Katja Petzold

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Articles

Article: NUCLEIC ACIDS RESEARCH. 2025;53(8):gkaf364
Mapping effective microRNA pairing beyond the seed using abasic modifications
Kosek DM; Petzold K; Andersson ER
Journal article: ANGEWANDTE CHEMIE-INTERNATIONAL EDITION. 2024;64(10):e202421062
Investigating Interaction Dynamics of an Enantioselective Peptide-Catalyzed Acylation Reaction
Brauser M; Petzold K; Thiele CM
Article: BRITISH JOURNAL OF PHARMACOLOGY. 2024;181(20):3819-3835
NanoBiT- and NanoBiT/BRET-based assays allow the analysis of binding kinetics of Wnt-3a to endogenous Frizzled 7 in a colorectal cancer model
Gratz L; Sajkowska-Kozielewicz JJ; Wesslowski J; Kinsolving J; Bridge LJ; Petzold K; Davidson G; Schulte G; Kozielewicz P
Article: NUCLEIC ACIDS RESEARCH. 2023;51(20):11162-11177
Efficient 3′-pairing renders microRNA targeting less sensitive to mRNA seed accessibility
Kosek DM; Banijamali E; Becker W; Petzold K; Andersson ER
Article: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2023;145(19):10659-10668
Mass Spectrometry of RNA-Binding Proteins during Liquid-Liquid Phase Separation Reveals Distinct Assembly Mechanisms and Droplet Architectures
Sahin C; Motso A; Gu X; Feyrer H; Lama D; Arndt T; Rising A; Gese GV; Haellberg BM; Marklund EG; Schafer NP; Petzold K; Teilum K; Wolynes PG; Landreh M
Article: RNA. 2023;29(3):317-329
RNA:RNA interaction in ternary complexes resolved by chemical probing
Banijamali E; Baronti L; Becker W; Sajkowska-Kozielewicz JJ; Huang T; Palka C; Kosek D; Sweetapple L; Mueller J; Stone MD; Andersson ER; Petzold K
Article: NATURE COMMUNICATIONS. 2022;13(1):5750
ANGEL2 phosphatase activity is required for non-canonical mitochondrial RNA processing
Clemente P; Calvo-Garrido J; Pearce SF; Schober FA; Shigematsu M; Siira SJ; Laine I; Spahr H; Steinmetzger C; Petzold K; Kirino Y; Wibom R; Rackham O; Filipovska A; Rorbach J; Freyer C; Wredenberg A
Article: PLOS ONE. 2022;17(7):e0264662
Enzymatic incorporation of an isotope-labeled adenine into RNA for the study of conformational dynamics by NMR
Feyrer H; Gurdap CO; Marusic M; Schlagnitweit J; Petzold K
Article: NATURE PROTOCOLS. 2021;16(11):5146-5170
Mutate-and-chemical-shift-fingerprint (MCSF) to characterize excited states in RNA using NMR spectroscopy
Riad M; Hopkins N; Baronti L; Karlsson H; Schlagnitweit J; Petzold K
Journal article: JOVE-JOURNAL OF VISUALIZED EXPERIMENTS. 2021;(173)
Practical Aspects of Sample Preparation and Setup of ¹H R_1ρ Relaxation Dispersion Experiments of RNA
Feyrer H; Schlagnitweit J; Petzold K
Article: JOVE-JOURNAL OF VISUALIZED EXPERIMENTS. 2021;(173)
Practical Aspects of Sample Preparation and Setup of ¹H R₁ρ Relaxation Dispersion Experiments of RNA
Feyrer H; Schlagnitweit J; Petzold K
Article: CURRENT PROTOCOLS. 2021;1(6):e159
Production of Structured RNA Fragments by In Vitro Transcription and HPLC Purification
Karlsson H; Feyrer H; Baronti L; Petzold K
Article: BIOMOLECULAR NMR ASSIGNMENTS. 2021;15(1):203-211
¹H, ¹³C and ¹⁵N chemical shift assignment of the stem-loop 5a from the 5′-UTR of SARS-CoV-2
Schnieders R; Peter SA; Banijamali E; Riad M; Altincekic N; Bains JK; Ceylan B; Fuertig B; Gruen JT; Hengesbach M; Hohmann KF; Hymon D; Knezic B; Oxenfarth A; Petzold K; Qureshi NS; Richter C; Schlagnitweit J; Schlundt A; Schwalbe H; Stirnal E; Sudakov A; Voegele J; Wacker A; Weigand JE; Wirmer-Bartoschek J; Woehnert J
Article: NUCLEIC ACIDS RESEARCH. 2020;48(22):12415-12435
Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy
