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Good morning.
Good morning.

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I don't know about you, but I can't
take too many more nights like this.

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I confess, I haven't gotten a thing
done for so many nights in a row now,

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but what a game! How many of
you saw the game? Excellent.

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Very good, very good. You have
your priorities straight in

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the world. Very good. Well,
if it's possible to get your

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minds off Curt Schilling last night,
and off more importantly tonight.

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Perhaps we can spend a bit of time
this morning in the meanwhile with

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whatever spare neurons you have
talking about recombinant DNA for a

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bit, OK? What we talked about last
time was different ways to clone

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your gene based on its properties.
We started off with cloning by

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complementation, right,
the idea that if you took a

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library of clones, you
would be able to put it into

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bacteria and select a bacterium
whose phenotype had been restored by

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virtue of having the plasmid.
You would complement the defect.

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You'd find the clone you wanted
because it complemented the defect.

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That's great if you can put it
into an organism that has a defect.

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You can do it with bacteria.
You can do that with yeast.

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It's harder to do with large
organisms because you can't inject

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enough of them with different clones
to be able to make that practical

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unless you're working in cell
culture or some very small,

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fast growing organism. We
talked about being able to use a

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protein sequence, reverse
translating that protein

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sequence in the computer from amino
acid sequence to nucleotide sequence,

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and using the nucleotide sequence to
design a probe to hybridize back to

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the genome. That works fine
if you have a protein sequence.

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But the last topic we talked about
that I wanted to just touch on again

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this morning was suppose you were
trying to clone the gene that causes

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a certain human disease,
and you have no idea what the

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protein was. Then, you
can't use its amino acid

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sequence because you don't have the
protein. What can you possibly do

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when all you know is that you have
a gene which causes a genetic defect

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that causes a disease? And I
said you could clone it using

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the ideas of genetic mapping,
position, the things that Sturtevant

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developed. And, I
touched on it briefly,

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and I want to just touch on it a
bit more because some people had some

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questions about it. And
I've set up a very simple

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example to show you. Suppose
that, to make it easy,

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we're working in a fruit fly
first. We're working drosophila, and

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suppose that the true picture of the
underlying chromosome is like this.

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There's a locus that could either
have a mutant allele M or the wild

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type allele plus. There's
a bunch of other loci along

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the chromosome. And, let's
suppose we know all of

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where they are and all that.
And, they have two alternative

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alleles. At this locus
the alleles are orange

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or pink. At this locus I'll
call the alleles orange or pink.

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Now, these are different loci.
These are different alleles. I've

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just called them orange and pink in
both cases so I don't have a rainbow

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of colors up here to confuse
us. But all I mean is there's two

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possible alleles here, two
alleles here, two alleles here.

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This is the diseased
gene we're interested in,

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and these are passive markers.
These are other markers along the

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chromosome. If we were
to set up a cross between

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heterozygotes, a
heterozygote here,

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and a heterozygote here, and
it were the case that on the

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chromosome bearing the mutant allele,
it happened that at these three

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markers we had orange alleles.
I don't know what they are, but

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whatever these orange alleles are,
they might be a visible phenotype,

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forked or yellow or bristled.
They could be a DNA sequence

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difference. They could be whatever
you want, but let's suppose the M

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chromosome has a set of alleles that
are different in each location than

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the plus chromosome. Then,
when we look at the offspring

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that come out of this cross,
let's only, for the sake of

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simplicity, look at those offspring
who are homozygous mutants.

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Well, in general, if there's
been no crossover here,

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then the M chromosome
will have orange, orange,

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orange, orange, orange, orange.
If there's been a crossover,

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however, it could go orange,
orange, pink on one of those

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chromosomes. Or if there's
been crossovers like this,

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it could go orange, orange, pink
on one chromosome, and orange,

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pink, pink on the other
chromosome. It could even,

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in the extreme, have had
crossovers very close to

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the gene maybe here, and even
maybe here. And you've got

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orange, pink, pink,
and pink, pink, pink.

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But if we look at the many
segregates, you know from genetic

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mapping that the closer the
locus is to the disease gene,

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the more strongly correlated
the inheritance will be,

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the tighter the linkage will be.
This is nothing more than linkage

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mapping. But now,
suppose we were doing

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linkage mapping, but for
the sake of argument the

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whole genome had already been
sequenced. Suppose the genome had

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been sequenced in a cross, and
the whole genome of the fruit

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fly had been sequenced
which it has been sequenced.

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And, we looked at a cross
and we looked at the mutants.

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And what we did was we tried
different positions along the genome.

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And at each position, we
had some genetic marker.

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And that genetic marker might be
as simple as the fact that at that

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position, maybe there is an A
in the DNA sequence on one of the

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chromosomes, and maybe I don't
know a G in the other sequence.

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And over here, this marker might
be, there's a T in some particular

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position, and there's a C
in some particular position.

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If we could assay that, if
we could tell, we could look

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whether this spelling variation is
closely correlated with the mutant.

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And this spelling variation
is closely correlated with the

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inheritance of the mutant allele.
And we could just try up and down

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the genome, different sites of
spelling difference as if they were

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genetic markers in our cross because
they are genetic markers in our

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cross, and see which one
is most tightly correlated.

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The minute we get any
genetic sequence difference,

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that shows co-inheritance linkage
in this cross, we know that this spot

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in the genome must be
nearby our mutation.

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So, we'll try one closer, and
we'll try one on the other side.

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And, what you do is you test
sites of genetic variation,

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first to find one that
shows any co-inheritance.

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And once you've got that, you
try ones closer, and closer,

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and closer. Last time I
talked about the process of,

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if you had one of those markers
you could use it to isolate the next

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clone and the next clone and the
next clone. But you know what I

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realized? That's so old fashioned.
We might as well deal with the fact

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we have a sequence of the genome.
No more would you ever isolate the

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next clone and the next
clone and the next clone.

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You just look it up in the computer.
So, even if you have the whole

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sequence of the genome, we
have to figure out what part of

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it was co-inherited along with this
disease, and that's the way you do

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it, OK? Genetic mapping, ust
as Sturtevant invented it,

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can be applied if you have a
whole sequence of the genome,

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and enough sites of variation.
And, I've drawn it for a fruit fly

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cross, but this could equally
well be cystic fibrosis.

