Publications

ZORA Publication List

Publications

• 2024

  • Journal Article

    • Musiari, Anastasia; Reichenbach, María; Gallo, Sofia; Sigel, Roland K O (2024). Corrin Ring Modifications Reveal the Chemical and Spatial Requirements for the B$_1$$_2$ $btuB$ Riboswitch Interaction. Chemistry, 30(49):e202401800.
    • Steffen, Fabio D; Cunha, Richard A; Sigel, Roland K O; Börner, Richard (2024). FRET-guided modeling of nucleic acids. Nucleic Acids Research, 52(13):e59.
    • Götz, Markus; Barth, Anders; Bohr, Søren S R; Börner, Richard; Chen, Jixin; Cordes, Thorben; Erie, Dorothy A; Gebhardt, Christian; Hadzic, Mélodie C A S; Hamilton, George L; Hatzakis, Nikos S; Hugel, Thorsten; Kisley, Lydia; Lamb, Don C; de Lannoy, Carlos; Mahn, Chelsea; Dunukara, Dushani; de Ridder, Dick; Sanabria, Hugo; Schimpf, Julia; Seidel, Claus A M; Sigel, Roland K O; Sletfjerding, Magnus B; Thomsen, Johannes; Vollmar, Leonie; Wanninger, Simon; Weninger, Keith R; Xu, Pengning; Schmid, Sonja (2024). Reply to: On the statistical foundation of a recent single molecule FRET benchmark. Nature Communications, 15(1):3626.
    • Kienbeck, Kasimir; Malfertheiner, Lukas; Zelger-Paulus, Susann; Johannsen, Silke; von Mering, Christian; Sigel, Roland K O (2024). From Enigma to Revelation: Unravelling Biological Functions of Ubiquitous Small Ribozymes. Chimia, 78(4):200-204.
    • Kienbeck, Kasimir; Malfertheiner, Lukas; Zelger-Paulus, Susann; Johannsen, Silke; von Mering, Christian; Sigel, Roland K O (2024). Identification of HDV-like theta ribozymes involved in tRNA-based recoding of gut bacteriophages. Nature Communications, 15(1):1559.

• 2023

  • Journal Article

    • Craig, James S; Melidis, Larry; Williams, Hugo D; Dettmer, Samuel J; Heidecker, Alexandra A; Altmann, Philipp J; Guan, Shengyang; Campbell, Callum; Browning, Douglas F; Sigel, Roland K O; Johannsen, Silke; Egan, Ross T; Aikman, Brech; Casini, Angela; Pöthig, Alexander; Hannon, Michael J (2023). Organometallic Pillarplexes That Bind DNA 4-Way Holliday Junctions and Forks. Journal of the American Chemical Society, 145(25):13570-13580.
    • Amadei, Fabio; Reichenbach, Maria; Gallo, Sofia; Sigel, Roland K O (2023). The structural features of the ligand-free moaA riboswitch and its ion-dependent folding. Journal of Inorganic Biochemistry, 242:112153.
    • Ahunbay, Esra; Zelger-Paulus, Susann; Sigel, Roland K O (2023). Group II Introns: Highly Structured yet Dynamic. Chimia, 77(4):235-241.
    • Schmid, N; Bruderer, S; Paruzzo, F; Fischetti, G; Toscano, G; Graf, D; Fey, M; Henrici, A; Ziebart, V; Heitmann, B; Grabner, H; Wegner, Jan Dirk; Sigel, R K O; Wilhelm, D (2023). Deconvolution of 1D NMR spectra: A deep learning-based approach. Journal of Magnetic Resonance, 347:107357.

