From discovery to potential application: engineering a novel M23 peptidase to combat Listeria monocytogenes.

Kaus-Drobek M, Nowacka M, Gewartowska M, Korzeniowska Nee Wiweger M, Jensen MR, Møretrø T, Heir E, Nowak E, Sabała I.

Sci Rep. 2025

Activity and structure of human (d)CTP deaminase CDADC1.

Slyvka A, Rathore I, Yang R, Gewartowska O, Kanai T, Lountos GT, Skowronek K, Czarnocki-Cieciura M, Wlodawer A, Bochtler M.

Proc Natl Acad Sci U S A. 2025

Tailoring Alkyl Side Chains of Ionizable Amino-Polyesters for Enhanced In Vivo mRNA Delivery.

López Espinar A, Mulder LM, Elkhashab M, Khan Z, Czarnocki-Cieciura M, Aburto MR, Vucen S, Kowalski PS.

ACS Appl Bio Mater. 2025

Re-adenylation by TENT5A enhances efficacy of SARS-CoV-2 mRNA vaccines.

Krawczyk PS, Mazur M, Orzeł W, Gewartowska O, Jeleń S, Antczak W, Kasztelan K, Brouze A, Matylla-Kulińska K, Gumińska N, Tarkowski B, Owczarek EP, Affek K, Turowski P, Tudek A, Sroka M, Śpiewla T, Kusio-Kobiałka M, Wesołowska A, Nowis D, Golab J, Kowalska J, Jemielity J, Dziembowski A, Mroczek S.

Nature. 2025

Structural and biochemical characterization of the 3'-5' tRNA splicing ligases.

Chamera S, Zajko W, Czarnocki-Cieciura M, Jaciuk M, Koziej Ł, Nowak J, Wycisk K, Sroka M, Chramiec-Głąbik A, Śmietański M, Gołębiowski F, Warmiński M, Jemielity J, Glatt S, Nowotny M.

J Biol Chem. 2025

Data storage based on the absence of nucleotides using a bacteriophage abortive infection system reverse transcriptase.

Bajc G, Pavlin A, Figiel M, Zajko W, Nowotny M, Butala M.

Lab Chip. 2025

Structural and biochemical characterization of cauliflower mosaic virus reverse transcriptase.

Prabaharan C, Figiel M, Szczepanowski RH, Skowronek K, Zajko W, Thangaraj V, Chamera S, Nowak E, Nowotny M.

J Biol Chem. 2024

Structure-functional characterization of Lactococcus AbiA phage defense system.

Gapińska M, Zajko W, Skowronek K, Figiel M, Krawczyk PS, Egorov AA, Dziembowski A, Johansson MJO, Nowotny M.

Nucleic Acids Res. 2024

Despite the odds: formation of the SARS-CoV-2 methylation complex.

Matsuda A, Plewka J, Rawski M, Mourão A, Zajko W, Siebenmorgen T, Kresik L, Lis K, Jones AN, Pachota M, Karim A, Hartman K, Nirwal S, Sonani R, Chykunova Y, Minia I, Mak P, Landthaler M, Nowotny M, Dubin G, Sattler M, Suder P, Popowicz GM, Pyrć K, Czarna A.

Nucleic Acids Res. 2024

Drug repurposing screen to identify inhibitors of the RNA polymerase (nsp12) and helicase (nsp13) from SARS-CoV-2 replication and transcription complex.

Kuzikov M, Reinshagen J, Wycisk K, Corona A, Esposito F, Malune P, Manelfi C, Iaconis D, Beccari A, Tramontano E, Nowotny M, Windshügel B, Gribbon P, Zaliani A.

Virus Res.. 2024

Cryo-EM structure of rotavirus B NSP2 reveals its unique tertiary architecture.

Chamera S, Wycisk K, Czarnocki-Cieciura M, Nowotny M.

J Virol. 2024

Structure-Based Discovery of High-Affinity Small Molecule Ligands and Development of Tool Probes to Study the Role of Chitinase-3-Like Protein 1.

Czestkowski W, Krzemiński Ł, Piotrowicz MC, Mazur M, Pluta E, Andryianau G, Koralewski R, Matyszewski K, Olejniczak S, Kowalski M, Lisiecka K, Kozieł R, Piwowar K, Papiernik D, Nowotny M, Napiórkowska-Gromadzka A, Nowak E, Niedziałek D, Wieczorek G, Siwińska A, Rejczak T, Jędrzejczak K, Mulewski K, Olczak J, Zasłona Z, Gołębiowski A, Drzewicka K, Bartoszewicz A.

