Congratulations, Randi!

Today Randi passed her PhD candidacy exam with flying colors. Randi’s thesis committee grilled her about her thesis project and any other scientific topic. Randi remained poised throughout the exam and handled all the questions to the satisfaction of the committee. This is a big milestone in Randi’s progression to earning her PhD and an excellent accomplishment.

Excellent job, Randi! The whole lab is very proud of you!

Nature Methods publication out this week!

This week our recent studies in collaboration with the Fishel lab were published in Nature Methods “Widespread nuclease contamination in commonly used oxygen-scavenging systems“.

Single molecule fluorescent systems have become increasingly common tools to observe protein-DNA interactions in real time. In order to preserve the fluorophores, oxygen-scavenging systems are added to the reaction flow cells. During our single molecule analysis of retroviral integrase complexes interacting with DNA, we discovered that the oxygen-scavenging systems damage the DNA, largely by nicking.

The nicking of DNA is important especially during single molecule analysis of DNA repair systems. Those studies may be confounded by unexpected and unrecognized nicks in the DNA.

We also report a method to purify one oxygen-scavenging system so that it no longer has DNA nicking activity. A simple size exclusion column is able to purify the protocatechuic acid-protocatechuate-3,4-dioxygenase (PCA-PCD) oxygen scavenger system.

Congratulations, Miguel, on your first publication!

Full citation:

Senavirathne, G., J. Liu, M.A. Lopez Jr., J. Hanne, J. Martin-Loepez, J-B. Lee, K.E. Yoder, and R. Fishel. 2015. Widespread nuclease contamination in commonly used oxygen-scavenging systems. Nature Methods. 12:901.