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The only difference is if we're
doing this in human families and

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it's cystic fibrosis we
don't have as many offspring.

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So, we have to pool data
from many families. And,

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we can't arrange it so that every
family has exactly the same orange

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alleles up here and pink alleles
down there, but computers can deal

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with that. They can still figure
out the correlation across many

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families, and you find the spot
in the genome where for many,

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many, many families the kids who
all got the disease show correlated

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inheritance with this marker.
And that eventually pins you down

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to a region of the genome. It
pins you down to those genetic

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markers that show the
absolute tightest correlation,

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tight correlation, and
that's where you look.

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And in that fashion, people
went being able to map the

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location of Huntington's
Disease in 1984 to, by now,

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mapping the locations of more than
1, 00 different human genetic diseases

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where people didn't know the protein
in advance. They did it entirely

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based on this positional mapping.
So, Sturtevant's idea, which I like

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so much, has played itself out
so beautifully now in the area of

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modern molecular
medicine. OK. So, onward.

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I want to talk about a few other
variations on the theme rather

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quickly, and then I think I want
to talk about how you analyze your

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clones. First,
variations on cloning,

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I should just at least mention
it. We talked about cloning in an

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autonomously replicating
plasmid in a bacteria.

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So, you go to a bacteria.
They have some autonomously

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replicated pieces of DNA.
There are circles. You can clone

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in them, and you can typically,
these things are on the order of,

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I don't know, 1,000 to 2,000 to 5,
00 bases can be readily cloned in

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these plasmids.
You can do more,

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but that's a typical kind
of number is the insert size,

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typically. But we in the lab
go up to much higher numbers

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like 10,000 sometimes. You can
also, if you wanted to study

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yeast, it turns out yeast
happily have plasmids as well,

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and you can do a similar
sort of thing for yeast.

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It turns out that instead of using
plasmids, you can use bacterial

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viruses. These bacterial viruses
have all different shapes as we've

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talked about, circular or linear,
and they can typically hold, oh, 15,

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00-40,000. Some of these
viruses are quite big.

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The bacteriophage lambda
tends to carry a lot of stuff.

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And, it can replicate. So,
you could do the same thing to

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that. You can even use viruses that
infect mammalian cells and there are

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all sorts of viruses now
that people clone in again,

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linear or circular. I don't
know, for mammalian cells,

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you often, the viruses like 1,000-5,
00. You can even make artificial

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whole chromosomes now.
You can do this in yeast.

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Artificial chromosomes are called
YACs. They have all the little

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machinery, little telomeres on
them, little centromeres. They have a

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selectable marker, and then
you can clone into it your

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piece of DNA. And these can take
up to a million bases of DNA.

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So, if you wanted, there are
bacterial artificial chromosomes.

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They're called BACs if they're
in bacteria. And recently,

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people have developed artificial
chromosome systems for mammalian

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cells, and specifically human cells.
And they're called unfortunately

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MACs and HACs and things like that.
Basically, any molecule that can

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replicate in any system, some
smart molecular biologist will

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come along and say, how do
I use that for my purpose,

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to stick my DNA in it, and get
it to replicate in this organism?

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And so, if something's not
on this list, it will be soon,

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OK? Now, here's another thing.
This is cloning chunks of DNA.

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Just to have the piece of DNA in a
library, but suppose we want to do

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more than just have the DNA
sitting there in the bacterium,

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suppose what I'd really like
to do is take a bacterium,

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E coli, and put it to work for us.
Maybe what I'd like to do is take a

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plasmid and insert in that
plasmid the gene for human insulin.

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So, I'm going to take the DNA locus
corresponding to human insulin,

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clone it into my plasmid. Maybe
I'll have isolated it from my

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library because, let's
see, insulin's protein

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sequence is known so I could
reverse translate it to a nucleotide

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sequence. So, I
could probe a library.

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So, I could find the clone that has
insulin. Now what I'd like to do is

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persuade this bacteria not just to
carry the DNA but to make insulin

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for me. Would that be useful?
Yeah, how did people used to get

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insulin? Cadavers, dead
bodies; it would be much easier

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to get them from a fermenter,
right, to get insulin from a

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fermenter, if you could
just ask E coli to make it.

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So, if we put it into E coli,
will it make insulin for us?

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Here's the human locus, DNA
for insulin. Will it make

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insulin? Let's see, how
do you make a protein?

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You've got to start by making RNA,
right? You've got to transcribe the

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gene. Will E coli
transcribe this gene?

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Well, why? It's got a promoter,
right? It's got the insulin

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promoter. There we go. The
insulin promoter is here.

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So, E coli will come along to the
insulin promoter and start making

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RNA? No, it turns out that
promoters in humans and promoters in

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bacteria are sufficiently different.
They don't work across species.

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They won't recognize the human
promoter. Too bad. Any ideas?

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Yep? Stick a bacterial promoter
there. Good, you're acting like a

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good molecular biology designer here.
Let's put a bacterial promoter here.

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It will recognize its own promoter.
That's great. Then, let's put the

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DNA for the human insulin gene here.
And now, maybe we'll put the Lac

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operon, and when it has lactose
it'll start making RNA from the

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human insulin gene. And
it'll start translating it.

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And, we get insulin.
Any problems? Well,

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will it make any, for starters?
What's another aspect of mammalian

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genes that's different
from bacterial genes?

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Processing, what kind of processing
with the RNA? And the splicing,

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ooh, the insulin gene has introns
that have to be spliced out.

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So, this is going to make some
RNA, insulin RNA, and it needs to be

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processed like this. Will
bacteria carry on our splicing

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for us? They don't do splicing.
Yep? Well, that's a very

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interesting question
because we haven't. But,

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what do you propose? You see,
I've just taken a piece of

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human DNA from the human genome,
which encodes the introns and the

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exons. But, you seem to have
a solution to our problem,

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and what would that be? So,
instead of making a library of

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genomic DNA, what you're
suggesting is a radical idea.