J Med Chem. 2024

Structures of annexin A2-PS DNA complexes show dominance of hydrophobic interactions in phosphorothioate binding.

Hyjek-Składanowska M, Anderson BA, Mykhaylyk V, Orr C, Wagner A, Poznański JT, Skowronek K, Seth P, Nowotny M.

Nucleic Acids Res.. 2023

Arginase 1/2 inhibitor OATD-02: from discovery to first-in-man setup in cancer immunotherapy.

Borek B, Nowicka J, Gzik A, Dziegielewski M, Jedrzejczak K, Brzezinska J, Grzybowski M, Stanczak P, Pomper P, Zagozdzon A, Rejczak T, Matyszewski K, Golebiowski A, Olczak J, Lisiecki K, Tyszkiewicz M, Kania M, Piasecka S, Cabaj A, Dera P, Mulewski K, Chrzanowski J, Kusmirek D, Sobolewska E, Magdycz M, Mucha L, Masnyk M, Golab J, Nowotny M, Nowak E, Napiorkowska-Gromadzka A, Pikul S, Jazwiec R, Dzwonek K, Dobrzanski P, Meyring M, Skowronek K, Iwanowski P, Zaslona Z, Blaszczyk R.

Mol Cancer Ther.. 2023

Mechanism of RecF–RecO–RecR cooperation in bacterial homologous recombination.

Nirwal S, Czarnocki-Cieciura M, Chaudhary A, Zajko W, Skowronek K, Chamera S, Figiel M, Nowotny M.

Nat Struct Mol Biol.. 2023

Structure of human TRPM8 channel.

Palchevskyi S, Czarnocki-Cieciura M, Vistoli G, Gervasoni S, Nowak E, Beccari AR, Nowotny M, Talarico C.

Commun Biol.. 2023

Rep protein accommodates together dsDNA and ssDNA which enables a loop-back mechanism to plasmid DNA replication initiation.

Wegrzyn K, Oliwa M, Nowacka M, Zabrocka E, Bury K, Purzycki P, Czaplewska P, Pipka J, Giraldo R, Konieczny I.

Nucleic Acids Res.. 2023

Mechanism of protein-primed template-independent DNA synthesis by Abi polymerases.

Figiel M, Gapińska M, Czarnocki-Cieciura M, Zajko W, Sroka M, Skowronek K, Nowotny M.

Nucleic Acids Res. 2022

Structural basis of transposon end recognition explains central features of Tn7 transposition systems.

Kaczmarska Z, Czarnocki-Cieciura M, Górecka-Minakowska KM, Wingo RJ, Jackiewicz J, Zajko W, Poznański JT, Rawski M, Grant T, Peters JE, Nowotny M.

Mol Cell.. 2022

Natural Compounds Inhibit SARS-CoV-2 nsp13 Unwinding and ATPase Enzyme Activities.

Corona A, Wycisk K, Talarico C, Manelfi C, Milia J, Cannalire R, Esposito F, Gribbon P, Zaliani A, Iaconis D, Beccari AR, Summa V, Nowotny M, Tramontano E.

ACS Pharmacol Transl Sci. 2022

The Pet127 protein is a mitochondrial 5'-to-3' exoribonuclease from the PD-(D/E)XK superfamily involved in RNA maturation and intron degradation in yeasts.

Labedzka-Dmoch K, Razew M, Gapinska M, Piatkowski J, Kolondra A, Salmonowicz H, Wenda JM, Nowotny M, Golik P.

RNA. 2022

A heterotypic assembly mechanism regulates CHIP E3 ligase activity.

Das A, Thapa P, Santiago U, Shanmugam N, Banasiak K, Dabrowska K, Nolte H, Szulc NA, Gathungu RM, Cysewski D, Krüger M, Dadlez M, Nowotny M, Camacho CJ, Hoppe T, Pokrzywa W.

EMBO J. . 2022

Structures of substrate complexes of foamy viral protease-reverse transcriptase.

Nowacka M, Nowak E, Czarnocki-Cieciura M, Jackiewicz J, Skowronek K, Szczepanowski R, Wöhrl BM, Nowotny M.

