Protocol detail

Monitoring DNA Modifications by PE Analysis

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The DNA modifications introduced by DMS, KMnO₄, or P1 nuclease (Sigma, Merck KGaA, Darmstadt, Germany) were monitored by PE analysis. The reaction conditions, mixture separation, and product visualization were described previously [42 (link)]. The gels were scanned using a Typhoon FLA 9500 (GE Healthcare, Chicago, IL, USA) and analyzed using ImageQuant (GE Healthcare, Chicago, IL, USA) and imagej (imagej.nih.gov/ij/">https://imagej.nih.gov/ij/ accessed on 13 June 2021).

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Jaworski P., Zyla-Uklejewicz D., Nowaczyk-Cieszewska M., Donczew R., Mielke T., Weigel C, & Zawilak-Pawlik A. (2021). Putative Cooperative ATP–DnaA Binding to Double-Stranded DnaA Box and Single-Stranded DnaA-Trio Motif upon Helicobacter pylori Replication Initiation Complex Assembly. International Journal of Molecular Sciences, 22(12), 6643.

Publication 2021

KMnO4 P1 nuclease Typhoon FLA 9500 ImageQuant imagej

Gels Reaction conditions Typhoon

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Variable analysis

independent variables

DNA modifications introduced by DMS, KMnO4, or P1 nuclease (Sigma, Merck KGaA, Darmstadt, Germany)

dependent variables

DNA modifications monitored by PE analysis

control variables

Reaction conditions
Mixture separation
Product visualization

controls

Positive controls not explicitly mentioned
Negative controls not explicitly mentioned

Annotations

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