Quantitative understanding of target recognition on DNA based on directional zipping processes

Publications

Peer reviewed articles (14)

Probing the stability of the SpCas9–DNA complex after cleavage

Author(s): Pierre Aldag, Fabian Welzel, Leonhard Jakob, Andreas Schmidbauer, Marius Rutkauskas, Fergus Fettes, Dina Grohmann, Ralf Seidel
Published in: Nucleic Acids Research, 49, 2021, Page(s) 12411–12421, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab1072

Miniature type V-F CRISPR-Cas nucleases enable targeted DNA modification in cells.

Author(s): G Bigelyte, J K Young, T Karvelis, K Budre, R Zedaveinyte, V Djukanovic, Elizabeth V Ginkel, S Paulraj, S Gasior, S Jones, L Feigenbutz, G St. Clair, P Barone, J Bohn, A Acharya, G Zastrow-Hayes, S Henkel-Heinecke, A Silanskas, R Seidel, V Siksnys.
Published in: Nature Communications, 12, 2021, Page(s) 6191, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-26469-4

The CDK1-TOPBP1-PLK1 axis regulates the Bloom's syndrome helicase BLM to suppress crossover recombination in somatic cells

Author(s): Balbo Pogliano C, Ceppi I, Giovannini S, Petroulaki V, Palmer N, Uliana F, Gatti M,Kasaciunaite K, Freire R, Seidel R, Altmeyer M, Cejka P, Matos J
Published in: Science Advances, 8, 2022, Page(s) eabk0221, ISSN 2375-2548
Publisher: American Association for the Advancement of Science
DOI: 10.1126/sciadv.abk0221

Primed CRISPR adaptation in Escherichia coli cells does not depend on conformational changes in the Cascade effector complex detected in Vitro

Author(s): Andrey Krivoy, Marius Rutkauskas, Konstantin Kuznedelov, Olga Musharova, Christophe Rouillon, Konstantin Severinov, Ralf Seidel
Published in: Nucleic Acids Research, 46/8, 2018, Page(s) 4087-4098, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gky219

Competing interaction partners modulate the activity of Sgs1 helicase during DNA end resection

Author(s): Kristina Kasaciunaite, Fergus Fettes, Maryna Levikova, Peter Daldrop, Roopesh Anand, Petr Cejka, Ralf Seidel
Published in: The EMBO Journal, 38/13, 2019, ISSN 0261-4189
Publisher: Nature Publishing Group
DOI: 10.15252/embj.2019101516

Decision-Making in Cascade Complexes Harboring crRNAs of Altered Length

Author(s): Inga Songailiene, Marius Rutkauskas, Tomas Sinkunas, Elena Manakova, Sabine Wittig, Carla Schmidt, Virginijus Siksnys, Ralf Seidel
Published in: Cell Reports, 28/12, 2019, Page(s) 3157-3166.e4, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2019.08.033

CtIP promotes the motor activity of DNA2 to accelerate long-range DNA end resection

Author(s): Ilaria Ceppi, Sean M. Howard, Kristina Kasaciunaite, Cosimo Pinto, Roopesh Anand, Ralf Seidel, Petr Cejka
Published in: Proceedings of the National Academy of Sciences, 117/16, 2020, Page(s) 8859-8869, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2001165117

Modeling DNA-Strand Displacement Reactions in the Presence of Base-Pair Mismatches

Author(s): Patrick Irmisch, Thomas E. Ouldridge, Ralf Seidel
Published in: Journal of the American Chemical Society, 2020, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.0c03105

Phosphorylation of the RecQ Helicase Sgs1/BLM Controls Its DNA Unwinding Activity during Meiosis and Mitosis

Author(s): Rokas Grigaitis, Lepakshi Ranjha, Philipp Wild, Kristina Kasaciunaite, Ilaria Ceppi, Vera Kissling, Adrian Henggeler, Aitor Susperregui, Matthias Peter, Ralf Seidel, Petr Cejka, Joao Matos
Published in: Developmental Cell, 53/6, 2020, Page(s) 706-723.e5, ISSN 1534-5807
Publisher: Cell Press
DOI: 10.1016/j.devcel.2020.05.016

A quantitative model for the dynamics of target recognition and off-target rejection by the CRISPR-Cas Cascade complex

Author(s): Marius Rutkauskas, Inga Songailiene,Patrick Irmisch,Felix E. Kemmerich, Tomas Sinkunas,Virginijus Siksnys, Ralf Seidel
Published in: Nature Communications, 13, 2022, Page(s) 7460, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-35116-5

Orthogonal Enzyme-Driven Timers for DNA Strand Displacement Reactions

Author(s): Juliette Bucci,Patrick Irmisch, Erica Del Grosso, Ralf Seidel, and Francesco Ricci
Published in: Journal of the American Chemical Society, 144, 2022, Page(s) 19791–19798, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.2c06599

Distinct RPA domains promote recruitment and the helicase-nuclease activities of Dna2

Author(s): Ananya Acharya, Kristina Kasaciunaite, Martin Göse, Vera Kissling, Raphaël Guérois, Ralf Seidel, Petr Cejka
Published in: Nature Communications, 12, 2021, Page(s) 6521, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-26863-y

Dissipative Control over the Toehold-Mediated DNA Strand Displacement Reaction

Author(s): Erica Del Grosso,Patrick Irmisch, Serena Gentile, Prof. Leonard J. Prins, Ralf Seidel, Francesco Ricci
Published in: Angewandte Chemie International Edition, 61, 2022, Page(s) e202201929, ISSN 1521-3757
Publisher: Wiley-VCH
DOI: 10.1002/anie.202201929

Mre11-Rad50 oligomerization promotes DNA double-strand break repair

Author(s): Vera M Kissling,Giordano Reginato, Eliana Bianco,Kristina Kasaciunaite, Janny Tilma, Gea Cereghetti, Natalie Schindler, Sung Sik Lee, Raphaël Guérois, Brian Luke, Ralf Seidel, Petr Cejka, Matthias Peter
Published in: Nature Communications, 13, 2022, Page(s) 2374, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-29841-0