J Virol.. 2021

Structural Insights into the Interaction of Clinically Relevant Phosphorothioate mRNA Cap Analogs with Translation Initiation Factor 4E Reveal Stabilization via Electrostatic Thio-Effect.

Warminski  M, Kowalska  J, Nowak E, Kubacka  D, Tibble  R, Kasprzyk  R, Sikorski  PJ, Gross  JD, Nowotny  M, Jemielity J.

ACS Chem Biol.. 2021

A combined structural and biochemical approach reveals translocation and stalling of UvrB on the DNA lesion as a mechanism of damage verification in bacterial nucleotide excision repair.

Jaciuk M, Swuec P, Gaur V, Kasprzak JM, Renault L, Dobrychłop M, Nirwal S, Bujnicki JM, Costa A, Nowotny M.

DNA Repair (Amst).. 2020

Origins of the increased affinity of phosphorothioate-modified therapeutic nucleic acids for proteins.

Hyjek-Składanowska M, Vickers T, Napiórkowska A, Anderson B, Tanowitz M, Crooke ST, Liang XH, Seth PP, Nowotny M.

J Am Chem Soc.. 2020

Human REXO2 Controls Short Mitochondrial RNAs Generated by mtRNA Processing and Decay Machinery to Prevent Accumulation of Double-Stranded RNA.

Szewczyk M, Malik D, Borowski LS, Czarnomska SD, Kotrys AV, Klosowska-Kosicka K, Nowotny M, Szczesny RJ.

Nucleic Acids Res.. 2020

Vimentin S-glutathionylation at Cys328 Inhibits Filament Elongation and Induces Severing of Mature Filaments in Vitro.

Kaus-Drobek M, Mücke N, Szczepanowski RH, Wedig T, Czarnocki-Cieciura M, Polakowska M, Herrmann H, Wysłouch-Cieszyńska A, Dadlez M.

FEBS J.. 2020

Structure and mechanism of CutA, RNA nucleotidyl transferase with an unusual preference for cytosine..

Malik D, Kobyłecki K, Krawczyk P, Poznański J, Jakielaszek A, Napiórkowska A, Dziembowski A, Tomecki R, Nowotny M.

Nucleic Acids Res.. 2020

Evolutionary History and Activity of RNase H1-Like Proteins in Arabidopsis thaliana.

Kuciński J, Chamera S, Kmera A, Rowley MJ, Fujii S, Khurana P, Nowotny M, Wierzbicki AT.

Plant Cell Physiol.. 2020

Disulfide bridge cross-linking between protein and the RNA backbone as a tool to study RNase H1.

Hyjek-Składanowska M, Stasińska AR, Napiórkowska-Gromadzka A, Bartłomiejczak A, Seth PP, Chmielewski MK, Nowotny M.

Bioorg Med Chem. . 2020

Discovery of OATD-01, a First-in-Class Chitinase Inhibitor as Potential New Therapeutics for Idiopathic Pulmonary Fibrosis.

Koralewski R, Dymek B, Mazur M, Sklepkiewicz P, Olejniczak S, Czestkowski W, Matyszewski K, Andryianau G, Niedziejko P, Kowalski M, Gruza M, Borek B, Jedrzejczak K, Bartoszewicz A, Pluta E, Rymaszewska A, Kania M, Rejczak T, Piasecka S, Mlacki M, Mazurkiewicz M, Piotrowicz M, Salamon M, Zagozdzon A, Napiorkowska-Gromadzka A, Bartlomiejczak A, Mozga W, Dobrzański P, Dzwonek K, Golab J, Nowotny M, Olczak J, Golebiowski A.

J Med Chem.. 2020

The expression of Rpb10, a small subunit common to RNA polymerases, is modulated by the R3H domain-containing Rbs1 protein and the Upf1 helicase.

Cieśla M, Turowski TW, Nowotny M, Tollervey D, Boguta M.

Nucleic Acids Res.. 2020

Crosslink and shield: protecting abasic sites from error-prone repair.

Nowotny M.

Nat Struct Mol Biol.. 2019

Recognition and processing of branched DNA substrates by Slx1-Slx4 nuclease.

Gaur V, Ziajko W, Nirwal S, Szlachcic A, Gapińska M, Nowotny M

Nucleic Acids Res.. 2019

RuvC uses dynamic probing of the Holliday junction substrate to achieve sequence specificity and efficient resolution.

