Asymmetric base-pair opening drives helicase unwinding dynamics

Francesco Colizzi; Cibran Perez-Gonzalez; Remi Fritzen; Yaakov Levy; Malcolm F. White; J. Carlos Penedo; Giovanni Bussi

doi:10.1073/pnas.1901086116

Asymmetric base-pair opening drives helicase unwinding dynamics

Francesco Colizzi^*, Cibran Perez-Gonzalez, Remi Fritzen, Yaakov Levy, Malcolm F. White, J. Carlos Penedo^*, Giovanni Bussi^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

The opening of a Watson–Crick double helix is required for crucial cellular processes, including replication, repair, and transcription. It has long been assumed that RNA or DNA base pairs are broken by the concerted symmetric movement of complementary nucleobases. By analyzing thousands of base-pair opening and closing events from molecular simulations, here, we uncover a systematic stepwise process driven by the asymmetric flipping-out probability of paired nucleobases. We demonstrate experimentally that such asymmetry strongly biases the unwinding efficiency of DNA helicases toward substrates that bear highly dynamic nucleobases, such as pyrimidines, on the displaced strand. Duplex substrates with identical thermodynamic stability are thus shown to be more easily unwound from one side than the other, in a quantifiable and predictable manner. Our results indicate a possible layer of gene regulation coded in the direction-dependent unwindability of the double helix.

Original language	English
Pages (from-to)	22471-22477
Number of pages	7
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	116
Issue number	45
Early online date	18 Oct 2019
DOIs	https://doi.org/10.1073/pnas.1901086116
Publication status	Published - 5 Nov 2019

Keywords

Double helix
Nucleic acids
Simulations
Experiments
Unwindability

Access to Document

10.1073/pnas.1901086116Licence: CC BY

Colizzi-2019-Asymmetric-base-pair-PNAS-CC
Copyright © 2019 the Author(s). Published by PNAS. This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY).
Final published version, 1.25 MBLicence: CC BY

Cite this

@article{d7604670ce7a40539b6cfcfee7c369cc,

title = "Asymmetric base-pair opening drives helicase unwinding dynamics",

abstract = "The opening of a Watson–Crick double helix is required for crucial cellular processes, including replication, repair, and transcription. It has long been assumed that RNA or DNA base pairs are broken by the concerted symmetric movement of complementary nucleobases. By analyzing thousands of base-pair opening and closing events from molecular simulations, here, we uncover a systematic stepwise process driven by the asymmetric flipping-out probability of paired nucleobases. We demonstrate experimentally that such asymmetry strongly biases the unwinding efficiency of DNA helicases toward substrates that bear highly dynamic nucleobases, such as pyrimidines, on the displaced strand. Duplex substrates with identical thermodynamic stability are thus shown to be more easily unwound from one side than the other, in a quantifiable and predictable manner. Our results indicate a possible layer of gene regulation coded in the direction-dependent unwindability of the double helix.",

keywords = "Double helix, Nucleic acids, Simulations, Experiments, Unwindability",

author = "Francesco Colizzi and Cibran Perez-Gonzalez and Remi Fritzen and Yaakov Levy and White, {Malcolm F.} and Penedo, {J. Carlos} and Giovanni Bussi",

note = "F.C. thanks Laur{\`e}ne Bastet, Gaston Giroux, and the Biblioth{\`e}que Roger-Maltais at UdeS for providing infrastructures and support. F.C. acknowledges sabbatical funding (2013 to 2015) from Romano Colizzi and Maria Gaudio in Taranto, Italy, and has received support by the European Union{\textquoteright}s Horizon 2020 Research and Innovation Programme under Marie Sk{\l}odowska-Curie Grant 752415. C.P.-G. thanks the Engineering and Physical Sciences Research Council (EPSRC) and the University of St. Andrews for financial support. Work in M.F.W. and J.C.P.{\textquoteright}s laboratories was supported by Grant 091825/Z/10/Z from the Wellcome Trust. G.B.{\textquoteright}s laboratory has received funding from the European Research Council (ERC) under the European Union{\textquoteright}s Seventh Framework Programme (FP/2007-2013)/ERC Grant 306662, S-RNA-S.",