• 2022

  • Journal Article

    • Götz, Markus; Barth, Anders; Bohr, Søren S -R; Börner, Richard; et al; Hadzic, Mélodie C A S; Sigel, Roland K O (2022). A blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories. Nature Communications, 13:5402.
    • McFadden, Ryan M L; Szunyogh, Dániel; Bravo‐Frank, Nicholas; Johannsen, Silke; Sigel, Roland K O; et al (2022). Magnesium(II)-ATP Complexes in 1-Ethyl-3-Methylimidazolium Acetate Solutions Characterized by 31Mg β-Radiation-Detected NMR Spectroscopy. Angewandte Chemie Internationale Edition, 61(35):e202207137.
    • Sigel, Astrid; Sigel, Helmut; Sigel, Roland K O (2022). Coordination Chemistry of Nucleotides and Antivirally Active Acyclic Nucleoside Phosphonates, including Mechanistic Considerations. Molecules, 27(9):2625.

  • Book Section

    • Ahunbay, Esra; Steffen, Fabio D; Zelger-Paulus, Susann; Sigel, Roland K O (2022). Chemical Dual End-Labeling of Large Ribozymes. In: Steger, Gerhard; Rosenbach, Hannah; Span, Ingrid. DNAzymes : Methods and Protocols. New York: Springer, 191-204.
    • Hadzic, Mélodie C A S; Sigel, Roland K O; Börner, Richard (2022). Single-Molecule Kinetic Studies of Nucleic Acids by Förster Resonance Energy Transfer. In: Steger, Gerhard; Rosenbach, Hannah; Span, Ingrid. DNAzymes : Methods and Protocols. New York: Springer, 173-190.
    • Fazliji, Besim; Ferreira Rodrigues, Carla; Wang, Haibo; Sigel, Roland K O (2022). Metal ion interactions with nucleic acids. In: Black, David. Reference Module in Chemistry, Molecular Sciences and Chemical Engineering / 2022. Waltham, MA: Elsevier, online.

• 2021

  • Journal Article

    • Steffen, Fabio D; Sigel, Roland K O; Börner, Richard (2021). FRETraj: integrating single-molecule spectroscopy with molecular dynamics. Bioinformatics, 37(21):3953-3955.
    • Gerhardy, Stefan; Oborská-Oplová, Michaela; Gillet, Ludovic; Börner, Richard; van Nues, Rob; Leitner, Alexander; Michel, Erich; Petkowski, Janusz J; Granneman, Sander; Sigel, Roland K O; Aebersold, Ruedi; Panse, Vikram Govind (2021). Puf6 primes 60S pre-ribosome nuclear export at low temperature. Nature Communications, 12:4696.
    • Anders, Ulrike; Gulotti-Georgieva, Maya; Zelger-Paulus, Susann; Hibti, Fatima-Ezzahra; Frydman, Chiraz; Suckau, Detlev; Sigel, Roland K O; Zenobi, Renato (2021). Screening for potential interaction partners with surface plasmon resonance imaging coupled to MALDI mass spectrometry. Analytical Biochemistry, 624:114195.

• 2020

  • Journal Article

    • Steffen, Fabio D; Khier, Mokrane; Kowerko, Danny; Cunha, Richard A; Börner, Richard; Sigel, Roland K O (2020). Metal ions and sugar puckering balance single-molecule kinetic heterogeneity in RNA and DNA tertiary contacts. Nature Communications, 11(1):104.

  • Book Section

    • Zhao, Meng; Börner, Richard; Sigel, Roland K O; Freisinger, Eva (2020). Site-Specific Dual-Color Labeling of Long RNAs. In: Heise, Tilman. RNA Chaperones. New York: Springer, 253-270.
    • Zelger-Paulus, Susann; Hadzic, Mélodie C A S; Sigel, Roland K O; Börner, Richard (2020). Encapsulation of Fluorescently Labeled RNAs into Surface-Tethered Vesicles for Single-Molecule FRET Studies in TIRF Microscopy. In: Arluison, Véronique; Wien, Frank. RNA Spectroscopy. New York: Springer, 1-16.

