hey guys I wanted to show you some more
stuff with nanome today, this is a very
useful tool for visualizing molecules
and proteins and things so let's go
ahead to RCSB database and let's type
in 1bna, what could that be?
let's take a look upload it and so we've
got some DNA specifically this is a
dodecamer of B-DNA which means we're
looking at 12 base pairs of DNA so i
wanted to show you this because you know
in biochemistry and biology we talk
about DNA a lot but we're usually using
some kind of reductive model some way of
visualizing it it's not so accurate but
you know we really want to get in here
and and look at DNA and see all the
atoms and see all the covalent bonds and
all the functional groups and you know
just really make sense of it and walk
through here so we can pull ourselves
right through this this helix and now I
want to show you some different ways to
visualize it because there's a lot of
stuff going on we see all these these
red spheres those are water molecules so
the hydrogens are implied but that can
sort of cloud what what we're looking at
it's important to know they're there
because they are interacting with the
phosphate backbone but we can get rid of
those and now that's a little bit
clearer and what else can we do to see
this a little more clearly we see this
the green ribbon here is meant to
represent the phosphate backbone but
it's a little bit in the way so we can
even toggle that let's get rid of that
ribbon and now we're really just seeing
the atoms the atoms and the bonds and
this is this is a good way to visualize
DNA this is more representative of what
DNA looks like then some of the pictures
we typically see in textbooks or when
we're you know trying to talk about
something else and we can look at this
in a few different ways we can use van
der waals view and here we can we can
very clearly see the the phosphate
backbone with this space-filling model
and that's wrapped around the side and
then we've got these base pairs in the
middle with all those blue nitrogen
atoms and we can look at this in a stick
view as well or a wire
you and these are just different ways of
representing the molecule all of which
are useful in their own ways again if we
look at this maybe from the top here we
can see all of the base pairs in the
center there and the phosphate backbone
wrapped around but let's go back to
ball-and-stick that is I find to be kind
of the best way to look at these and so
there it is there's DNA without the the
green ribbon and the waters and let's
really get in here now let's look we
want to take a look at these base pairs
can remember the base pairing that's
very important to understand in terms of
DNA's functionality and so here's a base
pair we can climb up the ladder rung by
rung so to speak
now here's another base pair and as
we're turning around we can keep
climbing up this spiral and so let's
look at this we've got a we've got a
guanine over here on the right and we've
got a cytosine over here on the left and
this is gonna make three hydrogen bonds
and we can really see these quite
clearly now the hydrogens are implied
but there's three here and we can even
measure the distances here we can
measure the distances between the base
pairs at each locus here each atom so
there's an NH to the carbonyl there's
one of those nitrogen's has a hydrogen
and then here's another NH to a carbonyl
so those are the three H bonds that are
made by a CG base pair and we can go
ahead and look let's hunt for an AT pair
now let's see if we can find an adenine
thymine so let's go ahead and move up
this up this thing here and okay looks
like looks like there's one right here
so let's zoom in now we've got we've got
adenine and thymine there and this one
is going to make two hydrogen bonds so
we can we can get the distances there as
well and that's why AT pairs are a
little bit weaker a little bit easier to
pry apart with AT pairs they only make
2 H-bonds instead of three and let's keep
climbing up the ladder and here we are
at the very top of our dodecamer so
that's only 12 base pairs recall that in
an you know in your
chromosomes we've
got DNA molecules with billions and
billions of base pairs so that's it I
just wanted to show you a little bit
about DNA and stay tuned as I show you
more molecules over time