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Let's instead take human RNA.
Here's some human RNA, lots of

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human RNA, a big collection of
human RNA. What was at the end of the

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human RNA: a poly(A) tail.
And what I understand you to be

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suggesting is if we take human
mRNAs, a whole collection of them,

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you want me to turn these mRNAs back
into DNA and clone them instead of

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using the chromosomal DNA. How
do I turn an RNA back to DNA?

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Is that possible? What do you
use: reverse transcriptase.

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We have to give it a primer.
So remember, five prime to three

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prime, we'd like to put
a primer going over here.

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Any ideas for a good primer?
Poly(T), isn't that convenient?

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One of the reasons that mammalian
messages have poly(A) tails is so

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that we are able to reverse
transcribe them using poly(T)

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primers. No, that's actually
not true. So, we use reverse

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transcriptase. And what
we can do is we'll copy

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this RNA into a strand
of DNA. There we go.

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Then what we'll do, next
step, is we'll take the DNA,

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and we'll copy back into
a second strand of DNA.

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And now, we have double-stranded
DNA whose sequence matches the

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already-processed mRNAs.
Sorry? So, the sequences would

244
00:17:21 --> 00:17:27
match the mRNAs. So what
you could do is instead of

245
00:17:27 --> 00:17:32
taking human DNA from the
nucleus, you could take RNAs,

246
00:17:32 --> 00:17:38
turn them back into DNA
by reverse transcriptase,

247
00:17:38 --> 00:17:43
and make a library now that
consists of zillions of inserts,

248
00:17:43 --> 00:17:49
each of which has what's
called a cDNA, a copied DNA,

249
00:17:49 --> 00:17:54
copied back from the RNA. The
great advantage of this is that

250
00:17:54 --> 00:18:00
the human cell has already
done the splicing, and so there

251
00:18:00 --> 00:18:05
are no introns left. Now,
when you stick it in a

252
00:18:05 --> 00:18:09
bacterium, the bacterium is
able to express this. It's able,

253
00:18:09 --> 00:18:13
if you give it its own bacterial
promoter, to make an RNA.

254
00:18:13 --> 00:18:17
And if you don't ask the
bacteria to have to splice,

255
00:18:17 --> 00:18:21
if you just give it a pre-spliced
piece of DNA that doesn't need

256
00:18:21 --> 00:18:25
splicing, it can translate that
DNA. Now, notice we used all of our

257
00:18:25 --> 00:18:29
tricks. You had to know
about reverse transcriptase,

258
00:18:29 --> 00:18:34
poly(A) tails, structures of genes,
introns, exons, yes, question?

259
00:18:34 --> 00:18:38
It doesn't. You do this in the test
tube. You purify human mRNA in the

260
00:18:38 --> 00:18:42
test tube. You take that mRNA in a
test tube, add reverse transcriptase,

261
00:18:42 --> 00:18:47
add poly(T), make this reaction of
RNA to DNA in the test tube go back.

262
00:18:47 --> 00:18:51
Where does it come from? Viruses
that copy themselves back for a

263
00:18:51 --> 00:18:56
living, right? So, again,
every single thing we're

264
00:18:56 --> 00:19:00
using comes from some living
organism that does this

265
00:19:00 --> 00:19:04
kind of stuff. And, when
I teach you about the

266
00:19:04 --> 00:19:08
facts of how viruses replicate or
what the structure of mRNAs look

267
00:19:08 --> 00:19:11
like or whatever, it's
because every bit of knowledge

268
00:19:11 --> 00:19:14
we get about the way biology works
turns into an incredibly powerful

269
00:19:14 --> 00:19:18
tool as it's turning out for us to
actually be able to further study

270
00:19:18 --> 00:19:21
biology. So, great.
So, where does reverse

271
00:19:21 --> 00:19:24
transcriptase come from now?
Originally they come from viruses

272
00:19:24 --> 00:19:28
that turn themselves back from RNA
to DNA. Now, how do you get reverse

273
00:19:28 --> 00:19:32
transcriptase?
Catalog, right,

274
00:19:32 --> 00:19:38
very good. All right, so
this is called, finally,

275
00:19:38 --> 00:19:44
a cDNA library. And, if
you had made a cDNA library,

276
00:19:44 --> 00:19:49
you would be able to screen the cDNA
library to find the gene for insulin.

277
00:19:49 --> 00:19:55
Is this useful?
This happens to be,

278
00:19:55 --> 00:20:01
for example, one of the consequences
of this was the biotechnology

279
00:20:01 --> 00:20:06
industry. OK, so if you
have any doubts about

280
00:20:06 --> 00:20:10
the usefulness of understanding
these abstract things about E coli

281
00:20:10 --> 00:20:14
and bacteria and stuff like
that, one of the consequences was

282
00:20:14 --> 00:20:18
Genentech, Biogen, and
Amgen, and if you just simply

283
00:20:18 --> 00:20:22
walk around Kendall Square, within
a mile of this place you will

284
00:20:22 --> 00:20:26
see laid out before you the
consequences of this ability,

285
00:20:26 --> 00:20:30
OK? It's transforming
Cambridge. Yes?

286
00:20:30 --> 00:20:36
And the world.
Yeah. Indeed.

287
00:20:36 --> 00:20:43
It might be that producing large
amounts of insulin was bad for the

288
00:20:43 --> 00:20:50
bacteria because there would be so
much protein it would clump and kill

289
00:20:50 --> 00:20:57
the bacteria. It might be that
insulin, for various reasons,

290
00:20:57 --> 00:21:04
might not fold appropriately
in the bacterial environment.

291
00:21:04 --> 00:21:07
And, this is why the biotechnology
industry has lots of smart people

292
00:21:07 --> 00:21:10
working in it because you're totally,
100% right. You might decide that

293
00:21:10 --> 00:21:13
instead of cloning it in bacteria
it's better to clone it in some

294
00:21:13 --> 00:21:16
insect cell in culture which, in
fact, people like to work with,

295
00:21:16 --> 00:21:19
or some other cell, or
a mammalian cell. And so,

296
00:21:19 --> 00:21:23
I simplify by saying put it in
coli, but in fact that might test six

297
00:21:23 --> 00:21:26
different cell lines, six
different host possibilities.

