusz Chworos, Stanislaw Wysocki
J Luminescence 2018, 196:81-89

Conjugate of PAMAM Dendrimer, Doxorubicin and Monoclonal Antibody-Trastuzumab: The New Approach of a Well-Known Strategy
Monika Marcinkowska, Ewelina Sobierajska, Maciej Stanczyk, Anna Janaszewska, Arkadiusz Chworos, Barbara Klajnert-Maculewicz
Polymers 2018, 10(2):187

Self-assembly nucleic acid-based biopolymers: learn from the nature
Pitchaya Pakornpadungsit, Wirasak Smitthipong, Arkadiusz Chworos
J Pol Res 2018, 25(2):45

Solvent effects on the photophysical properties of distyrylnaphthalene-based conjugated oligoelectrolytes
Agnieszka Kowalska-Baron, Remigiusz Zurawinski, Beata Lukasik, Arkadiusz Chworos, Stanislaw Wysocki
J Luminescence 2017, 192:359-370

Composing RNA Nanostructures from a Syntax of RNA Structural Modules
Cody Geary, Arkadiusz Chworos, Erik Verzemnieks, Neil R. Voss, Luc Jaeger
Nano Lett. 2017, 17(11):7095-7101

Facile synthesis of fluorescent distyrylnaphthalene derivatives for bioapplications,
Beata Lukasik, Justyna Milczarek, Pawlowska Roza, Remigiusz Zurawinski, Arkadiusz Chworos
New J Chemistry 2017, 41 (15): 6977-6980

Fluorescence and confocal imaging of mammalian cells using conjugated oligoelectrolytes with phenylenevinylene core.
Justyna Milczarek, Roza Pawlowska, Remigiusz Zurawinski, Beata Lukasik, Logan E. Garner, Arkadiusz Chworos
J Photochem Photobiol B. 2017, 170:40-48.

Designing synthetic RNA for delivery by nanoparticles
Dominika Jedrzejczyk, Edyta Gedaszewska-Darmach, Roza Pawlowska, Arkadiusz Chworos
J Phys Condens Matter. 2017 Mar 29;29(12):123001.

Supported Fluid Lipid Bilayer as a Scaffold to Direct Assembly of RNA Nanostructures
Aleksandra P. Dabkowska, Agnes Michanek, Luc Jaeger, Arkadiusz Chworos, Tommy Nylander, Emma Sparr
RNA structures: methods and protocol, Methods in Molecular Biology, 2017, 1632:107-122

RNA model evaluation based on MD simulation of four tRNA analogs
Anna Grzybkowska, Dominika Jedrzejczyk, Rostkowski Michal, Arkadiusz Chworos, Agnieszka Dybala-Defratyka
RSC Adv. 2016, 104(6):101778-101789

RNA fragments mimicking tRNA analogs interact with cytochrome c
Roza Pawlowska, Magdalena Janicka, Dominika Jedrzejczyk, Arkadiusz Chworos
Mol. Biol. Rep. 2016, 43(4):295-304. doi: 10.1007/s11033-016-3954-6

The alpha-thio and/or beta-gamma-hypophosphate analogs of ATP as cofactors of T4 DNA ligase
Roza Pawlowska, Korczynski Dariusz, Barbara Nawrot, Wojciech J. Stec, Arkadiusz Chworos
Bioorg Chem. 2016:110-5. doi: 10.1016/j.bioorg.2016.06.003

Assembly of RNA nanostructures on supported lipid bilayers
Aleksandra P. Dabkowska, Agnes Michanek, Luc Jaeger, Michael Rabe, Arkadiusz Chworos, Fredrik Hook, Tommy Nylande, Emma Sparr
Nanoscale, 2015, 7(2), 583-596

Bio-inspired nucleic acids based materials
Arkadiusz Chworos and Wirasak Smitthipong
Bio-Based Composites for High-Performance Materials: From Strategy to Industrial Application
CRC Press, Taylor & Francis, 2015, chapter 2, 43-58

Phenylenevinylene conjugated oligoelectrolytes as fluorescent dyes for mammalian cell imaging
Paulina Gwozdzinska, Roza Pawlowska, Justyna Milczarek, Logan E. Garner, Alexander W. Thomas, Guillermo C. Bazan, Arkadiusz Chworos
Chemical Communications, 2014, 50 (94), 14859-14861

