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A topological analysis of difference topology experiments of condensin with topoisomerase II.


ABSTRACT: An experimental technique called difference topology combined with the mathematics of tangle analysis has been used to unveil the structure of DNA bound by the Mu transpososome. However, difference topology experiments can be difficult and time consuming. We discuss a modification that greatly simplifies this experimental technique. This simple experiment involves using a topoisomerase to trap DNA crossings bound by a protein complex and then running a gel to determine the crossing number of the knotted product(s). We develop the mathematics needed to analyze the results and apply these results to model the topology of DNA bound by 13S condensin and by the condensin MukB.

SUBMITTER: Kim S 

PROVIDER: S-EPMC7132813 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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A topological analysis of difference topology experiments of condensin with topoisomerase II.

Kim Soojeong S   Darcy Isabel K IK  

Biology open 20200403 4


An experimental technique called difference topology combined with the mathematics of tangle analysis has been used to unveil the structure of DNA bound by the Mu transpososome. However, difference topology experiments can be difficult and time consuming. We discuss a modification that greatly simplifies this experimental technique. This simple experiment involves using a topoisomerase to trap DNA crossings bound by a protein complex and then running a gel to determine the crossing number of the  ...[more]

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