WATSURF 2013 Day 8 and interesting papers

Today was a lull for me in the conference, so I decided to catch up a bit on the latest literature.  Before getting to that, though, we also took a trip in the afternoon to the Mer de Glace, the longest glacier in France.

Here's the group at the bus stop to go to Chamonix:

Here's what it looks like once you get to the told of Montenvers.  There's a hotel at the top (who stays there?), and a gondola that takes you partway down (the rest is by stairs) to a grotto in the glacier that they carve out anew every year:

 
One of the most impressive things on the way down is that they have little plaques indicating the level of the glacier at various times in the past 25 years.  Here's the plaque for 1990.  For a sense of scale, the dots towards the bottom are people skiing on the glacier.  It's more or less at the same height as the snow line on the other side.

Here's what the grotto looks like inside (close to the entrance, where there's enough light):

Now back to business!  I wrote down a few neat factoids from some of the talks today.  From Giusseppe Zaccai (ILL, Grenoble, France), I learned that trehalose, a disaccharide, can form a glass that protects protein structures (so they don't denature) and effectively can replace water (except that it freezes dynamics); this effect is used by some insects and plants to survive dry conditions for up to years.  From Wolfgang Doster (TU München, Germany), I learned that there is nice data for a "phase diagram" of cytochrome C, which denatures under both cold and high pressure conditions (in Doster and Friedrich in Protein Folding Handbook, Part 1 (wiley VCH 2005)).  From Davide Orsi (PhD student in U. of Parma, Italy), I learned that giant lipid vesicles (microns in radius R) have surfaces that fluctuate very appreciably under thermal motions, and that the fluctuations projected onto the equatorial plane for modes 5+ are well-described by that of a planar elastic sheet of side-length 2 pi R.

Now for some interesting papers that came out today:

* Wei et al, "Mapping the Thermal Behavior of DNA Origami Nanostructures", J. Am. Chem. Soc. 135, 6165−6176 (2013): They put FRET fluorophores into two adjacent staple strands of a DNA origami sheet to monitor assembly kinetics.  Find very cooperative assembly/melting transition over just a few degrees C (with only a little hysteresis), but different parts of the structure seem to assemble at slightly different temperatures.  If they remove some (even most!) staple strands far from the fluorophores, little change in kinetics observed, but if they remove the immediate neighbors of the fluorophores, assembly/melting transition broadens enormously (evidence for local cooperativity).  For 3D DNA origamis (log-cabin style), hysteresis is much larger.

* Ruff et al, "Precision Templating with DNA of a Virus-like Particle with Peptide Nanostructures", J. Am. Chem. Soc. 135, 6211−6219 (2013): A nice synthetic assembly system where mushroom-like particles (stem is protein coiled-coil, cap is long PEG) attach at their base to dsDNA, form something that looks like a rod virus.

* Roy et al, "Silver Nanoassemblies Constructed from Boranephosphonate DNA", J. Am. Chem. Soc. 135, 6234−6241 (2013): This is cool!  Apparently, you can make ssDNA where the phosphate ions have one oxygen replaced by a BH_3 group.  Upon exposure to a silver salt, silver granules form around the BH_3's.  So if you "boronate" an arbitrary subset of staple strands in a DNA origami, you can grow silver granules in arbitrary pattern on the origami.  Maybe an interesting step towards nanoelectronics?

* Lee et al, "Integration of Gold Nanoparticles into Bilayer Structures via Adaptive Surface Chemistry", J. Am. Chem. Soc. 135, 5950−5953 (2013): Another cool idea: you coat a gold nanoparticle with both hydrophilic and hydrophobic polymers, which are mobile on the surface (at least under the conditions they used).  Then, when you expose lipid vesicles to these particles, they can insert into the membrane thanks to the hydrophobic polymers mixing with the interior of the bilayer, while the hydrophilic polymers act as a kind of extension of the lipid bilayer around the nanoparticle.  You can incorporate very large particles, and also many particles in one vescicle.

* Xin et al, "Regulation of an Enzyme Cascade Reaction by a DNA Machine", Small, (online, no issue/page yet) (2013): Another interesting idea with DNA: Arrange two enzymes that work in cascade (the product of A is the substrate of B) at the ends of a DNA "hinge".  The hinge is held together by a piece of ssDNA, which is floppy, so the enzymes tend to be closeby => fast reaction.  Now add a complementary "fuel" strand, with a toehold, to make the hinge a rigid (and longer) dsDNA.  This separates the two enzymes in space, so the reactive slows down.  If you add an "antifuel" strand that is complementary to the whole fuel strand, the hinge becomes floppy ssDNA again.  As a result, you can switch between fast and slow catalysis by adding or removing fuel strands.