Wacker A; Weigand JE; Akabayov SR; Altincekic N; Bains JK; Banijamali E; Binas O; Castillo-Martinez J; Cetiner E; Ceylan B; Chiu L-Y; Davila-Calderon J; Dhamotharan K; Duchardt-Ferner E; Ferner J; Frydman L; Fuertig B; Gallego J; Gruen JT; Hacker C; Haddad C; Haehnke M; Hengesbach M; Hiller F; Hohmann KF; Hymon D; de Jesus V; Jonker H; Keller H; Knezic B; Landgraf T; Loehr F; Luo L; Mertinkus KR; Muhs C; Novakovic M; Oxenfarth A; Palomino-Schatzlein M; Petzold K; Peter SA; Pyper DJ; Qureshi NS; Riad M; Richter C; Saxena K; Schamber T; Scherf T; Schlagnitweit J; Schlundt A; Schnieders R; Schwalbe H; Simba-Lahuasi A; Sreeramulu S; Stirnal E; Sudakov A; Tants J-N; Tolbert BS; Voegele J; Weiss L; Wirmer-Bartoschek J; Martin MAW; Wohnert J; Zetzsche H
Article: RNA. 2020;26(8):1023-1037
A robust and versatile method for production and purification of large-scale RNA samples for structural biology
Karlsson H; Baronti L; Petzold K
Article: NATURE. 2020;583(7814):139-144
Base-pair conformational switch modulates miR-34a targeting of Sirt1 mRNA
Baronti L; Guzzetti I; Ebrahimi P; Friebe Sandoz S; Steiner E; Schlagnitweit J; Fromm B; Silva L; Fontana C; Chen AA; Petzold K
Article: MOLECULES. 2020;25(5):E1142-1142
One-Pot Production of RNA in High Yield and Purity Through Cleaving Tandem Transcripts
Feyrer H; Munteanu R; Baronti L; Petzold K
Journal article: CHEMBIOCHEM. 2019;20(21):2683
Front Cover: RNA Dynamics by NMR Spectroscopy (ChemBioChem 21/2019)
Marušič M; Schlagnitweit J; Petzold K
Article: CHEMBIOCHEM. 2019;20(19):2474-2478
Observing an Antisense Drug Complex in Intact Human Cells by in-Cell NMR Spectroscopy
Schlagnitweit J; Sandoz SF; Jaworski A; Guzzetti I; Aussenac F; Carbajo RJ; Chiarparin E; Pell AJ; Petzold K
Article: METHODS. 2019;162:96-107
A two-dimensional replica-exchange molecular dynamics method for simulating RNA folding using sparse experimental restraints
Ebrahimi P; Kaur S; Baronti L; Petzold K; Chen AA
Article: CHEMISTRY-A EUROPEAN JOURNAL. 2018;24(23):6067-6070
Efficient Detection of Structure and Dynamics in Unlabeled RNAs: The SELOPE Approach
Schlagnitweit J; Steiner E; Karlsson H; Petzold K
Article: JOURNAL OF BIOMOLECULAR NMR. 2017;69(2):93-99
Comprehensive analysis of NMR data using advanced line shape fitting
Niklasson M; Otten R; Ahlner A; Andresen C; Schlagnitweit J; Petzold K; Lundstrom P
Journal article: ANGEWANDTE CHEMIE-INTERNATIONAL EDITION. 2016;128(51):16101-16104
Capturing Excited States in the Fast‐Intermediate Exchange Limit in Biological Systems Using 1H NMR Spectroscopy
Steiner E; Schlagnitweit J; Lundström P; Petzold K
Article: ANGEWANDTE CHEMIE-INTERNATIONAL EDITION. 2016;55(51):15869-15872
Capturing Excited States in the Fast-Intermediate Exchange Limit in Biological Systems Using ¹HNMR Spectroscopy
Steiner E; Schlagnitweit J; Lundstrom P; Petzold K
Article: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2015;137(40):12954-12965
Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings
Salmon L; Giambasu GM; Nikolova EN; Petzold K; Bhattacharya A; Case DA; Al-Hashimi HM
Article: NATURE. 2015;519(7543):315-320
Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes
Kimsey IJ; Petzold K; Sathyamoorthy B; Stein ZW; Al-Hashimi HM
Journal article: NEPHROLOGY DIALYSIS TRANSPLANTATION. 2014;29(12):2353
Building a network of ADPKD reference centres across Europe: the EuroCYST initiative (vol 29, pg 26, 2014)
Petzold K; Gansevoort RT; Ong ACM; Devuyst O; Rotar L; Eckardt K-U; Koettgen A; Pirson Y; Remuzzi G; Sandford R; Tesar V; Ecder T; Chaveau D; Torra R; Budde K; Le Meur Y; Wuethrich RP; Serra AL
Journal article: RESPIROLOGY. 2014;19(1):67-73
Interaction of cyclic mechanical stretch and toll-like receptor 4-mediated innate immunity in rat alveolar type II cells
Kuhn H; Petzold K; Hammerschmidt S; Wirtz H
Article: JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY. 2013;28(1):78-88
Synthesis, 2D-NMR and molecular modelling studies of pentacycloundecane lactam-peptides and peptoids as potential HIV-1 wild type C-SA protease inhibitors
Makatini MM; Petzold K; Alves CN; Arvidsson PI; Honarparvar B; Govender P; Govender T; Kruger HG; Sayed Y; Lameira J; Maguire GEM; Soliman MES
