Scanning a DNA molecule for bound proteins using hybrid magnetic and optical tweezers

Scanning a DNA molecule for bound proteins using hybrid magnetic and optical tweezers

Van Loenhout, M.T.
De Vlaminck, I.
Flebus, B.
Den Blanken, J.F.
Zweifel, L.P.
Hooning, K.M.
Kerssemakers, J.W.
Dekker, C.

Applied Sciences

BN/Bionanoscience

2013-06-03

The functional state of the genome is determined by its interactions with proteins that bind, modify, and move along the DNA. To determine the positions and binding strength of proteins localized on DNA we have developed a combined magnetic and optical tweezers apparatus that allows for both sensitive and label-free detection. A DNA loop, that acts as a scanning probe, is created by looping an optically trapped DNA tether around a DNA molecule that is held with magnetic tweezers. Upon scanning the loop along the ?-DNA molecule, EcoRI proteins were detected with ?17 nm spatial resolution. An offset of 33±5 nm for the detected protein positions was found between back and forwards scans, corresponding to the size of the DNA loop and in agreement with theoretical estimates. At higher applied stretching forces, the scanning loop was able to remove bound proteins from the DNA, showing that the method is in principle also capable of measuring the binding strength of proteins to DNA with a force resolution of 0.1 pN/[Formula: see text]. The use of magnetic tweezers in this assay allows the facile preparation of many single-molecule tethers, which can be scanned one after the other, while it also allows for direct control of the supercoiling state of the DNA molecule, making it uniquely suitable to address the effects of torque on protein-DNA interactions.

http://resolver.tudelft.nl/uuid:c8f21905-e951-4c54-8421-32dade46edb9

https://doi.org/10.1371/journal.pone.0065329

Public Library of Science

1932-6203

PLoS One, 8 (6), 2013

Institutional Repository

journal article

© 2013 The Author(s)
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