Publications

43. Annecke, H. T. P & Eidelpes R, Feyrer H., Gürdap C, Ilgen J., Dasgupta R., Petzold K Optimising In-cell NMR Acquisition for Nucleic Acids. JBNMR 2024 

42. Brauser M., Petzold K., Thiele C.M. Investigating Interaction Dynamics of an Enantioselective Peptide Catalyzed Acylation Reaction. Angew Chem Int Ed 2024, e202421062. doi: 10.1002/anie.202421062

41. Dasgupta R., Becker W., Petzold K. Elucidating microRNA-34a organisation within Human Argonaute-2 by NMR. Nucleic Acids Res. 2024. NAR doi: https://doi.org/10.1093/nar/gkae744

40. Sweetapple L., Kosek D.M., Banijamali E., Becker W., Müller J., Karadiakos C., Baronti L., Guzzetti I., Schritt D., Chen A., Andersson E.R*., Petzold K*. Biophysics of microRNA-34a targeting and its influence on down-regulation 2024. bioRxiv doi: 10.1101/2024.02.14.580117.

*Shared corresponding and last author

39. Kosek DM, Banijamali E, Becker W, Petzold K*, Andersson ER*. Efficient 3′-pairing renders microRNA targeting less sensitive to mRNA seed accessibility. Nucleic Acids Res. 2023 Nov 10;51(20):11162-11177.  doi: 10.1093/nar/gkad795.

*Shared corresponding and last author

38. C. Sahin, A. Motso, X. Gu, H. Feyrer, D. Lama, T. Arndt, A. Rising, G. Valentin Gese, B. M. Hällberg, E. G. Marklund, N. P. Schafer, K. Petzold, K. Teilum, P. G. Wolynes, and M. Landreh. Mass Spectrometry of RNA-Binding Proteins during Liquid–Liquid Phase Separation Reveals Distinct Assembly Mechanisms and Droplet Architectures. Journal of the American Chemical Society 2023 doi: 10.1021/jacs.3c00932

37. Grätz L, Sajkowska-Kozielewicz JJ, Wesslowski J, Kinsolving J, Bridge LJ, Petzold K, Davidson G, Schulte G, Kozielewicz P. NanoBiT- and NanoBiT/BRET-based assays allow the analysis of binding kinetics of WNT-3A to endogenous Frizzled 7 in a colorectal cancer model. Br J Pharmacol. 2023 Apr 13. doi: 10.1111/bph.16090. 

36.  E. Banijamali, L. Baronti, W. Becker, J. J. Sajkowska-Kozielewicz, T. Huang, C. Palka, D. Kosek, L. Sweetapple, J. Müller, M. Stone, E. R. Andersson, K. Petzold.  RNA:RNA Interaction in Ternary Complexes Resolved by Chemical Probing. RNA 2022, doi:10.1261/rna.079190.122

35. P. Clemente, J. Calvo-Garrido, S. F. Pearce, F. A. Schober, M. Shigematsu, S. J. Siira, I. Laine, H. Spåhr, C. Steinmetzger, K. Petzold, Y. Kirino, R. Wibom, O. Rackham, A. Filipovska, J. Rorbach, C. Freyer, A. Wredenberg. ANGEL2 phosphatase activity is required for non-canonical mitochondrial RNA processing. Nat Commun 2022, doi: 10.1038/s41467-022-33368-9

34. H. Feyrer, CO. Gurdap, M. Marušič, J. Schlagnitweit and K. Petzold. Enzymatic incorporation of isotope-labeled adenine into RNA for the study of conformational dynamics by NMR. PLoS ONE 2022, doi: doi.org/10.1371/journal.pone.0264662

33. M. Riad, N. Hopkins, L. Baronti, H. Karlsson, J. Schlagnitweit and K. Petzold. Mutate-and-Chemical-Shift-Fingerprint (MCSF) to characterize excited states in RNA using NMR spectroscopy. Nature Protocols 2021, doi:10.1038/s41596-021-00606-1

32. H. Karlsson, H. Feyrer, L. Baronti,  and K. Petzold. Production of structured RNA fragments by in vitro transcription and HPLC purification. Current Protocols 2021, doi: 10.1002/cpz1.159

31. H. Feyrer, J. Schlagnitweit, and K. Petzold “Practical aspects of sample preparation and setup of 1H R1ρ relaxation dispersion experiments of RNA” JOVE 2021, doi: 10.3791/62470.