Article: RSC ADVANCES. 2013;3(45):23355-23360
Investigation and folding pattern of L-ido and D-gluco peptides by EASY ROESY NMR and X-ray
Pawar SA; Jabgunde AM; Petzold K; Maguire GEM; Dhavale DD; Kruger HG; Govender T
Article: NATURE. 2012;491(7426):724-728
Visualizing transient low-populated structures of RNA
Dethoff EA; Petzold K; Chugh J; Casiano-Negroni A; Al-Hashimi HM
Article: EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY. 2012;57:459-467
Synthesis, screening and computational investigation of pentacycloundecane-peptoids as potent CSA-HIV PR inhibitors
Makatini MM; Petzold K; Arvidsson PI; Honarparvar B; Govender T; Maguire GEM; Parboosing R; Sayed Y; Soliman MES; Kruger HG
Journal article: CHEMMEDCHEM. 2012;7(6):938
Inside Cover: Pentacycloundecane‐diol‐Based HIV‐1 Protease Inhibitors: Biological Screening, 2D NMR, and Molecular Simulation Studies (ChemMedChem 6/2012)
Honarparvar B; Makatini MM; Pawar SA; Petzold K; Soliman MES; Arvidsson PI; Sayed Y; Govender T; Maguire GEM; Kruger HG
Article: CHEMMEDCHEM. 2012;7(6):1009-1019
Pentacycloundecane-diol-Based HIV-1 Protease Inhibitors: Biological Screening, 2D NMR, and Molecular Simulation Studies
Honarparvar B; Makatini MM; Pawar SA; Petzold K; Soliman MES; Arvidsson PI; Sayed Y; Govender T; Maguire GEM; Kruger HG
Article: EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY. 2011;46(9):3976-3985
Synthesis and structural studies of pentacycloundecane-based HIV-1 PR inhibitors: A hybrid 2D NMR and docking/QM/MM/MD approach
Makatini MM; Petzold K; Sriharsha SN; Ndlovu N; Soliman MES; Honarparvar B; Parboosing R; Naidoo A; Arvidsson PI; Sayed Y; Govender P; Maguire GEM; Kruger HG; Govender T
Article: BIOORGANIC & MEDICINAL CHEMISTRY LETTERS. 2011;21(8):2274-2277
Pentacycloundecane-based inhibitors of wild-type C-South African HIV-protease
Makatini MM; Petzold K; Sriharsha SN; Soliman MES; Honarparvar B; Arvidsson PI; Sayed Y; Govender P; Maguire GEM; Kruger HG; Govender T
Article: STRUCTURAL CHEMISTRY. 2011;22(1):161-166
Synthesis and NMR elucidation of homoisoflavanone analogues
Shaikh M; Petzold K; Kruger HG; du Toit K
Article: TETRAHEDRON ASYMMETRY. 2010;21(23):2859-2867
Novel tetrahydroisoquinoline based organocatalysts for asymmetric Diels-Alder reactions: insight into the catalytic mode using ROESY NMR and DFT studies
Naicker T; Petzold K; Singh T; Arvidsson PI; Kruger HG; Maguire GEM; Govender T
Article: MOLECULAR MICROBIOLOGY. 2010;77(6):1539-1555
Biochemical and functional characterization of Helicobacter pylori vesicles
Olofsson A; Vallstrom A; Petzold K; Tegtmeyer N; Schleucher J; Carlsson S; Haas R; Backert S; Wai SN; Grobner G; Arnqvist A
Article: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2009;131(40):14150-14151
Semiconstant-Time P,H-COSY NMR: Analysis of Complex Mixtures of Phospholipids Originating from Helicobacter pylori
Petzold K; Olofsson A; Arnqvist A; Grobner G; Schleucher J
Article: CHEMISTRY-A EUROPEAN JOURNAL. 2009;15(3):585-588
EASY ROESY: Reliable Cross-Peak Integration in Adiabatic Symmetrized ROESY
Thiele CM; Petzold K; Schleucher J
Article: ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS. 2008;474(1):39-47
Folding of the αII-spectrin SH3 domain under physiological salt conditions
Petzold K; Ohman A; Backman L
Article: NUCLEIC ACIDS RESEARCH. 2007;35(20):6854-6861
Conserved nucleotides in an RNA essential for hepatitis B virus replication show distinct mobility patterns
Petzold K; Duchardt E; Flodell S; Larsson G; Kidd-Ljunggren K; Wijmenga S; Schleucher J
Article: CELLULAR & MOLECULAR BIOLOGY LETTERS. 2005;10(4):595-612
Folding of spectrin's SH3 domain in the presence of spectrin repeats
Robertsson J; Petzold K; Löfvenberg L; Backman L
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All other publications

