Then we pour it into a gel casting “mold” & add a well comb to leave spaces to load our samples into. And let it cool. As it cools, it goes from clear to cloudy as it transforms from a liquid to a gel. That’s a change we can see, but the cooler stuff is happening at a level we can’t see.
As it cools, agarose’s molecules run out of the energy needed to wriggle around freely, so they settle down in the most comfortable position, which happens to be a convenient mesh. At the molecular structural level, each of agarose’s “strands of yarn” is a chain of about 400 subunits (so 800 individual sugars). When they have enough energy (high enough temps) they move around lots & don’t have a defined structure. We call this a “random coil” structure.
BUT when it starts to cool, it loses its energy so tries to settle in the most comfortable position (if you can’t move you at least want to be comfy). The 3,6-anhydro-L-galactose makes this “tricky” because 2 of its “legs” form a “bridge” across the ring which is kinda awkward. As a result, the most comfortable position is a helical form ➿. 2 strands of yarn wrap around each other in an antiparallel double helix (like in your DNA, but these helices are left-handed (do a thumbs up with your left hand & follow your fingers) unlike the right-handed helices of your DNA) w/frayed ends
These joined helices can still move around, but as a group. As you cool it down further, they start joining up to other helices (AGGREGATING)) to to form bigger bundles of helices (supercoils). Cool it down even further & the frayed ends start getting tanged up w/frayed ends of other helix bundles, so the helices start clumping up. BUT they still have that water coat & can’t get too close, so you get a porous mesh w/water trapped inside - perfect for DNA to swim through!
more about all sorts of things: #365DaysOfScience All (with topics listed) 👉 bit.ly/2OllAB0 or search blog: thebumblingbiochemist.com
As someone who works completely in a dry lab, I found it's so eye opening to see how the small mesh is made. Pretty cool
Then we pour it into a gel casting “mold” & add a well comb to leave spaces to load our samples into. And let it cool. As it cools, it goes from clear to cloudy as it transforms from a liquid to a gel. That’s a change we can see, but the cooler stuff is happening at a level we can’t see.
As it cools, agarose’s molecules run out of the energy needed to wriggle around freely, so they settle down in the most comfortable position, which happens to be a convenient mesh. At the molecular structural level, each of agarose’s “strands of yarn” is a chain of about 400 subunits (so 800 individual sugars). When they have enough energy (high enough temps) they move around lots & don’t have a defined structure. We call this a “random coil” structure.
BUT when it starts to cool, it loses its energy so tries to settle in the most comfortable position (if you can’t move you at least want to be comfy). The 3,6-anhydro-L-galactose makes this “tricky” because 2 of its “legs” form a “bridge” across the ring which is kinda awkward. As a result, the most comfortable position is a helical form ➿. 2 strands of yarn wrap around each other in an antiparallel double helix (like in your DNA, but these helices are left-handed (do a thumbs up with your left hand & follow your fingers) unlike the right-handed helices of your DNA) w/frayed ends
These joined helices can still move around, but as a group. As you cool it down further, they start joining up to other helices (AGGREGATING)) to to form bigger bundles of helices (supercoils). Cool it down even further & the frayed ends start getting tanged up w/frayed ends of other helix bundles, so the helices start clumping up. BUT they still have that water coat & can’t get too close, so you get a porous mesh w/water trapped inside - perfect for DNA to swim through!
more about all sorts of things: #365DaysOfScience All (with topics listed) 👉 bit.ly/2OllAB0 or search blog: thebumblingbiochemist.com