year = "2019",

month = nov,

day = "5",

doi = "10.1073/pnas.1901086116",

language = "English",

volume = "116",

pages = "22471--22477",

journal = "Proceedings of the National Academy of Sciences of the United States of America",

issn = "0027-8424",

publisher = "NATL ACAD SCIENCES",

number = "45",

}

TY - JOUR

T1 - Asymmetric base-pair opening drives helicase unwinding dynamics

AU - Colizzi, Francesco

AU - Perez-Gonzalez, Cibran

AU - Fritzen, Remi

AU - Levy, Yaakov

AU - White, Malcolm F.

AU - Penedo, J. Carlos

AU - Bussi, Giovanni

N1 - F.C. thanks Laurène Bastet, Gaston Giroux, and the Bibliothèque Roger-Maltais at UdeS for providing infrastructures and support. F.C. acknowledges sabbatical funding (2013 to 2015) from Romano Colizzi and Maria Gaudio in Taranto, Italy, and has received support by the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie Grant 752415. C.P.-G. thanks the Engineering and Physical Sciences Research Council (EPSRC) and the University of St. Andrews for financial support. Work in M.F.W. and J.C.P.’s laboratories was supported by Grant 091825/Z/10/Z from the Wellcome Trust. G.B.’s laboratory has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant 306662, S-RNA-S.

PY - 2019/11/5

Y1 - 2019/11/5

N2 - The opening of a Watson–Crick double helix is required for crucial cellular processes, including replication, repair, and transcription. It has long been assumed that RNA or DNA base pairs are broken by the concerted symmetric movement of complementary nucleobases. By analyzing thousands of base-pair opening and closing events from molecular simulations, here, we uncover a systematic stepwise process driven by the asymmetric flipping-out probability of paired nucleobases. We demonstrate experimentally that such asymmetry strongly biases the unwinding efficiency of DNA helicases toward substrates that bear highly dynamic nucleobases, such as pyrimidines, on the displaced strand. Duplex substrates with identical thermodynamic stability are thus shown to be more easily unwound from one side than the other, in a quantifiable and predictable manner. Our results indicate a possible layer of gene regulation coded in the direction-dependent unwindability of the double helix.

AB - The opening of a Watson–Crick double helix is required for crucial cellular processes, including replication, repair, and transcription. It has long been assumed that RNA or DNA base pairs are broken by the concerted symmetric movement of complementary nucleobases. By analyzing thousands of base-pair opening and closing events from molecular simulations, here, we uncover a systematic stepwise process driven by the asymmetric flipping-out probability of paired nucleobases. We demonstrate experimentally that such asymmetry strongly biases the unwinding efficiency of DNA helicases toward substrates that bear highly dynamic nucleobases, such as pyrimidines, on the displaced strand. Duplex substrates with identical thermodynamic stability are thus shown to be more easily unwound from one side than the other, in a quantifiable and predictable manner. Our results indicate a possible layer of gene regulation coded in the direction-dependent unwindability of the double helix.

KW - Double helix

KW - Nucleic acids

KW - Simulations

KW - Experiments

KW - Unwindability

UR - https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1901086116/-/DCSupplemental

U2 - 10.1073/pnas.1901086116

DO - 10.1073/pnas.1901086116

M3 - Article

C2 - 31628254

SN - 0027-8424

VL - 116

SP - 22471

EP - 22477

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

IS - 45

ER -

Asymmetric base-pair opening drives helicase unwinding dynamics

Abstract

Keywords

Access to Document

Other files and links

Fingerprint

Multifunctional molecular machines: multifunctional molecular machines acting on DNA

Multifunctional molecular machines: Multifunctional molecular machines acting on DNA: the XPD and XPB helicases

Carlos Penedo