Conference publication: BIOPHYSICAL JOURNAL. 2023;122(3):27A
RNA excited states by NMR and their impact on function
Petzold K
Conference publication: PROTEIN SCIENCE. 2023;32(12)
Mass Spectrometry and Molecular Dynamics Simulations Untangles Structure and Function of Protein Condensates
Sahin C; Motso A; Gu X; Feyrer H; Lama D; Arndt T; Rising A; Gese GV; Hallberg M; Marklund EG; Schafer NP; Petzold K; Teilum K
Preprint: BIORXIV. 2022
Mass spectrometry of RNA-binding proteins during liquid-liquid phase separation reveals distinct assembly mechanisms and droplet architectures
Sahin C; Motso A; Gu X; Feyrer H; Lama D; Arndt T; Rising A; Gese GV; Hällberg M; Marklund E; Schafer N; Petzold K; Teilum K; Wolynes P; Landreh M
Preprint: BIORXIV. 2022
Receptor levels determine binding affinity of WNT-3A to Frizzled 7 in a colorectal cancer model
Grätz L; Sajkowska-Kozielewicz J; Wesslowski J; Petzold K; Davidson G; Schulte G; Kozielewicz P
Preprint: BIORXIV. 2022
Purely enzymatic incorporation of an isotope-labeled adenine into RNA for the study of conformational dynamics by NMR
Feyrer H; Gurdap CO; Marušič M; Schlagnitweit J; Petzold K
Corrigendum: NUCLEIC ACIDS RESEARCH. 2021;49(12):7204-7205
Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy (vol 48, pg 12415, 2020)
Wacker A; Weigand JE; Akabayov SR; Altincekic N; Bains JK; Banijamali E; Binas O; Castillo-Martinez J; Cetiner E; Ceylan B; Chiu L-Y; Davila-Calderon J; Dhamotharan K; Duchardt-Ferner E; Ferner J; Frydman L; Fuertig B; Gallego J; Gruen JT; Hacker C; Haddad C; Haehnke M; Hengesbach M; Hiller F; Hohmann KF; Hymon D; de Jesus V; Jonker H; Keller H; Knezic B; Landgraf T; Loehr F; Luo L; Mertinkus KR; Muhs C; Novakovic M; Oxenfarth A; Palomino-Schaetzlein M; Petzold K; Peter SA; Pyper DJ; Qureshi NS; Riad M; Richter C; Saxena K; Schamber T; Scherf T; Schlagnitweit J; Schlundt A; Schnieders R; Schwalbe H; Simba-Lahuasi A; Sreeramulu S; Stirnal E; Sudakov A; Tants J-N; Tolbert BS; Voegele J; Weiss L; Wirmer-Bartoschek J; Martin MAW; Woehnert J; Zetzsche H
Conference publication: BIOPHYSICAL JOURNAL. 2021;120(3):286A
Single Base-Pair Conformational Switch Modulates miR-34a Targeting of Sirt1 mRNA
Petzold K
Review: CHEMBIOCHEM. 2019;20(21):2685-2710
RNA Dynamics by NMR Spectroscopy
Marusic M; Schlagnitweit J; Petzold K
Preprint: BIORXIV. 2019
Observing an antisense drug complex in intact human cells by in-cell NMR
Schlagnitweit J; Sandoz SF; Jaworski A; Guzzetti I; Aussenac F; Carbajo RJ; Chiarparin E; Pell AJ; Petzold K
Review: ANALYTICAL AND BIOANALYTICAL CHEMISTRY. 2018;410(14):3239-3252
A guide to large-scale RNA sample preparation
Baronti L; Karlsson H; Marusic M; Petzold K
Conference publication: FASEB JOURNAL. 2015;29
Correlation between Bacillus subtilis RNase P Conformational Change and Dynamics of P4 Helix Mimic in RNase P RNA
Chen Y; Frank A; Petzold K; Liu X; Brooks CIII; Al-Hashimi H; Fierke C
Conference publication: ACTA PHYSIOLOGICA. 2014;210:74
Renal xxpression of FGF23 and peripheral resistance to elevated FGF23 in rodent models of polycystic kidney disease
Spichtig D; Zhang H; Mohebbi N; Pavik I; Petzold K; Stange G; Saleh L; Biber J; Jaeger P; Serra AL; Wagner CA
Conference publication: FASEB JOURNAL. 2013;27:96.1
Predictive Understanding of RNA Dynamic Behavior: Bringing Order to Disorder
Al-Hashimi H; Petzold K; Chugh J; Mustoe T; Dethoff E; Brooks CIII
Other: NATURE CHEMISTRY. 2011;3(12):913-915
RNA STRUCTURE Adding a second dimension
Petzold K; Al-Hashimi HM
Conference publication: BIOPHYSICAL JOURNAL. 2009;96(3):409A
Helicobacter Pylori: How is Adhesin BabA, a Blood Group Antigen Binding Membrane Protein, Involved in Bacterial Adherence?
Petzold K; Olofsson A; Arnqvist A; Boren T; Grobner G; Schleucher J
Conference publication: ZOONOSES AND PUBLIC HEALTH. 2007;54:93-94
Helicobacter pylori outer membrane vesicles and properties for intimate host interactions
Olofsson A; Baeckstroem A; Petzold K; Groebner G; Wai SN; Carlsson S; Schleucher J; Arnqvist A
Conference publication: BIOPHYSICAL JOURNAL. 2007;:435A
Helicobacter pylori:: Functional insight into the action of its blood group antigen binding Adhesin BabA, a membrane protein.
Petzold K; Bugaytsova J; Olofsson A; Arnqvist A; Aisenbrey C; Boren T; Schleucher J; Grobner G