DNA-functionalized polystyrene particles and their controlled self-assembly
Rungsima Chollakup, Wirasak Smitthipong, Arkadiusz Chworos
RSC Advances, 2014, 4 (58), 30648-30653

Cytochrome c interaction with tRNA, the new properties of the known molecules
Roza Pawlowska, Dominika Jedrzejczyk, Magdalena Janicka, Anna Graczyk and Arkadiusz Chworos
Acta Biochimica Polonica, 2014, S1, P7.35, 155

Structural analogs of tRNA form a Complex with Cytochrome C
Roza Pawlowska, Dominika Jedrzejczyk, Magdalena Janicka, Arkadiusz Chworos
FEBS Letters 281, 2014, S1, 398

Anna Graczyk, Dominika Jedrzejczyk, Roza Pawlowska, Arkadiusz Chworos
The Complex of tRNA with Cytochrome C in Gel Studies
Collection Symposium Series, 2014, 14, 283-284

Rational design of RNA nanoparticles and nanoarrays
Arkadiusz Chworos
RNA Nanotechnology
Pan Stanford Publishing, 2014, chapter 11, 213-234

RNA nanoparticles for gene expression regulation
Roza Pawlowska, Paulina Gwozdzinska and Arkadiusz Chworos
Nucleic Acids Nanotechnologies in Medicine: Diagnosis and Treatment of Diseases
Springer, 2013, chapter 11, 263-290

Supramolecular cooperative-assembly of polyelectrolyte films
Rungsima Chollakup, Wirasak Smitthipong and Arkadiusz Chworos
RSC Advances, 2013, 3, 4745-4749

Distyrylbenzene oligoelectrolyte (DSBN+) for human cervical carcinoma cells imaging
Roza Pawlowska, Paulina Gwozdzinska, Logan Garner and Arkadiusz Chworos
MRS Symposium Proceedings, Cambridge University Press, 2013, vol. 1569

From Bioorganic Chemistry to Chemical Biology (Od chemii bioorganicznej do biologii chemicznej)
Wojciech T. Markiewicz, Henryk Koroniak, Arkadiusz Chworos, Piotr Mucha, Jan Barciszewski
Misja Nauk Chemicznych, Wydawnictwo Nauka I Innowacja, 2011, 27, 109-124 (book chapter)

Effect of the Peptide Secondary Structure on the Peptide Amphiphile Supramolecular Structure and Interactions
Dimitris Missirlis, Arkadiusz Chworos, Caroline J. Fu, Htet A. Khant, Daniel V. Krogstad, Matthew Tirrell
Langmuir, 2011, 27, 6163_6170

Self-Assembly of an Optically Active Conjugated Oligoelectrolyte
Julia H. Ortony, Tirtha Chatterjee, Logan E. Garner, Arkadiusz Chworos, Alexander Mikhailovsky, Edward J. Kramer Guillermo C. Bazan
JACS, 2011, 133, 8380-8387

Promoting RNA helical stacking via A-minor junctions
Cody Geary, Arkadiusz Chworos, Luc Jaeger
Nucleic Acids Research, 2011, 39(2), 1066-1080

Self-Assembling RNA Nanorings Based on RNAI/II Inverse Kissing Complexes
Wade W. Grabow, Paul Zakrevsky, Kirill Afonin, Arkadiusz Chworos, Bruce A. Shapiro, Luc Jaeger
Nano Lett., 2011, 11(2), 878-887

Improved isolation of proteins tagged with glutathione S-transferase
Nicholas K. Vinckier, Arkadiusz Chworos, Stanley M. Parsons
Protein Expression And Purification, 2011, 75(2), 161-164

A polyhedron made of tRNAs
Isil Severcan, Cody Geary, Arkadiusz Chworos, Neil Voss, Erica Jacovetty, Luc Jaeger
Nature Chemistry, 2010, 2, 772-779 (high impact)

Modification of the Optoelectronic Properties of Membranes via Insertion of Amphiphilic Phenylenevinylene Oligoelectrolytes
Logan E. Garner, Juhyun Park, Scott M. Dyar, Arkadiusz Chworos, James J. Sumner, Guillermo C. Bazan
JACS, 2010, 132 (29), 10042-10052