298
00:21:26 --> 00:21:29
They might have to take the
insulin out and refold it in vitro

299
00:21:29 --> 00:21:33
and things like that.
You're totally right.

300
00:21:33 --> 00:21:37
This is actually something that
requires work to do it right,

301
00:21:37 --> 00:21:42
just like building an
airplane requires work.

302
00:21:42 --> 00:21:47
I could tell you Bernoulli's
principles, but then Boeing does

303
00:21:47 --> 00:21:51
more than just writes down
Bernoulli's principles.

304
00:21:51 --> 00:21:56
OK, so onward. Now, I'd like to
turn next to analyzing your clone.

305
00:21:56 --> 00:22:00
Analyzing the clone, so suppose
we have, maybe it's by positional

306
00:22:00 --> 00:22:05
cloning, maybe it's by cDNA cloning,
but one way or the other we've got

307
00:22:05 --> 00:22:10
us a clone that we're
very interested in.

308
00:22:10 --> 00:22:14
Maybe it has the insulin gene.
Maybe it has the Huntington's

309
00:22:14 --> 00:22:18
disease gene. Whatever it is,
we're going to want to study it.

310
00:22:18 --> 00:22:22
And at the moment, I haven't told
you how I would even read its DNA

311
00:22:22 --> 00:22:26
sequence or analyze its DNA.
So, the first step is, of course,

312
00:22:26 --> 00:22:31
I have to purify the plasmid. And,
it turns out that that can be done.

313
00:22:31 --> 00:22:34
There are simple biochemical
techniques, as I mentioned in a

314
00:22:34 --> 00:22:37
previous lecture, that
allow you to grow up a lot of

315
00:22:37 --> 00:22:40
the bacteria, crack them open,
and the plasmid being a little

316
00:22:40 --> 00:22:43
circle, and being a little more
tightly super-coiled and wound up

317
00:22:43 --> 00:22:46
has somewhat different physical
properties. And you can use those

318
00:22:46 --> 00:22:50
to purify the plasmid. So,
plasmid preps are not hard to

319
00:22:50 --> 00:22:53
do. You can get a fairly pure
collection of the plasmid.

320
00:22:53 --> 00:22:56
Now, suppose I've done this for,
oh, I don't know, let's take my

321
00:22:56 --> 00:23:00
first example, orange mutants.
Suppose I tried to rescue bacteria

322
00:23:00 --> 00:23:04
that were orange minus,
and suppose I found that 50

323
00:23:04 --> 00:23:08
different plasmids rescued my orange
mutant because I transformed a lot

324
00:23:08 --> 00:23:12
of plasmids in, I plated
it, and 50 colonies grew up.

325
00:23:12 --> 00:23:16
Are they all the same
thing or are they different?

326
00:23:16 --> 00:23:20
Is there any quickie way to take a
look at these 50 plasmids and see if

327
00:23:20 --> 00:23:24
they're identical or fairly close,
or obviously different? Well, I'd

328
00:23:24 --> 00:23:28
like to take some way to take the
DNA from the plasmid and analyze it

329
00:23:28 --> 00:23:32
kind of easily. I
might want to see,

330
00:23:32 --> 00:23:37
like, how big is the insert?
Right, that'd be one way,

331
00:23:37 --> 00:23:43
if they had different sized inserts
so they couldn't be the same thing.

332
00:23:43 --> 00:23:49
So, maybe what I could do is how do
I clone this? I used EcoRI sites I

333
00:23:49 --> 00:23:55
recall. So, I have EcoRI sites here.
Suppose I were to take this DNA,

334
00:23:55 --> 00:24:02
and I were to now cut the DNA
from the plasmid with EcoRI.

335
00:24:02 --> 00:24:09
Then, what I would get
is two separate molecules.

336
00:24:09 --> 00:24:16
I would get the vector and the
insert. How could I see how big

337
00:24:16 --> 00:24:24
they were? Gels, gel
electrophoresis is the way to do

338
00:24:24 --> 00:24:29
that. So, I take a gel. A
gel is a slab of gelatin,

339
00:24:29 --> 00:24:33
Jell-O, OK, and normally it's
laid flat, but I'm going to do it

340
00:24:33 --> 00:24:37
vertically here. I load
into the top of it here a

341
00:24:37 --> 00:24:41
little bit of my DNA, this
whole mixture. I take the

342
00:24:41 --> 00:24:45
plasmid. I cut it. I put
it in here. DNA's positive

343
00:24:45 --> 00:24:49
charge or negative charge?
Negative. So, where should I put

344
00:24:49 --> 00:24:53
the positive pull? On
the bottom, well done.

345
00:24:53 --> 00:24:57
That's often not done, and to
the detriment of the experiment.

346
00:24:57 --> 00:25:01
If you put the positive pull here,
it goes the wrong way, and everybody

347
00:25:01 --> 00:25:05
has to do that at least once.
So, what'll happen is the DNA

348
00:25:05 --> 00:25:11
fragments move through, and
the smaller fragments move

349
00:25:11 --> 00:25:16
faster than the big fragments,
right? If something's little, it'll

350
00:25:16 --> 00:25:22
move fast. If something's big,
it moves slowly: little, big.

351
00:25:22 --> 00:25:27
Smaller moves faster because it
wiggles through the little pores in

352
00:25:27 --> 00:25:33
the gel better. So, suppose
I were to do this for a

353
00:25:33 --> 00:25:39
bunch of plasmids, and
what I saw was this.

354
00:25:39 --> 00:25:47
First order, what do you guess?
Sorry? Top road's probably the

355
00:25:47 --> 00:25:55
plasmid vector. This
is probably the vector,

356
00:25:55 --> 00:26:03
and what do I know about the
inserts? At least two inserts,

357
00:26:03 --> 00:26:09
at least two distinct inserts.
Now, if I wanted to be sure that was

358
00:26:09 --> 00:26:13
the vector, maybe what I
could do is take another row,

359
00:26:13 --> 00:26:17
and run a known amount of the vector,
take the vector alone and I could

360
00:26:17 --> 00:26:21
check that the vector alone runs
over here. And maybe I might take

361
00:26:21 --> 00:26:25
some other known molecules.
These would be called molecular

362
00:26:25 --> 00:26:29
weight standards. So, if
I run some knowns in one of

363
00:26:29 --> 00:26:33
the lanes of the gel, I
can even measure and say,

364
00:26:33 --> 00:26:37
ah-ha, the insert is somewhere
between the size of this one and the

365
00:26:37 --> 00:26:40
size of that one. And so,
I get a little ruler that I

366
00:26:40 --> 00:26:43
can put on the gel. So, in
fact, that's the first thing

367
00:26:43 --> 00:26:46
you would do is you
digest your clone that way.