30. R. Schnieders, S. A. Peter, E. Banijamali, M. Riad, N. Altincekic, J. K. Bains, B. Ceylan, B. Fürtig, J. T. Grün, M. Hengesbach, K. F. Hohmann, D. Hymon, B. Knezic, A. Oxenfarth, K. Petzold, N. S. Qureshi, C. Richter, J. Schlagnitweit, A. Schlundt, H. Schwalbe, E. Stirnal, A. Sudakov, J. Vögele, A. Wacker, J. E. Weigand, J. Wirmer-Bartoschek & J. Wöhnert “1H, 13C and 15N chemical shift assignment of the stem-loop 5a from the 5′-UTR of SARS-CoV-2” Journal of Biomolecular NMR Assignments 2021, doi: 10.1007/s12104-021-10007-w

29. Wacker, J. E. Weigand, S. R. Akabayov, N. Altincekic, J. K. Bains, E. Banijamali, O. Binas, J. Castillo-Martinez, E. Cetiner, B. Ceylan, L.-Y. Chiu, J. Davila-Calderon, K. Dhamotharan, E. Duchardt-Ferner, J. Ferner, L. Frydman, B. Fürtig, J. Gallego, J. T. Grün, C. Hacker, C. Haddad, M. Hähnke, M. Hengesbach, F. Hiller, K. F. Hohmann, D. Hymon, V. de Jesus, H. Jonker, H. Keller, B. Knezic, T. Landgraf, F. Löhr, L. Luo, K. R. Mertinkus, C. Muhs, M. Novakovic, A. Oxenfarth, M. Palomino-Schätzlein, K. Petzold, S. A. Peter, D. J. Pyper, N. S. Qureshi, M. Riad, C. Richter, K. Saxena, T. Schamber, T. Scherf, J. Schlagnitweit, A. Schlundt, R. Schnieders, H. Schwalbe, A. Simba-Lahuasi, S. Sreeramulu, E. Stirnal, A. Sudakov, J.-N. Tants, B. S. Tolbert, J. Vögele, L. Weiß, J. Wirmer-Bartoschek, M. A. Wirtz Martin, J. Wöhnert & H. Zetzsche “Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy” Nucleic Acid Research2020, doi: 10.1093/nar/gkaa1013

28. L. Baronti, I. Guzzetti^†, P. Ebrahimi^†, S. Friebe Sandoz^†, E. Steiner^†, J. Schlagnitweit, B. Fromm, L. Silva, C. Fontana, A. Chen and K. Petzold “Base-pair conformational switch modulates miR-34a targeting of Sirt1 mRNA” Nature 2020, doi: 10.1038/s41586-020-2336-3

^† These people contributed equally

News & Views: “From transient recognition to efficient silencing: a RISCky business”

27. H. Karlsson, L. Baronti and K. Petzold “A robust and versatile method for production and purification of large-scale RNA samples for structural biology” RNA 2020, doi: 10.1261/rna.075697.120

26. H. Feyrer, R. Munteanu, L. Baronti and K. Petzold “One-Pot Production of RNA in High Yield and Purity Through Cleaving Tandem Transcripts” Molecules 2020, 25(5), 1142.