Górecka KM, Krepl M, Szlachcic A, Poznański J, Šponer J, Nowotny M.

Nat Commun.. 2019

RNases H: Structure and mechanism.

Hyjek M, Figiel M, Nowotny M.

DNA Repair (Amst). 2019

Mechanism of polypurine tract primer generation by HIV-1 reverse transcriptase.

Figiel M, Krepl M, Park S, Poznański J, Skowronek K, Gołąb A, Ha T, Šponer J, Nowotny M.

J Biol Chem. 2018

5′-Phosphorothiolate Dinucleotide Cap Analogues: Reagents for Messenger RNA Modification and Potent Small-Molecular Inhibitors of Decapping Enzymes.

Wojtczak BA, Sikorski PJ, Fac-Dabrowska K, Nowicka A, Warminski M, Kubacka D, Nowak E, Nowotny M, Kowalska J, Jemielity J.

J Am Chem Soc.. 2018

Structural analysis of mtEXO mitochondrial RNA degradosome reveals tight coupling of nuclease and helicase components.

Razew M, Warkocki Z, Taube M, Kolondra A, Czarnocki-Cieciura M, Nowak E, Labedzka-Dmoch K, Kawinska A, Piatkowski J, Golik P, Kozak M, Dziembowski A, Nowotny M.

Nat Commun.. 2018

The siRNA suppressor RTL1 is redox-regulated through glutathionylation of a conserved cysteine in the double-stranded-RNA-binding domain.

Charbonnel C, Niazi AK, Elvira-Matelot E, Nowak E, Zytnicki M, de Bures A, Jobet E, Opsomer A, Shamandi N, Nowotny M, Carapito C, Reichheld J-P, Vaucheret H, Saez-Vasquez J.

Nucleic Acids Res.. 2017

mRNA cap analogues substituted in the tetraphosphate chain with CX2: identification of O-to-CCl2 as the first bridging modification that confers resistance to decapping without impairing translation.

Rydzik AM, Warminski M, Sikorski PJ, Baranowski MR, Walczak S, Kowalska J, Zuberek J, Lukaszewicz M, Nowak E, W Claridge TD, Darzynkiewicz E, Nowotny M, Jemielity J.

Nucleic Acids Res. 2017

Chapter Six - Structural Studies of RNases H2 as an Example of Crystal Structure Determination of Protein–Nucleic Acid Complexes

Figiel M, Nowotny M

Methods in Enzymology. 2017

Coordination between the polymerase and RNase H activity of HIV-1 reverse transcriptase

Figiel M, Krepl M, Poznanski J, Golab A, Šponer J, Nowotny M

Nucleic Acids Res.. 2017

Structure and mechanism of nucleases regulated by SLX4

Nowotny M, Gaur V

Curr Opin Struct Biol. 2016

A short splicing isoform of HBS1L links the cytoplasmic exosome and SKI complexes in humans

Kalisiak K, Kuliński TM, Tomecki R, Cysewski D, Pietras Z, Chlebowski A, Kowalska K, Dziembowski A

Nucleic Acids Res. 2016

Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli

Stracy M, Jaciuk M, Uphoff S, Kapanidis AN, Nowotny M, Sherratt DJ, Zawadzki P

Nat Commun.. 2016

Helicobacter pylori HP0377, a member of the Dsb family, is an untypical multifunctional CcmG that cooperates with dimeric thioldisulfide oxidase HP0231

Roszczenko P, Grzeszczuk M, Kobierecka P, Wywial E, Urbanowicz P, Wincek P, Nowak E, Jagusztyn-Krynicka EK

BMC Microbiol.. 2015

Structural and Mechanistic Analysis of the Slx1-Slx4 Endonuclease

Gaur V, Wyatt HDM, Komorowska W, Szczepanowski RH, de Sanctis D, Gorecka KM, West SC, Nowotny M

Cell Reports. 2015

Functional and evolutionary analyses of Helicobacter pylori HP0231 (DsbK) protein with strong oxidative and chaperone activity characterized by a highly diverged dimerization domain

Bocian-Ostrzycka KM, Łasica AM, Dunin-Horkawicz S, Grzeszczuk MJ, Drabik K, Dobosz AM, Godlewska R, Nowak E, Collet J-F, Jagusztyn-Krynicka EK

Frontiers in Microbiology. 2015

Crystal structure of RNase H3-substrate complex reveals parallel evolution of RNA/DNA hybrid recognition.