368
00:26:46 --> 00:26:49
Now, does the fact that these
guys have exactly the same,

369
00:26:49 --> 00:26:52
apparently, size on the gel mean
that they're the exact same piece of

370
00:26:52 --> 00:26:55
DNA? No, because you can't even
actually tell it's exactly the same.

371
00:26:55 --> 00:26:59
There's a limit to how
precisely you can measure it.

372
00:26:59 --> 00:27:04
So, what else could you do? You
could try another restriction

373
00:27:04 --> 00:27:10
enzyme. It turns out that since
there are so many restriction

374
00:27:10 --> 00:27:15
enzymes in the catalog,
if I take a piece of DNA,

375
00:27:15 --> 00:27:21
maybe that Eco fragment, I could
try cutting it with HinDIII.

376
00:27:21 --> 00:27:26
And when I cut it with HinDIII,
I'm going to get three distinct

377
00:27:26 --> 00:27:32
lengths. I could try cutting
it with, oh, I don't know,

378
00:27:32 --> 00:27:37
pick another enzyme, BamHI.
When I cut it with BamHI,

379
00:27:37 --> 00:27:43
I'll get some other lengths.
And, how to get these lengths by

380
00:27:43 --> 00:27:48
adding these, by running them out
on a gel and looking at their sizes.

381
00:27:48 --> 00:27:54
What if I added both HinDIII
and BamHI to my test tube?

382
00:27:54 --> 00:28:00
I'd cut at both sites.
So, I'd cut here, here,

383
00:28:00 --> 00:28:06
here, here, here. So,
this is cut with HinDIII,

384
00:28:06 --> 00:28:12
here cut with BamHI, here cut
with both and I could measure these

385
00:28:12 --> 00:28:19
lengths. So, suppose I gave
you this as a computer problem,

386
00:28:19 --> 00:28:25
I have a string and it's an unknown
string, and I cut it at two places

387
00:28:25 --> 00:28:31
and I get these lengths, X1, X2, X3.
And then I take that same string and

388
00:28:31 --> 00:28:35
I cut it at other positions, Y1,
Y2, and Y3 are the lengths that

389
00:28:35 --> 00:28:39
result. And then suppose I now
cut it at both of the sites,

390
00:28:39 --> 00:28:43
and I measure it, and I get Z1,
Z2, Z3, Z4, Z5. If I gave you all

391
00:28:43 --> 00:28:48
those numbers, could you
figure out where the sites

392
00:28:48 --> 00:28:52
must be? Probably. It
turns out to be a reasonably

393
00:28:52 --> 00:28:56
doable computer problem, although
it can get a little hard in

394
00:28:56 --> 00:29:00
places. And you could
try a third enzyme and

395
00:29:00 --> 00:29:03
a fourth enzyme, and it's
a cute exercise to write

396
00:29:03 --> 00:29:07
yourself a little piece of code that
will figure out where the sites are

397
00:29:07 --> 00:29:10
based on the lengths. The
reason it occasionally gets

398
00:29:10 --> 00:29:13
funny what if Z3 and Z4 are exactly
the same length and they run on top

399
00:29:13 --> 00:29:16
of each other in the gel,
and there are special cases.

400
00:29:16 --> 00:29:20
But you can kind of reconstruct
where those restriction sites must

401
00:29:20 --> 00:29:23
be just by writing a good piece
of code that'll put these pieces

402
00:29:23 --> 00:29:26
together. This is called
restriction mapping,

403
00:29:26 --> 00:29:30
and it's great fun. Everybody
likes to do this once.

404
00:29:30 --> 00:29:33
But, it's only a limited
amount of information, right,

405
00:29:33 --> 00:29:36
because you get where the sites are,
and I guess if I gave you ten clones

406
00:29:36 --> 00:29:40
and they all had exactly
the same restriction maps,

407
00:29:40 --> 00:29:43
the exact same positions
of these restriction sites,

408
00:29:43 --> 00:29:47
you'd feel pretty confident
they were the same clone.

409
00:29:47 --> 00:29:50
But you still wouldn't really know
much about the clone other than it

410
00:29:50 --> 00:29:53
had two HinDIII sites and two BamHI
sites, and here's where they were.

411
00:29:53 --> 00:29:57
What do you really want to
know about this clone? It's

412
00:29:57 --> 00:30:02
DNA sequence, right? Let's
not settle for anything less

413
00:30:02 --> 00:30:10
than the exact nucleotide
sequence of the clone. So,

414
00:30:10 --> 00:30:18
that's really the last key
topic is sequencing DNA.

415
00:30:18 --> 00:30:26
How are you going to sequence
DNA? Well, suppose I give you some

416
00:30:26 --> 00:30:34
double strand of DNA,
five prime to three prime,

417
00:30:34 --> 00:30:42
five prime, three prime,
double stranded DNA.

418
00:30:42 --> 00:30:47
Let me heat it up. What
happens when I heat up DNA?

419
00:30:47 --> 00:30:52
It melts the hydrogen bonds, the
non-covalent hydrogen bonds here

420
00:30:52 --> 00:30:57
break, and I got my two
strands separated. Now,

421
00:30:57 --> 00:31:02
what I'd like to do is I want to
start reading out this DNA sequence.

422
00:31:02 --> 00:31:08
So, I'm going to make me a primer.
Now, golly, here's a primer.

423
00:31:08 --> 00:31:14
You're going to ask me, how
did I even know what primer to

424
00:31:14 --> 00:31:21
use if I don't know the DNA
sequence? How can I make a primer?