25. P. Ebrahimi, S.Kaur, L. Baronti, K. Petzold  and A. Chen “A two-dimensional Replica-Exchange Molecular Dynamics method for simulating RNA folding using sparse experimental restraints” Methods 162-163:96-107, 2019
24. M. Marušić, J. Schlagnitweit and K. Petzold “RNA dynamics by NMR” ChemBioChem 2019, 20, 2685-2710 

23. J. Schlagnitweit, S. Friebe Sandoz, A. Jaworski, I. Guzzetti, F. Aussenac, R. J. Carbajo, E. Chiarparin, A. J. Pell and K. Petzold*, “Observing an antisense drug complex in intact human cells by in-cell NMR” ChemBioChem, 20(19): 2474-2478, 2019

22. J. Schlagnitweit, E. Steiner, H. Karlsson and K. Petzold “Efficient detection of structure and dynamics in unlabeled RNAs: the SELOPE approach” Chemistry – A European Journal; 24(23):6067-6070, 2018.

21. L. Baronti, H. Karlsson, M. Marušić, K. Petzold  “A guide to large-scale RNA sample preparation” Analytical and Bioanalytical Chemistry, 1-14 Volume 410, Issue 14, pp 3239–3252, 2018

20. M. Niklasson, R. Otten, A. Ahlner^†, C. Andresen^†, J. Schlagnitweit^†, K. Petzold and P. Lundström “Comprehensive analysis of NMR data using advanced line shape fitting” J Biomol NMR  69: pp 93-99, 2017.
^† These people contributed equally

19. E. Steiner, J. Schlagnitweit, P. Lundström and K. Petzold. “Capturing Excited States in the Fast-Intermediate Exchange Time-Limit in Biological Systems Using ¹H NMR Spectroscopy”, Angew Chem Int Edit 2016, 55 (51), 15869–15872, 2016.    

18. L. Salmon, G.M. Giambaşu, E.N. Nikolova, K. Petzold, A. Bhattacharya, D.A. Case, H.M. Al-Hashimi. “Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings.” J Am Chem Soc., 137 (40), pp 12954–12965, 2015

17. I.J. Kimsey, K. Petzold, B. Sathyamoorthy, Z.W. Stein and H.M. Al-Hashimi “Visualizing Transient Watson-Crick Like Mispairs in DNA and RNA Duplexes” Nature, 519 (7543), pp 315-320, 2015

ISI web of knowledge data base: As of March/April 2018, this highly cited paper received enough citations to place it in the top 1% of the academic field of Biology & Biochemistry based on a highly cited threshold for the field and publication year 

16. S.A. Pawar, A.M. Jabgunde, K. Petzold, G.E.M. Maguire, D.D. Dhavale, H.G. Kruger and T.Govender, “Investigation and folding pattern of L-ido and D-gluco peptides by EASY ROESY NMR and X-ray”, RSC Advances, 3, 23355- 23369, 2013

15. M.M. Makatini, K. Petzold, C.N. Alves, P.I. Arvidsson, B. Honarparvar, P. Govender,. T. Govender., H.G. Kruger,. Y. Sayed, J. Lameira, G.E.M. Maguire,and M.E.S. Soliman “Synthesis, 2D-NMR and Molecular Modelling Studies of Pentacyclo-Undecane Lactam Peptides and Peptoids as Potential HIV-1 Wild type C-SA Protease Inhibitors”, Journal of Enzyme Inhibition And Medicinal Chemistry, 28(1): 78–88, 2013

14. E.A. Dethoff^†, K. Petzold^†, J. Chugh^†, A. Casiano-Negroni and H.M. Al-Hashimi, “Visualizing Transient Low-Populated Structures of RNA”, Nature; 491 (7426), pp 724-728, 2012 

^† These people contributed equally 

Four times recommended by the Faculty1000 and current Top10 in overall ranking and 2nd in structural biology Highlighted in Nature Methods Dec. 2012

13. B. Honarparvar, M.M. Makatini, S.A. Pawar, K. Petzold, M.E.S. Soliman, P.I. Arvidsson, Y. Sayed, T. Govender, G.E.M. Maguireand H.G. Kruger.“Pentacycloundecane-Diol-Based HIV-1 Protease Inhibitors: Biological Screening, 2D NMR, and Molecular Simulations Studies”, ChemMedChem, 7(6), pp 1009-19, 2012