Figiel M, Nowotny M.

Nucleic Acids Res.. 2014

Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding

Miętus M, Nowak E, Jaciuk M, Kustosz P, Studnicka J, Nowotny M

Nucleic Acids Res. 2014

The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification

Majorek KA, Dunin-Horkawicz S, Steczkiewicz K, Muszewska A, Nowotny M, Ginalski K, Bujnicki JM

Nucleic Acids Res.. 2014

Multiple myeloma-associated hDIS3 mutations cause perturbations in cellular RNA metabolism and suggest hDIS3 PIN domain as a potential drug target

Tomecki R, Drazkowska K, Kucinski I, Stodus K, Szczesny RJ, Gruchota J, Owczarek EP, Kalisiak K, Dziembowski A

Nucleic Acids Res.. 2014

Ty3 reverse transcriptase complexed with an RNA-DNA hybrid shows structural and functional asymmetry

Nowak E, Miller JT, Bona MK, Studnicka J, Szczepanowski RH, Jurkowski J, Le Grice SFJ, Nowotny M

Nature Structural & Molecular Biology. 2014

Structural analysis of human 2′-O-ribose methyltransferases involved in mRNA cap structure formation

Smietanski M, Werner M, Purta E, Kaminska KH, Stepinski J, Darzynkiewicz E, Nowotny M, Bujnicki JM

Nat Commun. 2014

Structural and biochemical insights to the role of the CCR4-NOT complex and DDX6 ATPase in microRNA repression.

Mathys H, Basquin J, Ozgur S, Czarnocki-Cieciura M, Bonneau F, Aartse A, Dziembowski A, Nowotny M, Conti E, Filipowicz W.

Mol Cell.. 2014

Crystal structure of RuvC resolvase in complex with Holliday junction substrate

Górecka KM, Komorowska W, Nowotny M

Nucleic Acids Res. 2013

Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid

Nowak E, Potrzebowski W, Konarev PV, Rausch JW, Bona MK, Svergun DI, Bujnicki JM, Le Grice SF, Nowotny M

Nucleic Acids Res. 2013

RNase H2 roles in genome integrity revealed by unlinking its activities

Chon H, Sparks JL, Rychlik M, Nowotny M, Burgers PM, Crouch RJ, Cerritelli SM

Nucleic Acids Res. 2013

Sequence-specific cleavage of the RNA strand in DNA-RNA hybrids by the fusion of ribonuclease H with a zinc finger

Sulej AA, Tuszynska I, Skowronek KJ, Nowotny M, Bujnicki JM

Nucleic Acids Res. 2012

The structural and biochemical characterization of human RNase H2 complex reveals the molecular basis for substrate recognition and Aicardi-Goutières syndrome defects

Figiel M, Chon H, Cerritelli SM, Cybulska M, Crouch RJ, Nowotny M

J Biol Chem. 2011

Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations

Rosta E, Nowotny M, Yang W, Hummer G

J Am Chem Soc.. 2011

Structure of UvrA nucleotide excision repair protein in complex with modified DNA.

Jaciuk M, Nowak E, Skowronek K, Tańska A, Nowotny M

Nat Struct Mol Biol. 2011

Crystal structures of RNase H2 in complex with nucleic acid reveal the mechanism of RNA-DNA junction recognition and cleavage.

Rychlik MP, Chon H, Cerritelli SM, Klimek P, Crouch RJ, Nowotny M

Mol Cell. 2010

Structural and functional modules in RNA interference

Nowotny M, Yang W

Curr Opin Struct Biol. 2009

Retroviral integrase superfamily: the structural perspective.

Nowotny M

EMBO Rep. 2009

Human Sgt1 binds HSP90 through the CHORD-Sgt1 domain and not the tetratricopeptide repeat domain.

Lee YT, Jacob J, Michowski W, Nowotny M, Kuznicki J, Chazin WJ.

J Biol Chem.. 2004

Characterization of the interaction of calcyclin (S100A6) and calcyclin-binding protein.

Nowotny M, Bhattacharya S, Filipek A, Krezel AM, Chazin W, Kuznicki J.

J Biol Chem.. 2000