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Double-stranded RNA bending by AU-tract sequences

View ORCID ProfileAlberto Marin-Gonzalez, View ORCID ProfileClara Aicart-Ramos, Mikel Marin-Baquero, View ORCID ProfileAlejandro Martín-González, View ORCID ProfileMaarit Suomalainen, Abhilash Kannan, View ORCID ProfileJ. G. Vilhena, View ORCID ProfileUrs F. Greber, View ORCID ProfileFernando Moreno-Herrero, View ORCID ProfileRubén Pérez
doi: https://doi.org/10.1101/2020.02.17.952044
Alberto Marin-Gonzalez
1Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
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Clara Aicart-Ramos
1Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
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Mikel Marin-Baquero
1Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
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Alejandro Martín-González
1Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
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Maarit Suomalainen
2Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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Abhilash Kannan
2Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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J. G. Vilhena
3Physics Department, University of Basel, Basel, Switzerland
4Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
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Urs F. Greber
2Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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Fernando Moreno-Herrero
1Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
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  • For correspondence: fernando.moreno@cnb.csic.es ruben.perez@uam.es
Rubén Pérez
4Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
5IFIMAC - Condensed Matter Physics Center, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
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  • For correspondence: fernando.moreno@cnb.csic.es ruben.perez@uam.es
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ABSTRACT

Sequence-dependent structural deformations of the DNA double helix (dsDNA) have been extensively studied, where adenine tracts (A-tracts) provide a striking example for global bending in the molecule. In contrast to dsDNA, much less is known about how the nucleotide sequence affects bending deformations of double-stranded RNA (dsRNA). Using all-atom microsecond long molecular dynamics simulations we found a sequence motif consisting of alternating adenines and uracils, or AU-tracts, that bend the dsRNA helix by locally compressing the major groove. We experimentally tested this prediction using atomic force microscopy (AFM) imaging of long dsRNA molecules containing phased AU-tracts. AFM images revealed a clear intrinsic bend in these AU-tracts molecules, as quantified by a significantly lower persistence length compared to dsRNA molecules of arbitrary sequence. The bent structure of AU-tracts here described might play a role in sequence-specific recognition of dsRNAs by dsRNA-interacting proteins or impact the folding of RNA into intricate tertiary and quaternary structures.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted February 17, 2020.
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Double-stranded RNA bending by AU-tract sequences
Alberto Marin-Gonzalez, Clara Aicart-Ramos, Mikel Marin-Baquero, Alejandro Martín-González, Maarit Suomalainen, Abhilash Kannan, J. G. Vilhena, Urs F. Greber, Fernando Moreno-Herrero, Rubén Pérez
bioRxiv 2020.02.17.952044; doi: https://doi.org/10.1101/2020.02.17.952044
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Double-stranded RNA bending by AU-tract sequences
Alberto Marin-Gonzalez, Clara Aicart-Ramos, Mikel Marin-Baquero, Alejandro Martín-González, Maarit Suomalainen, Abhilash Kannan, J. G. Vilhena, Urs F. Greber, Fernando Moreno-Herrero, Rubén Pérez
bioRxiv 2020.02.17.952044; doi: https://doi.org/10.1101/2020.02.17.952044

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