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

Soojeong Kim; Isabel K Darcy

doi:10.1242/bio.048603

Back

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

Journal article

Open access

Peer reviewed

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

Soojeong Kim and Isabel K Darcy

Biology Open, Vol.9(4), bio048603

04/03/2020

DOI: 10.1242/bio.048603

Files and links (1)

url

https://doi.org/10.1242/bio.048603View

Published (Version of record) Open Access

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.

Difference topology experiment

DNA topology

Tangle analysis

Condensin

Details

Title: Subtitle: A topological analysis of difference topology experiments of condensin with topoisomerase II
Creators: Soojeong Kim
Isabel K Darcy - University of Iowa
Resource Type: Journal article
Publication Details: Biology Open, Vol.9(4), bio048603
DOI: 10.1242/bio.048603
NLM abbreviation: Biol Open
ISSN: 2046-6390
Grant note: DOI: 10.13039/501100003725, name: National Research Foundation of Korea, award: NRF2017R1D1A1B03028460
Language: English
Date published: 04/03/2020
Academic Unit: Mathematics
Record Identifier: 9984242446202771

Metrics

30 Record Views