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Issue 7, 2010
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Digestion of individual DNA molecules by λ-exonuclease at liquid–solid interface

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Abstract

Enzyme digestion of single DNA molecules was directly observed in real time by dual-color total internal reflection fluorescence microscopy (TIRFM). Individual λ-DNA molecules labeled with the fluorescent dye, YOYO-1, were stretched in a laminar flow stream and immobilized on a bare fused-silica prism surface based on hydrophobic and electrostatic interactions. Enzyme digestion was initiated by the influx of λ-exonuclease enzyme via capillary force. When the dye : bp ratio was higher than 1 : 20, the exact digestion rate could not be measured because of induced photocleavage of the DNA molecules. At a dye : bp ratio of 1 : 50, shortening of the DNA strand was recorded in real time. Unlike previous studies, the length-based digestion rate of λ-exonuclease showed 3 distinct values in the range of 0.173(±0.024) to 0.462(±0.152) µm s−1 at 37 °C. That is, different enzyme molecules exhibit different digestion dynamics. Digestion was also monitored based on the decrease in fluorescence intensity, but uncertainties were much larger due to the distance dependent excitation intensity in the TIRF mode.

Graphical abstract: Digestion of individual DNA molecules by λ-exonuclease at liquid–solid interface

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Supplementary files

Article information


Submitted
15 Mar 2010
Accepted
13 Apr 2010
First published
30 Apr 2010

Analyst, 2010,135, 1759-1764
Article type
Paper

Digestion of individual DNA molecules by λ-exonuclease at liquid–solid interface

S. H. Kang, S. Lee and E. S. Yeung, Analyst, 2010, 135, 1759 DOI: 10.1039/C0AN00145G

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