425
00:31:21 --> 00:31:27
Hold that question. Make sure I
remember to come back and answer

426
00:31:27 --> 00:31:34
that, OK? But for the moment,
grant me that I have a primer here.

427
00:31:34 --> 00:31:39
What I'd like to do is
add DNA polymerase. So,

428
00:31:39 --> 00:31:45
let's add some DNA polymerase.
And, I'd like to add nucleotide

429
00:31:45 --> 00:31:50
triphosphates,
dNTPs, the dATP,

430
00:31:50 --> 00:31:56
dCTP, the dGTP, dTTP, and
if I add DNA polymerase and I

431
00:31:56 --> 00:32:02
add my nucleotides, what
does Arthur Kornberg tell us

432
00:32:02 --> 00:32:07
will happen? It'll
start polymerizing,

433
00:32:07 --> 00:32:13
right? And, it'll stop there. So,
the polymerase knows the bases,

434
00:32:13 --> 00:32:18
right? It knows what base to put
in because polymerase is very smart.

435
00:32:18 --> 00:32:24
So, the bases get put in correctly.
The only problem is, how do we get

436
00:32:24 --> 00:32:30
polymerase to tell
us what it just did?

437
00:32:30 --> 00:32:37
Here's a cute trick.
This is, by the way,

438
00:32:37 --> 00:32:44
a cute trick that won the Nobel
Prize. So, suppose my primer is

439
00:32:44 --> 00:32:51
like this: five prime, T,
A, A, T, T, C, T, and the

440
00:32:51 --> 00:32:58
template strand here, A, T,
T, A, A, G, A, now let's keep

441
00:32:58 --> 00:33:05
going, A, T, G,
C, C, A, A, T, G,

442
00:33:05 --> 00:33:14
G, A, T, T, A, five prime.
So, there's my primer.

443
00:33:14 --> 00:33:26
There's my template. I'm going
to start adding. Well, let's

444
00:33:26 --> 00:33:37
add our polymerase.
Let's add our dNTPs,

445
00:33:37 --> 00:33:47
polymerase, dATP, dCTP, dTTP,
dGTP, and then I want to add a

446
00:33:47 --> 00:33:58
special extra good old
ingredient into this.

447
00:33:58 --> 00:34:07
The special extra ingredient
I want to add is a defective T,

448
00:34:07 --> 00:34:17
a defective dTTP. What do I mean
by defective? I mean chemically

449
00:34:17 --> 00:34:27
modified in such a way that
it can't be extended, that you

450
00:34:27 --> 00:34:36
can't extend past it. So
now, let's follow my reaction.

451
00:34:36 --> 00:34:44
I'm going to start with, I'm just
going to write them down here,

452
00:34:44 --> 00:34:52
T, A, A, T, T, C, T. What's the
next base I'm going to put in?

453
00:34:52 --> 00:35:00
T, OK? Is that a defective
T or a good T? I don't know.

454
00:35:00 --> 00:35:05
It could be. Maybe it's a defective
T, which I'll put a little star

455
00:35:05 --> 00:35:11
there, OK? If so, what
happens to my polymerase?

456
00:35:11 --> 00:35:17
It stops. It can't go any further.
It can't go any further because the

457
00:35:17 --> 00:35:22
T's defective. But what
if it wasn't a defective T?

458
00:35:22 --> 00:35:28
What if it was a good T? Then
what goes on? The polymerase

459
00:35:28 --> 00:35:34
will put in, keep going guys. A,
C, G, G, and what does it put in

460
00:35:34 --> 00:35:39
now? T,
right? Now,

461
00:35:39 --> 00:35:45
is that a defective T?
Maybe. We don't know.

462
00:35:45 --> 00:35:50
If it is a defective T,
it stops there. Otherwise,

463
00:35:50 --> 00:35:56
polymerase goes here, and
the next space is what?

464
00:35:56 --> 00:36:02
T, and is that a
defective T? Maybe.

465
00:36:02 --> 00:36:09
And, if it's not a defective T,
then polymerase goes on, puts in an

466
00:36:09 --> 00:36:16
A, puts in a G, a
C, C, and then a T.

467
00:36:16 --> 00:36:23
And maybe that's defective.
All right, which of these

468
00:36:23 --> 00:36:31
possibilities is what polymerase
does when I throw it in?

469
00:36:31 --> 00:36:35
Well, all of them. There's
a lot of molecules there.

470
00:36:35 --> 00:36:39
Some of the molecules, by chance,
happen to install a defective T,

471
00:36:39 --> 00:36:43
and they grind to a halt here.
Sometimes, a good T's put in and the

472
00:36:43 --> 00:36:47
molecules stop here.
Sometimes they stop here,

473
00:36:47 --> 00:36:51
and if I start with a big collection
of primers in a lot of my template

474
00:36:51 --> 00:36:55
DNA, I'm going to get this whole
collection of different molecules of

475
00:36:55 --> 00:36:59
different lengths.
What lengths do I get?

476
00:36:59 --> 00:37:04
The lengths correspond precisely
to the positions of the Ts.

477
00:37:04 --> 00:37:10
I get a series of molecules
whose lengths perfectly match the

478
00:37:10 --> 00:37:16
positions of Ts.
Well, first off,

479
00:37:16 --> 00:37:23
how do I measure their lengths?
Run a gel, bingo, run a gel.

480
00:37:23 --> 00:37:30
So, if I could run a gel that could
separate nucleotides based on length

481
00:37:30 --> 00:37:37
that two next to each other,
another one up there, I'd see a

482
00:37:37 --> 00:37:44
small molecule,
length one, two,

483
00:37:44 --> 00:37:51
three, four, five, three,
six, eight, I'd see one of

484
00:37:51 --> 00:37:58
length eight. I'd see one of
length, what's the next one,

485
00:37:58 --> 00:38:05
13, eight, nine, ten,
13, 14, so eight, nine,

486
00:38:05 --> 00:38:12
ten, 11, 12, 13, 14, 15,
what's that, 13, 14, 15, 16,

487
00:38:12 --> 00:38:18
17, 18. OK, those would
be the positions at

488
00:38:18 --> 00:38:22
which I would see this T. So,
I'd need to have a special kind

489
00:38:22 --> 00:38:26
of gel that's so accurate that it
can separate single nucleotides,

490
00:38:26 --> 00:38:31
right, that the lengths,
but that can be done.

