April 21 2016 at 02:08AM

Today I Learned: 1) There are some super-useful, really intuitive rules for representing chemical reactions with differential equations, that let you take, say, the reaction system A + B -> C and write down some differential equations that describe the change of number of each species over time (in this case, dA/dt = -AB, dB/dt = -AB, and dC/dt = AB, up to a (rate) constant). Today I learned that you can derive these rules as the mean time values of the chemical master equation for the system, which is a more detailed, more-correct, stochastic description of the chemistry. 2) There's a new version of Cas9 on the market (metaphorically speaking). This one is a fusion of cas to cytidine deaminase, which converts C nucleotides into T nucleotides and G nucleotides into A nucleotides. As with most Cas fusions, the Cas bit of the enzyme targets the enzyme to specific sequences. The cytidine deaminase converts nucleotides, making this fusion a one-protein single-base pair editor! It's still rather restricted in some ways -- it can only convert C->T and G->A, for instance, and it doesn't actually have single-nucleotide precision (it affects everything in a 5bp window). Still, it's an awesome enzyme, as perhaps we might expect from a joint team of authors out of Harvard and MIT. Paper here (sadly, it's Nature, so you'll probably need a university connection to read it): http://ift.tt/1ScybRd Thanks to reddit and to Asher Rubin for alerting me to this article! 3) How the ColE1 plasmid origin* works. I've heard bits and pieces of how it functions before now, but I think I really more or less get it now...? So here's the basic idea -- ColE1 has a binding site for DNA polymerase, but it can't be replicated without an RNA primer. The origin provides this primer in the form of RNAII (kind of a dumb name, for multiple reasons), which is a 500-ish base pair RNA that folds up as it's transcribed, forming a secondary structure that places the end of itself right at the origin, where it acts as a primer. RNAII gets transcribed --> plasmid replicates. Importantly, the processing of RNAII is co-transcriptional -- there's never RNAII floating around in the cell, it just immediately gets turned into a primer. ...unless RNAI shows up, that is. RNAI is a cool little RNA species that sits entirely inside RNAII, and I do mean "entirely" -- its promoter, sequence, and terminator are all part of the RNAII sequence, but in reverse. Anyway, RNAI inhibits RNAII by binding to it, changing its secondary structure, and messing it up as a primer. I'm not *exactly* sure how this mechanism controls copy number... but I think it has to do with polymerases (or some other protein critical for plasmid replication to start) being really limiting. When there's only one plasmid, the polymerase/other molecule finds it and binds to it relatively quickly, but if there are a bunch of plasmids, the per-plasmid rate of replication slows way down as polymerase becomes limiting, but the rate of RNAI production (and inactivation of the plasmid's replication) remains the same. I don't find this totally satisfying, though, because on the surface it sounds like there should still be *some* replication, just not any faster than there would be with a lower copy number. *for those unfamiliar in the ways of molecular biology, a plasmid origin is the part of a plasmid that allows it to replicate. Part of an origin's job is to provide a place for the cell's replication machinery to sit down and start replicating the plasmid. The other part of the origin's job is to eventually *stop* replication so that the plasmid reaches some steady state concentration. Anybody have a more satisfying explanation? Thanks to Andrey Shur for teaching me more about ColE1