12. K. Petzold and H.M. Al-Hashimi, “RNA Structure: Adding a Second Dimension”, Nature Chemistry; 3 (12), pp 913-915, 2011

11. M.M. Makatini, K. Petzold, P.I. Arvidsson, B. Honarparvar, T, Govender, G.E. M. Maguire, R. Parboosing, Y. Sayed, M.E.S. Solimana, and H.G. Kruger, “Synthesis, screening and computational investigation of pentacycloundecane-peptoids as potent CSA-HIV PR inhibitors.”, European Journal of Medicinal Chemistry, 46(9), pp 913-915, 2011

10. M.M. Makatini, K. Petzold, S.N. Sriharsha, M.E.S. Soliman, B. Honarparvar, PI Arvidsson, Y. Sayed, P. Govender, G.E.M. Maguire, H.G. Kruger and T. Govender “Synthesis and Structural Studies of Pentacycloundecane-based HIV-1 PR Inhibitors: A Hybrid 2D-NMR and Docking/QM/MM/MD Approach”, European Journal of Medicinal Chemistry; 46 (9), pp 3976-3985, 2011

9. M. Shaikh, K. Petzold, H.G. Kruger and K. du Toit “Synthesis and NMR elucidation of homoisoflavanone analogues”, Structural Chemistry; 22 (1), pp 161-166, 2011

8. M.M. Makatini, K. Petzold, S.N. Sriharsha, M.E.S. Soliman, B. Honarparvar, PI Arvidsson, Y. Sayed, P. Govender, G.E.M. Maguire, H.G. Kruger and T. Govender “Pentacycloundecane-based inhibitors of Wild type C-South African HIV-protease”, Bioorganic & Medicinal Letters; 21 (8), pp 2274-2277, 2011

7. T. Naicker, K. Petzold, T. Singh, P.I. Arvidsson, H.G. Kruger, G.E.M. Maguire, T. Govender, “Novel tetrahydroisoquinoline based organocatalysts for asymmetric Diels-Alder reactions: insight into the catalytic mode using ROESY NMR and DFT studies”, Tetrahedron Asymmetry; 21 (23), pp 2859-2867, 2010

6. A. Olofsson, A. Vallström, K. Petzold, N. Tegtmeyer, J. Schleucher, S.C. Carlsson, R. Haas, S. Backert, S.N. Wai, G. Gröbner and A. Arnqvist “Biochemical and functional characterization of Helicobacter pylori vesicles”, Molecular Microbiology;77(6), pp 1539-1555, 2010

5. K. Petzold, A. Olofsson, A. Arnqvist, G. Gröbner and J. Schleucher “Semiconstant-Time P,H-COSY NMR: Analysis of Complex Mixtures of Phospholipids Originating from Helicobacter pylori”, Journal of the American Chemical Society;131 (40), pp 14150–14151, 2009

4. C.M. Thiele, K. Petzold and J. Schleucher “EASY ROESY: reliable cross-peak integration in adiabatic symmetrized ROESY”, Chemistry – A European Journal; 15 (3), pp 585-588, 2009

3. K. Petzold, A. Öhman and L. Backman “Folding of the -spectrin SH3 domain under in vivo conditions”, Archives of Biochemistry and Biophysics; 474(1), pp 39-47, 2008

2. K. Petzold, E. Duchardt, S. Flodell, G. Larsson, K. Kidd-Ljungren, S. Wijmenga, J. Schleucher “Conserved nucleotides in the hepatitis B virus reverse-transcriptase-binding RNA are mobile”, Nucleic Acids Research; 35(20), pp 6854-6861,2007

1. J. Robertsson, K. Petzold, L. Löfvenberg and L. Backman, “Folding of Spectrin’s SH3 domain in the presence of spectrin repeats”, Cellular &Molecular Biology Letters;10(4); pp 595-612,2005