Identification of Bacteria by Conjugated Oligoelectrolyte/Single-Stranded DNA Electrostatic Complexes
Aidee Duarte, Arkadiusz Chworos, Suvi F. Flagan, Grady Hanrahan, Guillermo C. Bazan
JACS, 2010, 132 (36), 12562-12564

Specific interaction of DNA-functionalized polymer colloids
Rungsima Chollakup, Wirasak Smitthipong and Arkadiusz Chworos
Polymer Chemistry, 2010, 1 (5), 658-662

A Tripod Molecular Tip for Single Molecule Ligand-Receptor Force Spectroscopy by AFM
Michael E. Drew, Arkadiusz Chworos, Emin Oroudjev, Helen Hansma, Yoko Yamakoshi
Langmuir, 2010, 26 (10), 7117-7125

Automatic Analysis of Conjugated Polyelectrolytes – DNA Interactions Based on Sequential Analysis of AFM Imaging
Arkadiusz Chworos, Boguslaw Obara
IEEE Transactions on Nanotechnology, 8, 2009, 457-462

Noncovalent Supramolecular Self-assembling Polyelectrolyte: Nucleic Acid Based Materials
Wirasak Smitthipong, Thorsten Neumann, Surekha Gajria, Youli Li, Arkadiusz Chworos, Luc Jaeger, and Matthew Tirrell
Macromolecules, 2009, 10, 221-228

Square-Shaped RNA Particles from Different RNA Folds
Isil Severcan, Cody Geary, Erik Verzemnieks, Arkadiusz Chworos, and Luc Jaeger
Nano Letters, 2009, vol 9, issue 3, 1270-1277

Preliminary structural investigations of the Eut-L shell protein of the ethanolamine ammonia-lyase metabolosome of Escherichia coli
Kiel Nikolakakis, Akashi Ohtaki, Keith Newton, Arkadiusz Chworos and Martin Sagermann
Acta Crystallographica, 2009, F65, 128_132

Anatomy and Growth Characteristics of Conjugated Polyelectrolyte/DNA Aggregates.
Chunyan Chi, Arkadiusz Chworos, Jinping Zhang, Alexander Mikhailovsky and Guillermo C. Bazan
Advanced Functional Materials, 18, 2008, 3606_3612 (journal cover)

Self-assembled Materials Containing Complementary Nucleobase Molecular Recognition.
Wirasak Smitthipong, Arkadiusz Chworos, Brian Lin, Thorsten Neumann, Surekha Gajria, Luc Jaeger and Matthew Tirrell
Mater. Res. Soc. Symp. Proc., 2008, 1094

Supramolecular Materials Comprising Nucleic Acid Biopolymers.
Wirasak Smitthipong, Thorsten Neumann, Arkadiusz Chworos, Luc Jaeger and Matthew Tirrell
Macromol. Symp., 264, 2008, 13-17

Nucleic acid foldamers: design, engineering and selection of programmable bio-materials with recognition, catalytic and self-assembly properties.
Arkadiusz Chworos and Luc Jaeger
Foldamer, by Wiley, 2007, Chapter 10 (book chapter)

Sculpting Responsive, Informational Nano-Particles with RNA
Cody Geary, Isil Severcan, Erik Verzemnieks, Arkadiusz Chworos and Luc Jaeger
Journal of Biomolecular Structure & Dynamics, 2007, 24, 703-704

The design and characterization of modular polyhedral architectures made of RNA
Isil Severcan, Cody Geary, Arkadiusz Chworos, Luc Jaeger
Biophysical Journal, 2007, 350a-351a Suppl. S

The architectonics of programmable RNA and DNA nanostructures
Luc Jaeger and Arkadiusz Chworos
Current Opinion of Structural Biology, 2006, 4, 531-543 (review)

From RNA Tectonics to Programmable Jigsaw Puzzles Made of RNA
Arkadiusz Chworos and Luc Jaeger
Proceedings Foundations of Nanoscience, 2005, 157-162

Controlled Spacing of Cationic Gold Nanoparticles by Nanocrown RNA
Alexey Y. Koyfman, Gary Braun, Sergei Magonov, Arkadiusz Chworos, Norbert O. Reich, and Luc Jaeger
JACS, 2005, 127, 11886-11887