Grants

Understanding ribosomal movements to develop new drug targets
Swedish Research Council
1 January 2019 - 31 December 2024
Cancer gate holder miR-34a: Understand the structure of the cell's environment
Swedish Cancer Society
1 January 2018
MicroRNA adjusts cancer: change the structure to select function
Swedish Cancer Society
1 January 2017
MicroRNA control of neural development: Dissecting biological function with atomic resolution
Knut and Alice Wallenberg Foundation
1 January 2016 - 1 January 2021
MicroRNA adjusts cancer: change the structure to select function
Swedish Cancer Society
1 January 2016
"RNA structure meets function"
Swedish Research Council
1 November 2015 - 30 November 2015
RNA switches – how structural changes influence the function
Swedish Foundation for Strategic Research
1 September 2015 - 31 August 2018
Structure and Dynamics of non-coding RNAs
Swedish Research Council
1 January 2015 - 31 December 2018
MicroRNA adjusts cancer: change the structure to select function
Swedish Cancer Society
1 January 2015
How RNAs move - dynamics of regulatory RNAs
Ragnar Söderberg Foundation
1 January 2015 - 31 December 2019
How do microRNAs select their targets
Novo Nordisk Foundation
1 July 2014 - 30 June 2015
Notification of the use of return grants for granted postdoctoral grants
Swedish Research Council
1 August 2013 - 31 July 2014

Employments

Principal Researcher, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 2022-

Degrees and Education

Docent, Karolinska Institutet, 2019

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