Using PhADE in single molecule fluorescence imaging

Anna Loveland, a postdoc in the Grigorieff Lab, has a new paper, A general approach to break the concentration barrier in single-molecule imaging” that appeared today in Nature Methods online. The paper is based on her PhD work, which was done jointly in the labs of Antoine van Oijen and Johannes Walter at Harvard.

Single-molecule fluorescence imaging is often incompatible with physiological protein concentrations, as fluorescence background overwhelms an individual molecule’s signal. Loveland et al. employ a new imaging approach called PhADE (photoactivation, diffusion and excitation). A protein of interest is fused to a photoactivatable protein (mKikGR) and introduced to its surface-immobilized substrate. After photoactivation of mKikGR near the surface, rapid diffusion of the unbound mKikGR fusion out of the detection volume eliminates background fluorescence, whereupon the bound molecules are imaged. The authors labeled the eukaryotic DNA replication protein flap endonuclease 1 with mKikGR and added it to replication-competent Xenopus laevis egg extracts. PhADE imaging of high concentrations of the fusion construct revealed its dynamics and micrometer-scale movements on individual, replicating DNA molecules. Because PhADE imaging is in principle compatible with any photoactivatable fluorophore, it should have broad applicability in revealing single-molecule dynamics and stoichiometry of macromolecular protein complexes at previously inaccessible fluorophore concentrations.

Anna B Loveland, Satoshi Habuchi, Johannes C Walte & Antoine M van Oijen (2012) A general approach to break the concentration barrier in single-molecule imaging. Nature Methods

How yeast switch mating type and why we care

For grad students needing background on work in the Haber lab studying DNA recombination and repair, there are a couple new papers out to help you. A new review by Prof. Haber entitled Mating-type genes and MAT switching in Saccharomyces cerevisiae in Genetics provides a detailed introduction to literature. There’s a lot there… as Jim says in the Acknowledgements

The part of this work that derives from my own lab has been carried out for more than 30 years by an exceptional contingent of graduate students, postdoctoral fellows, technicians, and Brandeis University undergraduates […]

If methods papers are what you need instead, check out Sugawara & Haber (2012), Monitoring DNA Recombination Initiated by HO Endonuclease in Methods in Molecular Biology.

Math graduate student training grant renewed

Mathematics Ph.D. students and faculty at Brandeis should be happy to learn that the department’s training grant from the US Dept. of Education’s Graduate Assistance in Areas of National Need (GAANN) program is being renewed for another three years. Training grants are a vital piece of the puzzle for supporting graduate education in the sciences, allowing Ph.D. students to focus on research.


Riboswitches and fluoride

Ronald Breaker (Yale and HHMI) gave an inspiring talk today to kick off this year’s Biochemistry-Biophysics Friday Lunchtime Pizza Talks series, discussing his lab’s work on Riboswitches: Biology’s Ancient Regulators. If you missed the talk, here’s a review that might help you catch up.

Breaker ended the talk by discussing the fluoride-sensing riboswitch, and pointing to the new avenues for research to which this called attention. Coincidentally(?), a new paper in PNAS is out today from Chris Miller‘s lab here at Brandeis on exactly that — take a look at Stockbridge et al., Fluoride resistance and transport by riboswitch-controlled CLC antiporters.


Tenure track faculty position, Biochemistry

The Department of Biochemistry at Brandeis University invites applications for a tenure-track faculty position, to begin Fall, 2013. We are searching for a creative scientist who will establish an independent research program and who in addition will maintain a strong interest in teaching Biochemistry at the undergraduate and graduate levels. The research program should address fundamental questions of biological, biochemical, or biophysical mechanism.

Brandeis University offers the rare combination of a vigorous research institution in a liberal-arts college setting. The suburban campus is located 20 minutes from Boston and Cambridge and is part of the vibrant community of academic and biotechnology centers in the Boston area.

The application should include a cover letter, curriculum vitae, statement of research accomplishments and future plans, and three letters of reference. Applications will be accepted only through Additional inquiries may be directed to Chris Miller, Professor of Biochemistry (

First consideration will be given to applications received by December 1, 2012. Brandeis University is an Equal Opportunity Employer, committed to building a culturally diverse intellectual community. We particularly welcome applications from women and minority candidates.

Writing on the ceiling

BrandeisNOW answers the question Who’s been writing on the Physics ceiling?

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