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Data and code for: Sequence specificity in DNA binding is mainly governed by association

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posted on 2021-12-21, 09:21 authored by Emil MarklundEmil Marklund, Guanzhong Mao, Jinwen Yuan, Spartak Zikrin, Eldar Abdurakhmanov, Sebastian Deindl, Johan Elf
Sequence-specific binding of proteins to DNA is essential for accessing genetic information. Here, we derive a simple equation for target-site recognition, which uncovers a previously unrecognized coupling between the macroscopic association and dissociation rates of the searching protein. Importantly, this relationship makes it possible to recover the relevant microscopic rates from experimentally determined macroscopic ones. This post contains kinetic data for the lac repressor and code to analyse and interpret the data in light of this theory.

File list:
- data_pbm.zip - Data-set for output generated using a protein binding microarray.

- data_tirf.zip - Data-set for output generated using TIRF based single molecule localisation microscopy.

- data_cas9.zip - Data-set for cas9 binding collected from literature.

- data_spr.zip - Data-set for output generated using surface plasmon resonance based methods.

- figure_scripts.zip - Set of scripts used to generate all figures. See README file inside for details.

Funding

The physics of genetic information processing

Swedish Research Council

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Determination of reaction mechanism and specificity in nucleotide sequence recognition

Swedish Research Council

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Single-Molecule And Structural Studies Of ATP-Dependent Chromatin Remodelling

European Research Council

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Biophysics in gene regulation - A genome wide approach

European Research Council

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KAW 2019.0306

KAW 2019.0439

KAW 2016.0077

History

Publisher

Uppsala University

Contact email

johan.elf@icm.uu.se

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