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okay guys first first thing I want to

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make a very large disclaimer that I have

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no knowledge of geology whatsoever I'm

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not sure why I'm in this session but I'm

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assuming it's appropriate and I would

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like to request exemption from any

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questions regarding Jamie's claims about

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iron and having nothing to ferric to

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ferrous having nothing to do with

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oxidation in the atmosphere okay so what

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I wanted to do is to talk about the iron

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the soluble form fe 2 plus and its role

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of biochemistry and early Earth so if we

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look at the history of biology not

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geology history of biology as you see

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here we see this large tree of life the

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tree of life in modern times is

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represented by three domains bacteria

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archaea and you carry a so if we walk

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back in time along that tree of life we

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get to what we call Luca last Universal

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common ancestor we've all heard of that

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by this point which we estimate roughly

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is about 3.9 billion years ago if we go

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farther back in time we get into this

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the squiggly line and the squiggle enos

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of this line all that means is that we

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are likely to have observed a lot of

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horizontal gene transfer during that

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time so even though last Universal

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common ancestor singular most likely

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it's a composite of multiple types of

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organisms and what we're really dealing

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with this far back in time is more like

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a soup or sea of different life-forms so

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what I want to talk about is this point

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of the RNA world hypothesis essentially

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in which we theorize there's some kind

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of primitive catalysis and maybe some

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metal assisted assembly back in that RNA

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world so the RNA world hypothesis

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essentially states that before modern

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biology which is DNA RNA and proteins of

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our modern times we have something

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called the RNA world in which RNA

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perform the roles of genetic storage and

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catalysis essentially all the functions

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that protein DNA and RNA do together

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today and this world is hypothesized to

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have occurred back in the early rkm yawn

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about 3.8 billion years ago very roughly

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so what do we know about modern RNA well

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one thing that we study a lot in our lab

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Lauren Williams lab at Georgia Tech is

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the relation

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between RNA and divalent cations

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especially magnesium so we know that our

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name magnesium have a very special

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relationship and it has to do with this

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magnesium being a divalent cation having

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two charges and really enjoying the

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opportunity whoops what did I do okay

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sorry I'm really liking to bond with

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those phosphates that form the DNA

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backbone of the RNA background in this

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case oops I did it again sorry about

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that and we know that I that magnesium

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also has very special role in the

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folding of large RNAs so there are

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certain if you have an RNA that's three

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thousand bases long such as what you see

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in the ribosome there are certain

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conformational spaces or certain

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three-dimensional shapes that that RNA

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cannot reach without the presence of

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magnesium in solution just because of

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its size and its charge density so we

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see this kind of special relationship in

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key lated magnesium motifs like those

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found in the ribosome believe there are

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23 of these magnesium chelation sites in

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the 23s ribosomal RNA we'll talk about

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biology more tomorrow but just know the

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ribosome is the thing that makes

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messenger RNA into proteins and all

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cells present in all cells completely

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ubiquitous but we see these on chelation

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complexes where we have two magnesium

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and we have multiple phosphates these

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are the phosphates on the back room

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interacting with the positive charge

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from the magnesium and then if we

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superimpose ribosomes from across the

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phylogenetic tree of modern life what we

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see is that these chelation complexes

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this geometry is conserved among all of

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life especially if the center of the

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ribosome from we're going to get the

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prize for them good slide changing this

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time so one thing we've done we have a

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research scientist in our lab and named

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Anton Petrov he's a quantum physicist

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and so he's looked at in silico meaning

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on computer in mathematical space the

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relationship between magnesium and RNA

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you see here calcium and are

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a its sodium and RNA trying to identify

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what is so special about magnesium that

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these other cations don't have and so

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what you can see in these quantum

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mechanical calculations in mathematical

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space is that the interaction energy

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between RNA and magnesium the

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interaction energy between those

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backbone phosphates and magnesium is

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much more spontaneous so interaction

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energies with very large negative number

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or more spontaneous we don't have to

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adding energy to them in order to the

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fore in order to form that structure but

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if we look at calcium or sodium we have

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a much lower negative number in the case

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of calcium or a positive number in the

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case of sodium indicating we need to add

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some energy to pour that structure to

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form now what we are interested in

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looking at is whether some other cations

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can play the role of magnesium and we

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thought we found one we're pretty sure

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we found one at this point so if we look

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at iron we put iron in place with

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magnesium in the same in the same

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mathematical space and then we minimized

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structure what we get is the same

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geometry in the backbone of the RNA with

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iron as we do with magnesium we believe

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that's because the charge density and

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the size of iron is so similar to

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magnesium much more similar than any

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other cation that we have biologically

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available and in the case of iron

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actually the interaction energy is a

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little bit more negative so the complex

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formation that's a little bit better

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with iron than with magnesium so based

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on this information what we've

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hypothesized is the back in the days

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when the earth was very unops Akande i

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don't think i have to go much into this

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at this point i've had a very good

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overview today so before protosynth

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photosynthesis and the great oxidation

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what we had as we've already heard is

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that the iron in the ocean be

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biologically available to plus form is

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probably much greater in concentrations

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than it is today and would have been

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much more biologically available I

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didn't want to mention that iron

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two-plus in the presence of oxygen gives

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rise to Fintan chemistry which can be

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toxic to to biology that's I did also

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want to show the banded iron formation

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that

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you've already seen so the theory is

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that it's oxygen increased in the

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atmosphere we have the interaction with

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the surface oceans and the iron

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precipitated out and form these banded

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iron formations and this one I believe

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is in Minnesota courtesy of Clark

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Johnson so our hypothesis is that iron

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back in the days when the earth was an

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optic actually played the role in RNA

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and played the role in life that

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magnesium plays today so we wondered

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whether we could recreate these early

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earth conditions remove the magnesium

