*: Authors contributed equally. #: Corresponding author(s).
M Pacesa*#, L Nickel*, C Schellhaas*, J Schmidt, E Pyatova, L Kissling, P Barendse, J Choudhury, S Kapoor, A Alcaraz-Serna, Y Cho, KH Ghamary, L Vinué, BJ Yachnin, AM Wollacott, S Buckley, AH Westphal, S Lindhoud, S Georgeon, CA Goverde, GN Hatzopoulos, P Gönczy, YD Muller, G Schwank, DC Swarts, AJ Vecchio, BL Schneider, S Ovchinnikov#, BE Correia# (2025) One-shot design of functional protein binders with BindCraft. Nature open access article link
P Bobadilla Ugarte, S Halter, SK Mutte, C Heijstek, T Niault, I Terenin, P Barendse, B Koopal, M Roosjen, S Boeren, V Hauryliuk, M Jinek, AH Westphal, DC Swarts# (2025) Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA. Molecular Cell 85(10). open access article link
T Niault, S van Houte, E Westra#, DC Swarts# (2025) Evolution and ecology of anti-defence systems in phages and plasmids. Current Biology 35(1). open access article link
SK Mutte*, P Barendse*, P Bobadilla Ugarte, DC Swarts# (2025) Distribution of bacterial DNA repair proteins and their co-occurrence with immune systems. Cell Reports 44(1). open access article link
F Raimondi, KM Siow, D Wrona, C Fuster-García, O Pastukhov, M Schmitz, K Bargsten, L Kissling, DC Swarts, G Andrieux, T Cathomen, U Modlich, M Jinek, U Siler, J Reichenbach# (2024) Gene editing of NCF1 loci is associated with homologous recombination and chromosomal rearrangements. Communications Biology 7, 1291. open access article link
L Olijslager, D Weijers, DC Swarts# (2024) Distribution of specific prokaryotic immune systems correlates with host optimal growth temperature. NAR Genomics & Bioinformatics 6(3) lqae105. open access article link
C Bastiaanssen*, P Bobadilla Ugarte*, K Kim*, G Finocchio*, Y Feng*, TA Anzelon, S Köstlebacher, D Tamarit, TJG Ettema, M Jinek, IJ MacRae, C Joo#, DC Swarts#, F Wu# (2024) RNA-guided RNA silencing by an Asgard archaeal Argonaute. Nature Communications 15 (5499). open access article link
G Finocchio*, B Koopal*, A Potocnik, C Heijstek, AH Westphal, M Jinek#, DC Swarts# (2024) Target DNA-dependent activation mechanism of the prokaryotic immune system SPARTA. Nucleic Acids Research, gkad1248. open access article link
DC Swarts# (2023) Keeping Cas9 out of the (R-)loop. Proc. Natl. Acad. Sci. USA 120 (34) 1-3. article link
PB Ugarte, P Barendse, DC Swarts# (2023) Argonaute proteins confer immunity in all domains of life. Current Opinion in Microbiology 74, 202313. open access article link
B Koopal, SK Mutte, DC Swarts# (2022) A long look at short prokaryotic Argonautes. Trends in Cell Biology 33(7) 605-618. article link | free access link | accepted manuscript (preprint)
A Potocnik, DC Swarts# (2022) Short prokaryotic Argonaute system repurposed as a nucleic acid detection tool. Clinical and Translational Medicine 12 (9) e1059-e1059. open access article link
B Koopal, A Potocnik, SK Mutte, S Lindhoud, C Aparicio Maldonado, JJM Vervoort, SJJ Brouns, DC Swarts# (2022) Short prokaryotic Argonaute systems trigger cell death upon detection of invading DNA. Cell 185(9) 1471-1486. open access article link | press release (EN) | press release (NL)
L van Oosten, JJ Altenburg, C Fougeroux, C Geertsema, F van den End, WAC Evers, AH Westphal, S Lindhoud, W van den Berg, DC Swarts, L Deurhof, A Suhrbier, TT Le, S Torres Morales, SK Myeni, M Kikkert, AF Sander, WA de Jongh, R Dagil, MA Nielsen, A Salanti, M Søgaard, TMP Keijzer, D Weijers, MHM Eppink, RH Wijffels, MM van Oers, DE Martens, and GP Pijlman#. (2021) Two-Component Nanoparticle Vaccine Displaying Glycosylated Spike S1 Domain Induces Neutralizing Antibody Response against SARS-CoV-2 Variants. MBio 12(5) e1813-1821. open access article link
DC Swarts# (2020) Prokaryotic Argonautes Function beyond immunity by Unlinking Replicating Chromosomes. Cell 182(6) 1381-1383. open access article link
DC Swarts# (2019) Making the cut(s): How Cas12a cleaves target and non-target DNA. Biochemical Society Transactions 47(5) 1499-1510. open access article link
JW Hegge*, DC Swarts*, SD Chandradoss, TJ Cui, J Kneppers, M Jinek, C Joo, J van der Oost# (2019) DNA-guided DNA cleavage at moderate temperatures by Clostridium butyricum Argonaute. Nucleic Acids Research 14(11) 5809-5821. open access article link
Selection of older publications
DC Swarts, M Jinek# (2019) Mechanistic insights into the cis- and trans-acting DNase activities of Cas12a. Molecular Cell, 73, 589–600.