491
00:38:31 --> 00:38:36
There's acrylamide, the
polymer that will do that.

492
00:38:36 --> 00:38:41
That'll tell me the exact lengths
of the T's. What else do I do?

493
00:38:41 --> 00:38:46
Well, let's obviously do
it from the other bases.

494
00:38:46 --> 00:38:52
Let's try defective A,
defective C, defective G.

495
00:38:52 --> 00:38:57
Let's see, if I got it right,
which we'll try, it ought to end up

496
00:38:57 --> 00:39:02
looking something like that.
And if not, you get the picture,

497
00:39:02 --> 00:39:07
that this ought to match up as to
which columns have which lengths.

498
00:39:07 --> 00:39:13
OK, I think I got it right.
That tells me the lengths of the

499
00:39:13 --> 00:39:18
molecules. So, I could
read off at sequence.

500
00:39:18 --> 00:39:23
The sequence of that molecule
ought to be, starting over there,

501
00:39:23 --> 00:39:29
the sequence of what I've added in,
ought to be something like T, A, C,

502
00:39:29 --> 00:39:34
G, G, T, T, A, C,
C, T, yep, it worked.

503
00:39:34 --> 00:39:39
It's exactly right. Bingo.
I can now read the sequence.

504
00:39:39 --> 00:39:44
Fred Sanger, a brilliant scientist,
thought up this method of just

505
00:39:44 --> 00:39:49
exploiting E coli's own polymerase
or other organism's own polymerases.

506
00:39:49 --> 00:39:54
So, copying and all the chemistry
that had to be done was thinking up

507
00:39:54 --> 00:40:00
a defective nucleotide
that could not be extended.

508
00:40:00 --> 00:40:10
It could obviously be inserted.
It can't be extended. So, one

509
00:40:10 --> 00:40:20
question is, what's a
defective nucleotide? Well,

510
00:40:20 --> 00:40:30
you will recall that our nucleotide
in the sugar phosphate chain

511
00:40:30 --> 00:40:37
is sitting like this. Let's
see, hanging off the one prime

512
00:40:37 --> 00:40:42
carbon is the base. This
is the one prime carbon,

513
00:40:42 --> 00:40:47
the two prime carbon, the three
prime carbon, the four prime carbon,

514
00:40:47 --> 00:40:52
the five prime carbon. What do we
know in DNA at the two prime carbon?

515
00:40:52 --> 00:40:57
Normally in ribose there
would be a hydroxyl here,

516
00:40:57 --> 00:41:02
right? But in deoxyribose,
there's just a hydrogen.

517
00:41:02 --> 00:41:11
So, if this is deoxyribose, so
a dNTP really means a two prime

518
00:41:11 --> 00:41:20
deoxyribose, where do I now attach
my next base in the sugar phosphate

519
00:41:20 --> 00:41:30
train? Three prime ends, and
what do I attach it to: the OH.

520
00:41:30 --> 00:41:35
What do you think would
happen if there's no OH there?

521
00:41:35 --> 00:41:40
You're stuck. All you've got
to do is take off that hydroxyl.

522
00:41:40 --> 00:41:45
No hydroxyl group. If you made
nucleotides that don't have that

523
00:41:45 --> 00:41:50
hydroxyl group, they
can't be extended.

524
00:41:50 --> 00:41:55
So, instead of these being just
deoxy at the two prime position,

525
00:41:55 --> 00:42:00
they are dideoxy,
deoxy at two positions.

526
00:42:00 --> 00:42:04
They are two prime, three
prime, dideoxynucleotides.

527
00:42:04 --> 00:42:09
That's it. Now, if you needed
to get two prime three prime

528
00:42:09 --> 00:42:13
dideoxynucleotides, they're
in the catalogue of course,

529
00:42:13 --> 00:42:18
right, because Fred Sanger had
to make them himself and all that,

530
00:42:18 --> 00:42:23
but you can just buy them now.
And so, you can do the sequence.

531
00:42:23 --> 00:42:28
A few other little
details here, though, guys.

532
00:42:28 --> 00:42:32
How do we see the DNA and the gel?
One possibility would be staining

533
00:42:32 --> 00:42:37
it. There are some dies
like ethidium bromide,

534
00:42:37 --> 00:42:42
and for doing your restriction
mapping, using a dye that sticks to

535
00:42:42 --> 00:42:47
DNA like ethidium bromide does is
pretty good. And then you put it

536
00:42:47 --> 00:42:52
under fluorescent light and
you look. For sequencing,

537
00:42:52 --> 00:42:57
the amount of DNA is so little that
it's hard to see with a dye by the

538
00:42:57 --> 00:43:02
naked eye, which is what you do
with restriction map. So, sorry?

539
00:43:02 --> 00:43:06
So, the first thing people did was
radioactive. What they did was they

540
00:43:06 --> 00:43:10
took a primer,
made it radioactive,

541
00:43:10 --> 00:43:14
and you did this whole sequencing
reaction with radioactive primer.

542
00:43:14 --> 00:43:18
Then, when you run the gel, you
take your gel and you expose it for

543
00:43:18 --> 00:43:22
some number of hours, eight
hours maybe, a piece of x-ray

544
00:43:22 --> 00:43:26
film, develop the x-ray film,
and you'll see that picture. So,

545
00:43:26 --> 00:43:30
one solution that you could do
to visualize is using radioactive

546
00:43:30 --> 00:43:37
nucleotides. So, we got
the defective nucleotide.

547
00:43:37 --> 00:43:45
We now need to visualize our
DNA. Let's visualize the sequence.

548
00:43:45 --> 00:43:54
One possibility: radioactive.
The second possibility, someone

549
00:43:54 --> 00:44:03
already mentioned
it, a fluorescent dye.

550
00:44:03 --> 00:44:10
Now, here, a fluorescent dye could
be put on, and you can't read it

551
00:44:10 --> 00:44:17
with your eye, but lasers
are very good at reading.