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remove the oxygen so that the iron would

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not eat up the RNA and see if we could

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find some kind of activity see if RNA

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would do something interesting in the

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presence of iron so one of the first

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things we did is evaluate like I said

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before magnesium is required for RNA to

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generate certain conformational States

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we wanted to see if iron in the presence

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of iron the same conformational states

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of RNA could be reached so if you look

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here along the x-axis this is

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essentially if you imagine this the five

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prime end of an RNA to the beginning of

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one strand of a molecule and you follow

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this along this would be the end of the

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Strand of the molecule and along the

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y-axis we have essentially the

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vulnerability of that molecule to some

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kind of external chemical modifying

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agent so along this chart along this

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graph the higher the peak the more

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vulnerable the RNA at that position in

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the molecule so if we look at the RNA

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and with sodium only we see one

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particular pattern of vulnerability

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along the bala Kuehl if we add magnesium

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we've changed the conformational state

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of RNA and we see a different pattern

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iron we see almost exactly the same

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pattern which is very interesting what

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we'd expect based on the in silico

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results right so if we look at a

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different kinds of enzymatic reaction we

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haven't talked about this yet but we

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will tomorrow morning ribozymes

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ribosomes are like machines like enzymes

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like protein machines in this case made

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of RNA that can do interesting things

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like like eight strands of our

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so they can reconnect two strands

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together to make one continuous backbone

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so what we see in this reaction if we

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test the ribozyme with iron in the

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absence of oxygen and we subject that to

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time what we see is that we get ligation

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product with magnesium which is well

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documented in the literature but in the

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absence of magnesium but the presence of

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iron we get a whole lot more like a shin

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product which is very cool we can take

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also take a ribozyme that does RNA

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backbone cleavage so it's separating the

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RNA backbone and over time look at the

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fraction of cleavage product we see that

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in the presence of magnesium the

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ribozyme cleaves in the presence of iron

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only we get a whole lot more cleavage

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project product so overall what this is

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telling us is that RNA catalytic RNA can

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be much more efficient in the presence

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of iron than they can be in magnesium as

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long as oxygen is absent as long as

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we're recapitulating those early earth

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conditions so the very last and most

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recent experiment that we performed this

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one's done by cha longshaw of our group

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please check this out this is a very

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very cool paper it was just accepted in

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nature chemistry so what we what cha

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long did is he took a colourless

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solution this is tetramethyl benzidine

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okay thank you this is a this is

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essentially a color eight indicator so

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if this tetramethyl benzidine is

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oxidized it's going to turn blue very

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simple so we take tetramethyl been

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setting which is here hydrogen peroxide

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which is here here put in the RNA put in

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the iron remove the oxygen but not

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necessarily in that order and we can

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monitor the rate of change of the color

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of the solution using a simple

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spectrophotometer very simple technique

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so we did this or chalam did this not me

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so if we monitor this over time 20

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minutes here's our solutions 6 micro

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molar iron hydrogen peroxide minus this

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is supposed to say 02 we can't have

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oxygen s reaction if we have no RNA in

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the solution we have no color change we

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have no electron transfer we add ATP 3

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closely spaced phosphate groups which we

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would expect to interact with the iron

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right we still see no electron transfer

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we add single-stranded RNA oligomer no

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electron transfer we get electron

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transfer we're expecting an increase in

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the blue color right which is going to

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increase this way double-stranded DNA

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nothing large viral genome nothing 23 s

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ribosomal RNA from thermus thermophilus

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voila we have electron transfer p for p

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suit 6 domain RNA which is a

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well-characterized RNA small RNA we also

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have electron transfer and trna also

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very well characterized electron

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transfer very cool we should be jumping

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up and down right now eh along so what

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is common among those three RNAs that

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the other the other single-stranded RNA

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the double-stranded DNA that showed no

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reaction whoa what is so special about

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this well one thing we know from looking

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at three dimensional crystal structures

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is that we have these special magnesium

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phosphate geometries going on here mag

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tRNA is probably the exception to that I

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don't know that one one of the magnesium

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phosphate backbone geometries has been

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observed in TNA tRNA but we do know that

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magnesium is very important to tRNA this

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reaction also has the same kinetics as

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what we call the michelis minton

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formalism so it can essentially complies

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with the traditional test for an enzyme

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which is cool means it saturates itself

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so if we limit the enzyme we have plenty

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of substrate at some point we're going

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to have so much substrate that we're not

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going to get any more catalysis per unit

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of substrate at it

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so conclusions the critical role of

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magnesium in RNA if we put it into a

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hypothesized early Earth's environment

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in the absence of oxygen can be better

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served by iron the relationship with

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iron and RNA provides a very needed link

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between the RNA world and the geologic

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record and that RNA may have originally

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served the soul roll them sorry iron may

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have originally served the made the

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predominant role in the early life and

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that was later replaced by the oxidation

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and that this new RNA world RNA with

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iron opens up a new realm of catalytic

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functions that have not been previously

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characterized I wanted to thank the real

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brains behind this not me shillong Shaw

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Anton Petrov dr. shreyas Denise Okafor

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graduate student and of course our

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wonderful p I Lauren Williams is always

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there for us as well as Steve Harvey

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Nick HUD dr. worked out and many others

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of our lab and this is our lab Lauren

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all right we can take one quick question

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um I saw that you had the sodium control

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for your putting RNA with different

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rounds have you tried any other divalent

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controls like biologically relevant like

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calcium or manganese ore no we have not

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one thing we do know is when we add

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magnesium to they'll elect the electron

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transfer reaction it kills it so even if

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we have iron there with RNA if we have

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magnesium there it's gone but we have

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not tried other cations and we don't

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have reason based on our end silico

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results to believe that those would

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actually support any kind of catalysis

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that's a great question manganese would