• 2019

  • Journal Article

    • Schmidt, Olivia P; Jurt, Simon; Johannsen, Silke; Karimi, Ashkan; Sigel, Roland K O; Luedtke, Nathan W (2019). Concerted dynamics of metallo-base pairs in an A/B-form helical transition. Nature Communications, 10:4818.
    • Istrate, Andrei; Johannsen, Silke; Istrate, Alena; Sigel, Roland K O; Leumann, Christian J (2019). NMR solution structure of tricyclo-DNA containing duplexes: insight into enhanced thermal stability and nuclease resistance. Nucleic Acids Research, 47(9):4872-4882.
    • Steffen, Fabio D; Börner, Richard; Freisinger, Eva; Sigel, Roland K O (2019). Stick, Flick, Click: DNA-guided Fluorescent Labeling of Long RNA for Single-molecule FRET. CHIMIA International Journal for Chemistry, 73(4):257-261.
    • Freisinger, Eva; Sigel, Roland K O (2019). The Bioinorganic Periodic Table. CHIMIA International Journal for Chemistry, 73(3):185-193.

• 2018

  • Journal Article

    • Paudel, Bishnu P; Fiorini, Erica; Börner, Richard; Sigel, Roland K O; Rueda, David S (2018). Optimal molecular crowding accelerates group II intron folding and maximizes catalysis. Proceedings of the National Academy of Sciences of the United States of America, 115(47):11917-11922.
    • Sigel, Astrid; Operschall, Bert P; Sigel, Roland K O; Sigel, Helmut (2018). Metal ion complexes of nucleoside phosphorothioates reflecting the ambivalent properties of lead(ii). New Journal of Chemistry, 42(10):7551-7559.
    • Hadzic, Mélodie C A S; Börner, Richard; König, Sebastian L B; Kowerko, Danny; Sigel, Roland K O (2018). Reliable State Identification and State Transition Detection in Fluorescence Intensity-Based Single-Molecule Förster Resonance Energy-Transfer Data. Journal of Physical Chemistry B, 122(23):6134-6147.
    • Börner, Richard; Kowerko, Danny; Hadzic, Mélodie C A S; König, Sebastian L B; Ritter, Marc; Sigel, Roland K O (2018). Simulations of camera-based single-molecule fluorescence experiments. PLoS ONE, 13(4):e0195277.
    • Freisinger, Eva; Sigel, Roland K O (2018). Celebrating Helmut Sigel. Journal of Biological Inorganic Chemistry, 23(1):1-5.
    • Gallo, Sofia; Sigel, Roland K O (2018). Covalent and non-covalent binding of platinated vitamin B 12 -derivatives to a B 12 responsive riboswitch. Inorganica Chimica Acta, 472:214-220.
    • Erat, Michèle C; Besic, Emina; Oberhuber, Michael; Johannsen, Silke; Sigel, Roland K O (2018). Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding. Journal of Biological Inorganic Chemistry, 23(1):167-177.
    • Zhao, Meng; Steffen, Fabio D; Börner, Richard; Schaffer, Michelle F; Sigel, Roland K O; Freisinger, Eva (2018). Site-specific dual-color labeling of long RNAs for single-molecule spectroscopy. Nucleic Acids Research, 46(3):e13-e13.

• 2017

  • Journal Article

    • Pechlaner, Maria; Dominguez-Martin, Alicia; Sigel, Roland K O (2017). Influence of pH and Mg(ii) on the catalytic core domain 5 of a bacterial group II intron. Dalton Transactions, 46(12):3989-3995.
    • Choudhary, Pallavi K; Gallo, Sofia; Sigel, Roland K O (2017). Tb3+-Cleavage Assays Reveal Specific Mg2+ Binding Sites Necessary to Pre-fold the btuB Riboswitch for AdoCbl Binding. Frontiers in Chemistry, 5:598.
    • Cao, Qian; Li, Yi; Freisinger, Eva; Qin, Peter Z; Sigel, Roland K O; Mao, Zong-Wan (2017). G-quadruplex DNA targeted metal complexes acting as potential anticancer drugs. Inorganic Chemistry Frontiers, 4(1):10-32.