Thermal stability analysis of self-assembling tRNA tecto-squares
Isil Severcan, Arkadiusz Chworos, Luc Jaeger
Biophysical Journal, 2005, 88, 571a-571a Part 2 Suppl. S

Building Programmable Jigsaw Puzzles with RNA
Arkadiusz Chworos, Isil Severcan, Alexey Y. Koyfman, Patrick Weinkam, Emin Oroudjev, Helen G. Hansma and Luc Jaeger
Science, 2004, 306, 2068-72 (high impact)

Comparison of the cleavage profiles of oligonucleotide duplexes with or without phosphorothioate linkages by using a chemical nuclease probe
Arkadiusz Chworos, Philippe Arnaud , Krystyna Zakrzewska, Piotr Guga, Genevi�ve Pratviel, Wojciech J. Stec and Bernard Meunier
J Biol Inorg Chem., 2004, 9, 374-84

Characterization of the dehydro-guanidinohydantoin oxidation product of guanine in a dinucleotide
Arkadiusz Chworos, Christel Seguy, Genevi�ve Pratviel, and Bernard Meunier
Chem Res Toxicol., 2002, 15, 1643-51

New examples of mixed seleno-sulfides; reactions with triphenylphosphine
Arkadiusz Chworos, Lucyna A. Wozniak and Wojciech J. Stec
Chem Commun., 2002, 7, 518-9

Guanine oxidation: NMR charakterization of a dehydro-guanidinohydantoin residue generated by a 2e-oxidation of d(GpT)
Arkadiusz Chworos, Yannick Coppel, Igor Dubey, Genevieve Pratviel and Bernard Meunier
J.Am.Chem.Soc., 2001, 123, 5867-5877

One-Pot Synthesis of Nucleoside 3-O-(S-Phenyl Methanephosphonothioate)s
Jaroslaw Pyzowski, Arkadiusz Chworos, Lucyna A. Wozniak, Wojciech J. Stec
Tetrahedron Letters, 2000, 41, 1223-1226

Stereochemical Correlation and Absolute Configuration Assignment for Thymidine 3-(S-Phenyl Methanephosphonothioate)
Arkadiusz Chworos and Lucyna A. Wozniak
Proceedings of the VIth Int. Symp. Solid Phase Synthesis & Combinatorial Chemical Libraries York, UK. 1999, entitled “Innovation and Perspectives in Solid Phase Synthesis & Combinatorial Libraries”, 2000, 43-46

The Synthesis of Unsymmetrical S1-(3-O-Thymidine-O-Methanephosphonyl)-S2-p-Nitrophenyl Disulfides and Their Reactions with Triphenylphosphine
Arkadiusz Chworos, Lucyna A. Wozniak and Wojciech J. Stec
Tetrahedron Letters, 2000, 41, 1219-1222

A Facile Conversion of Thio- and Selenophosphoric Acids and Their Derivatives into Fluoridates by Means of Reaction with Silver Fluoride
Arkadiusz Chworos and Lucyna A. Wozniak
Tetrahedron Letters, 1999, 41, 9337-9340

Mixed Phosphorus-Carboxylic Anhydrides as Synthons for Stereoselective Synthesis of [Rp]-Dinucleoside (3,5)-Methanephosphonates
Lucyna A.Wozniak, Arkadiusz Chworos and Wojciech J. Stec
Phosphorus,Sulfur and Silicon; 146, 1999, 649-652

Chemo- and Stereoselectivity of Nucleophilic Substitution at Phosphorus in Mixed Phosphorus-Carboxylic Anhydrides
Lucyna A.Wozniak, Arkadiusz Chworos and Wojciech J. Stec
Phosphorus,Sulfur and Silicon, 1999, 147, 1263-1264

Stereoselective Synthesis of [Rp]-Dinucleoside (3,5)-Methanephosphonates
Lucyna A.Wozniak, Arkadiusz Chworos and Wojciech J. Stec
Phosphorus,Sulfur and Silicon, 1999, 147, 1265-1266

Base-Dependent Regioselective and P-stereocontrolled Hydrolysis of Nucleoside 3-O-(O-2,4,6,-trimethylbenzoyl methanephosphonothioate)s
Lucyna A.Wozniak, Jaroslaw Pyzowski, Arkadiusz Chworos and Wojciech J. Stec
J.Org.Chem., 1998, 63, 9109-9112

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