Get out your crap hat!* Former Blockhead Elio Abbondanzieri (and a veritable horde of Zhuang lab grad students) has published a paper in Nature on HIV reverse transcriptase. Reverse transcriptase (RT) has two opposite activities: polynucleotide synthesis, and degradation. The active sites are at opposite ends of the molecule, so how it knows when to do what is a big open question. By labeling the RT and its substrates, they were able to detect the binding orientation of the RT, and thereby show that it binds in different orientations to elongation substrates and degradation substrates. Further, the use of a single molecule assay allowed them to assay rate constants, and show that occasionally RT will "flip" from one orientation to the other, and that these flipping rates can be affected by small molecules, such as Nevirapine, a drug which targets the HIV RT.
The paper made me wonder about optical trapping of RT to look at its processivity, but this has apparently been tried (by Elio, in fact), and its processivity is too low to make it worthwhile. I still wonder whether some kind of "fishing" assay could be developed, where multiple brief binding events could be recorded by dangling a bead with RT near a surface with substrate, or something like that.
*
UPDATE: I was apparently incorrect about the origin of the Crap Hat. As pointed out in the comments, the Crap Hat originated with Josh Shaevitz, not Elio Abbondanzieri. Going through the Block Lab archives, in fact, turned up several photos of people wearing Crap Hats at Josh's thesis defense. My sincerest apologies for the error!