  • Book Section

    • Palou-Mir, Joana; Barceló-Oliver, Miquel; Sigel, Roland K O (2017). The Role of Lead(II) in Nucleic Acids. In: Sigel, Astrid; Sigel, Helmut; Sigel, Roland K O. Lead: Its Effects on Environment and Health. Berlin: De Gruyter, 403-434.

  • Edited Scientific Work

    • Edited by: Sigel, Astrid; Sigel, Helmut; Sigel, Roland K O (2017). Berlin: De Gruyter. Metal Ions in Life Sciences.

• 2016

  • Journal Article

    • Schaffer, Michelle F; Peng, Guanya; Spingler, Bernhard; Schnabl, Joachim; Wang, Meitian; Olieric, Vincent; Sigel, Roland K O (2016). The X-ray Structures of Six Octameric RNA Duplexes in the Presence of Different Di- and Trivalent Cations. International Journal of Molecular Sciences, 17(7):988.
    • Skilandat, Miriam; Rowinska-Zyrek, Magdalena; Sigel, Roland K O (2016). Secondary structure confirmation and localization of Mg2+ions in the mammalian CPEB3 ribozyme. RNA, 22(5):750-763.
    • Steffen, Fabio D; Sigel, Roland K O; Börner, Richard (2016). An atomistic view on carbocyanine photophysics in the realm of RNA. Physical Chemistry Chemical Physics (PCCP), 18(42):29045-29055.
    • Guiset Miserachs, Helena; Donghi, Daniela; Börner, Richard; Johannsen, Silke; Sigel, Roland K O (2016). Distinct differences in metal ion specificity of RNA and DNA G-quadruplexes. Journal of Biological Inorganic Chemistry, 21(8):975-986.
    • Börner, Richard; Kowerko, Danny; Guiset Miserachs, Helena; Schaffer, Michelle F; Sigel, Roland K O (2016). Metal ion induced heterogeneity in RNA folding studied by smFRET. Coordination Chemistry Reviews, 327-328:123-142.
    • Egloff, David; Oleinich, Igor A; Zhao, Meng; König, Sebastian L B; Sigel, Roland K O; Freisinger, Eva (2016). Sequence-specific post-synthetic oligonucleotide labeling for single-molecule fluorescence applications. ACS Chemical Biology, 11(9):2558-2567.
    • Bartova, Simona; Alberti, Elena; Sigel, Roland K O; Donghi, Daniela (2016). Metal ion binding to an RNA internal loop. Inorganica Chimica Acta, 452:104-110.
    • Bartova, Simona; Pechlaner, Maria; Donghi, Daniela; Sigel, Roland K O (2016). Studying metal ion binding properties of a three-way junction RNA by heteronuclear NMR. Journal of Biological Inorganic Chemistry, 21(3):319-328.
    • Palou-Mir, Joana; Musiari, Anastasia; Sigel, Roland K O; Barceló-Oliver, Miquel (2016). Characterization of the full-length btuB riboswitch from Klebsiella pneumoniae. Journal of Inorganic Biochemistry, 160:106-113.

  • Edited Scientific Work

    • Edited by: Sigel, Astrid; Sigel, Helmut; Sigel, Roland K O (2016). Dordrecht NL: Springer. Metal Ions in Life Sciences.

• 2015

  • Journal Article

    • Pechlaner, Maria; Donghi, Daniela; Zelenay, Veronika; Sigel, Roland K O (2015). Protonation-Dependent Base Flipping at Neutral pH in the Catalytic Triad of a Self-Splicing Bacterial Group II Intron. Angewandte Chemie Internationale Edition, 54(33):9687-9690.
    • Böttcher, Albrecht; Kowerko, Danny; Sigel, Roland K O (2015). Explicit analytic equations for multimolecular thermal melting curves. Biophysical Chemistry, 202:32-39.

Pagination