552
00:44:17 --> 00:44:24
So, you might run a whole gel
here and have lasers scan it.

553
00:44:24 --> 00:44:31
But, you can actually do better
than that. Suppose I put my

554
00:44:31 --> 00:44:39
fluorescent dye on
my dideoxynucleotides.

555
00:44:39 --> 00:44:45
Suppose I put it on
my dideoxynucleotides,

556
00:44:45 --> 00:44:52
and suppose I even had enough
chemistry at my disposal that I

557
00:44:52 --> 00:44:59
could put a different color
of fluorescent dye on each

558
00:44:59 --> 00:45:05
of my nucleotides. Then,
whenever the dideoxy is put in

559
00:45:05 --> 00:45:09
to terminate the chain, it
carries with it its own color.

560
00:45:09 --> 00:45:14
Wouldn't that be cool? And, that's
what's done. Not just can you buy

561
00:45:14 --> 00:45:18
dideoxynucleotides now, but
you can buy the four different

562
00:45:18 --> 00:45:23
dideoxynucleotides each with
its own dye attached to it.

563
00:45:23 --> 00:45:27
So, there are di-dideoxies I guess,
sorry, but it's different di's,

564
00:45:27 --> 00:45:32
right? They're dye-dideoxies.
So, you could do that.

565
00:45:32 --> 00:45:36
And then what you get would be that
in this column you get this color.

566
00:45:36 --> 00:45:40
And in this column, you'd get this
color. And in this column you'd get

567
00:45:40 --> 00:45:44
this color, etc. I'm not
worrying about where they

568
00:45:44 --> 00:45:48
are here. And they'd all be
different colors and it would be

569
00:45:48 --> 00:45:52
very pretty. You know what?
Why do we need to run separate

570
00:45:52 --> 00:45:56
lanes anymore?
If we got a laser,

571
00:45:56 --> 00:46:00
we can tell the laser scan
it to tell it different. Stick

572
00:46:00 --> 00:46:05
it in one way. In fact,
what's done is stick it in

573
00:46:05 --> 00:46:13
a capillary tube, throw in
all four at the same time

574
00:46:13 --> 00:46:20
now, and as these fragments come by,
each has its own color. And all we

575
00:46:20 --> 00:46:28
need is a laser scanner capable
of sitting right here. Here's

576
00:46:28 --> 00:46:34
my laser scanner.
And the laser scanner,

577
00:46:34 --> 00:46:40
positive here, negative here,
as the DNA flows by through this

578
00:46:40 --> 00:46:46
polymer, the laser scanner reads
off which colors just went by.

579
00:46:46 --> 00:46:51
And it goes A color, C color,
T color, G color. That's it. So,

580
00:46:51 --> 00:46:57
there are actually machines now
that have 96 different capillaries.

581
00:46:57 --> 00:47:04
These are called capillary tubes.
And you can have 96 of them with

582
00:47:04 --> 00:47:12
laser scanning across,
and in each column now,

583
00:47:12 --> 00:47:20
it turns out that you can
read almost 1,000 letters,

584
00:47:20 --> 00:47:28
1,000 bases per column per capillary
times about 100 capillaries.

585
00:47:28 --> 00:47:36
Or in other words, you can read
out about 10^5 bases of information.

586
00:47:36 --> 00:47:40
You can read out 10^5 bases of
information in about two hours.

587
00:47:40 --> 00:47:45
Of course, you can do
that ten times a day. So,

588
00:47:45 --> 00:47:50
you can actually read out 10^6 or
about a million bases of information

589
00:47:50 --> 00:47:55
per machine. And here at MIT, we
have 100 of these machines. So,

590
00:47:55 --> 00:48:00
we actually can read out a little
shy of 100 million letters of DNA

591
00:48:00 --> 00:48:05
sequence per day,
which I mean is a lot.

592
00:48:05 --> 00:48:11
We read about 40 billion
letters per year here at MIT,

593
00:48:11 --> 00:48:17
and this is how we do it.
How much does a machine cost?

594
00:48:17 --> 00:48:23
List, or do you want a
deal? They list for $300,

595
00:48:23 --> 00:48:29
00, but if you buy in bulk, I
can do better. [LAUGHTER] We buy

596
00:48:29 --> 00:48:34
it in bulk, by the way. So
now, how are we going to get our

597
00:48:34 --> 00:48:38
primer there? That was the only
little bit we were missing is where

598
00:48:38 --> 00:48:42
did our primer come from? The
last little detail: here's my

599
00:48:42 --> 00:48:47
vector, remember, and I
want to sequence this insert.

600
00:48:47 --> 00:48:51
How am I going to get a primer in
the insert? I don't know what its

601
00:48:51 --> 00:48:56
sequence is. How do I even
start this? Sorry? Well,

602
00:48:56 --> 00:49:00
but that won't tell me what
the sequence is that I have to,

603
00:49:00 --> 00:49:05
I mean, I was looking to try to get
a primer that matches the insert.

604
00:49:05 --> 00:49:09
And I don't know what the insert is.
So, how am I going to get a primer?

605
00:49:09 --> 00:49:13
Oh, I know the vector.
The vector is well known.

606
00:49:13 --> 00:49:17
It sequence is in the catalog.
Let me instead just use a primer

607
00:49:17 --> 00:49:21
that happens to sit in the vector,
and I'll match to a known sequence

608
00:49:21 --> 00:49:25
to start with, and then
I'll sequence into my

609
00:49:25 --> 00:49:29
unknown territory. So, this
is how you get the initial

610
00:49:29 --> 00:49:33
primer was you arrange that your
initial primer is sitting in known

611
00:49:33 --> 00:49:37
vector sequence. All right,
so you can now sequence

612
00:49:37 --> 00:49:40
DNA. I've got to say, I've
taught this course for a little

613
00:49:40 --> 00:49:44
more than a decade,
and being able to say,

614
00:49:44 --> 00:49:47
now we can routinely sequence
about a million letters per machine,

615
00:49:47 --> 00:49:50
and 100 million letters per
day, and things like this was not

616
00:49:50 --> 00:49:53
routinely the case. When
we started teaching this

617
00:49:53 --> 49:58
course, I was
describing what we di