Martin Jinek 2 protocols

John Oost Department of Agrotechnology and Food Sciences, Wageningen University, the Netherlands, the Netherlands,
3 protocols

P Mohanraju Wageningen University and Research
1 protocol

Stan Brouns Department of Agrotechnology and Food Sciences, Wageningen University, the Netherlands
1 protocol
Aksiniya Asenova University of California, Davis
17 protocols

Arsalan Daudi University of California
157 protocols

Benoit Chassaing Georgia State University
14 protocols

Kabin Xie Huazhong Agricultural University
7 protocols

Daan C. Swarts
  • Post-Doc, Department of Biochemistry, University of Zurich, Switzerland
Research focus
  • Biochemistry
  • -Structural biology
    -Protein-nucleic acid interactions
  • 3 Author merit


PhD, Wageningen UR, 2015

Lab information

Martin Jinek lab


First author publications
8. JW Hegge*, DC Swarts*, J van der Oost (2017). Prokaryotic Argonaute proteins - novel genome-editing tools? Nature Reviews Microbiology nrmicro.2017.73
7. 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
6. 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
5. 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
4. 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
3. 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
2. 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
1. DC Swarts, C Mosterd, MWJ van Passel, SJJ Brouns (2012) CRISPR Interference Directs Strand Specific Spacer Acquisition. PLoS ONE, 7(4): e35888

Co-author publications
6. J van der Oost, DC Swarts, MM Jore (2014) Prokaryotic Argonautes – variations on the RNA interference theme. Microbial Cell, Vol. 1, Issue 5, 158-159
5. 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
4. 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
3. 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 Reviews Genetics, Vol. 46
2. CM Plugge, AM Henstra, P Worm, DC Swarts, AH Paultisch-Fuchs, JCM Scholten, A Lykidis, AL Lapidus, E Goltsman, E Kim, E McDonald, L Rohlin, BR Crable, RP Gunsalus, AJM Stams, MJ McInerney (2012) Complete genome sequence of Syntrophobacter fumaroxidans strain (MPOBT). Standards in Genomic Sciences, Vol. 7 91-106
1. F Blombach, H Launay, V Zorraquino, DC Swarts, LD Cabrita, D Benelli, J Christodoulou, P Londei, J van der Oost (2011) An HflX-Type GTPase from Sulfolobus solfataricus binds to the 50S Ribosomal Subunit in All Nucleotide-Bound States. Journal of Bacteriology, Vol. 193 2861-2867

Peer-reviewed protocol publications
2. DC Swarts, ER Westra, SJJ Brouns, J van der Oost (2014) Purification and Sequencing of DNA guides from Prokaryotic Argonaute. Bio-protocol, Vol 4, Issue 22
1. DC Swarts, MM Jore, John van der Oost (2014) Expression and Purification of the Thermus thermophilus Argonaute Protein. Bio-protocol, Vol 4, Issue 19

*These authors contributed equally
3 Protocols published
Heterologous Expression and Purification of the CRISPR-Cas12a/Cpf1 Protein
Authors:  Prarthana Mohanraju, John van der Oost, Martin Jinek and Daan C. Swarts, date: 05/05/2018, view: 16659, Q&A: 3
This protocol provides step by step instructions (Figure 1) for heterologous expression of Francisella novicida Cas12a (previously known as Cpf1) in Escherichia coli. It additionally includes a protocol for high-purity purification ...
Purification and Sequencing of DNA Guides from Prokaryotic Argonaute
Authors:  Daan C. Swarts, Edze R. Westra, Stan J. J. Brouns and John van der Oost, date: 11/20/2014, view: 13364, Q&A: 0
Some proteins utilize nucleic acids to guide them to complementary nucleic acid targets. One example is prokaryotic Argonaute protein, which, binds small single stranded DNA molecules as guides (Swarts et al., 2014). This protocol describes ...
3 Protocols reviewed
Determination of (p)ppGpp Levels During Stringent Response in Streptomyces coelicolor by Thin Layer Chromatography
Authors:  Smitha Sivapragasam and Anne Grove, date: 11/05/2016, view: 9538, Q&A: 0
The stringent response in bacteria is a stress response that is mediated by the signaling molecules guanosine tetraphosphate and pentaphosphate [(p)ppGpp], alarmones that are also directly related to virulence. Therefore, determination of (p)ppGpp ...
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Measurement of Intracellular cAMP Levels Using the Cyclic Nucleotide XP Enzymatic Immunoassay Kit in Bacteria
Authors:  Sarah K Giles, Uwe H Stroeher and Melissa H Brown, date: 04/20/2016, view: 10813, Q&A: 0
Cyclic AMP (cAMP) is a ubiquitous secondary signaling molecule, commonly associated with many bacterial processes, including the regulation of virulence factors, such as biofilms, pellicles and motility (Wolfgang, 2003). The quantity of available ...
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6 Protocols edited
Using CRISPR/Cas9 for Large Fragment Deletions in Saccharomyces cerevisiae
Authors:  Huanhuan Hao, Jing Huang, Tongtong Liu, Hui Tang and Liping Zhang, date: 07/20/2017, view: 11359, Q&A: 0
CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9) systems have emerged as a powerful tool for genome editing in many organisms. The wide use of CRISPR/Cas9 systems may be due to the fact that these ...
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Expression and Purification of the Cas10-Csm Complex from Staphylococci
Authors:  Lucy Chou-Zheng and Asma Hatoum-Aslan, date: 06/05/2017, view: 9455, Q&A: 0
CRISPR-Cas (Clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) is a class of prokaryotic immune systems that degrade foreign nucleic acids in a sequence-specific manner. These systems rely upon ribonucleoprotein ...
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