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Effect of DNA conformation on facilitated diffusion

Research output: Contribution to journalArticle

Original languageEnglish
Pages (from-to)582-588
Number of pages7
JournalBiochemical Society Transactions
Volume41
DOIs
StatePublished - Apr 2013

Abstract

Within a living cell, site-specific DNA-binding proteins need to search the whole genome to find a target of similar to 10-20 bp. That they find the target, and do so quickly, is vital for the correct functioning of the DNA, and of the cell as a whole. The current understanding is that this search is performed via facilitated diffusion, i.e. by combining three-dimensional bulk diffusion within the cytoplasm or nucleoplasm, with one-dimensional diffusion along the DNA backbone, to which the protein binds non-specifically. After reviewing the standard theory of facilitated diffusion, we discuss in the present article the still rather rare direct computer simulations of this process, focusing on the three-dimensional part of the search, and the effect of DNA looping and the general DNA conformation on its efficiency. We close by highlighting some open questions in this field.

    Research areas

  • Brownian dynamics simulations, DNA looping, facilitated diffusion, polymer physics, search on DNA, REPRESSOR-OPERATOR INTERACTION, BINDING PROTEINS, TARGET LOCATION, TRANSCRIPTION, ORGANIZATION, KINETICS, TRANSLOCATION, DYNAMICS, SEARCH, GENOME

ID: 17186090