DC Swarts# (2019) Stirring up the Type V Alphabet Soup. The CRISPR Journal, 2, 14-16.
DC Swarts, M Jinek# (2018) Cas9 versus Cas12a/Cpf1: structure-function comparisons and implications for genome editing. WIREs RNA, e1481, 1-19.
M Vlot, J Houkes, SJA Lochs, DC Swarts, P Zheng, T Kunne, P Mohanraju, C Anders, M Jinek, J van der Oost, MJ Dickman, SJJ Brouns# (2017) Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not by type V CRISPR-Cas effector complexes. Nucleic Acids Research, Vol. 46, Issue 2, 873-885.
J Hegge*, DC Swarts*, J van der Oost# (2017) Programmable DNA cleavage by prokaryotic Argonautes – Novel genome editing tools? Nature Reviews Microbiol. 16, 5-11.
DC Swarts, J van der Oost, M Jinek# (2017) Structural basis for guide RNA processing and seed-dependent DNA targeting by Cas12a. Molecular Cell 66, 221-233.
DC Swarts*, M Szczepaniak*, G Sheng*, SD Chandradoss, Y Zhu, EM Timmers, Y Zhang, H Zhao, J Lou, Y Wang, C Joo, J van der Oost# (2017) Autonomous generation and loading of DNA guides by bacterial Argonaute. Molecular Cell 65, 985-998.
DC Swarts, JW Hegge, I Hinojo, M Shiimori, M Ellis, J Dumrongkulraksa, RM Terns, MP Terns, J van der Oost# (2015) Argonaute of archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA. Nucleic Acids Research, 43: 5120-5129.
DC Swarts, JJ Koehorst, ER Westra, PJ Schaap, J van der Oost# (2015) Effects of Argonaute on gene expression in Thermus thermophilus. PLoS ONE, 10(4): e0124880.
DC Swarts, K Makarova, Y Wang, K Nakanishi, RF Ketting, EV Koonin, DJ Patel, J van der Oost# (2014) The evolutionary journey of Argonaute proteins. Nat. Struc. Mol. Biol. Vol. 21, 743-753.
DC Swarts*, MJ Jore*, ER Westra, Y Zhu, JH Janssen, AP Snijders, Y Wang, DJ Patel, J Berenguer, SJJ Brouns, J van der Oost# (2014) DNA-guided DNA interference by a prokaryotic Argonaute. Nature, Vol. 507, Issue 7491, 258-261.
G Sheng*, H Zhao*, J Wang, Y Rao, W Tian, DC Swarts, J van der Oost, DJ Patel, Y Wang# (2014) Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage. Proc. Natl. Acad. Sci. USA, Vol. 111, Issue 2, 652-657.
T Künne, DC Swarts, SJJ Brouns# (2014) Planting the seed: Target recognition of short guide RNAs. Trends in Microbiology, Vol. 22, Issue 2, 74-83.
ER Westra, DC Swarts, RHJ Staals, MM Jore, SJJ Brouns, J van der Oost# (2012) The CRISPRs, They Are A-Changin’: How Prokaryotes Generate Adaptive Immunity. Annual Review of Genetics, Vol. 46.
DC Swarts, C Mosterd, MWJ van Passel, SJJ Brouns# (2012) CRISPR Interference Directs Strand Specific Spacer Acquisition. PLoS ONE, 7(4): e35888.
THE SWARTS LAB 