1
00:00:06,310 --> 00:00:08,180
So far, there are a lot of
ways to clone genes.

2
00:00:08,180 --> 00:00:09,240
I've given you two.

3
00:00:09,240 --> 00:00:12,060
Later in the course, I'll give
you a third, but we cloned it

4
00:00:12,060 --> 00:00:13,870
here by its function,
complementation.

5
00:00:13,870 --> 00:00:15,350
We cloned it here on
the basis of the

6
00:00:15,350 --> 00:00:17,275
protein it actually made.

7
00:00:17,275 --> 00:00:19,580
Now, how do we analyze
these genes?

8
00:00:19,580 --> 00:00:21,270
How do you know which gene
we're dealing with?

9
00:00:21,270 --> 00:00:22,630
How do we study it?

10
00:00:22,630 --> 00:00:23,850
Let's turn to that.

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Analyzing our gene.

12
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Well, let's suppose we
have our cell, maybe

13
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it's our yeast cell.

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It's Arg1 again.

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We'll go back to yeast.

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It's got its yeast DNA it's also
got this circle that has

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our plasmid here.

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00:00:46,260 --> 00:00:48,250
Circle is plasmid.

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How are we going to
study that gene?

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00:00:50,020 --> 00:00:52,350
We know that yeast is
able to now grow.

21
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We can grow up that yeast.

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We can purify DNA from it.

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But wait a second.

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How do we get our plasmids away
from the chromosomal DNA?

25
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Aren't we back in the same
boat of you can't

26
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purify DNA from DNA?

27
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Thankfully, this is easy.

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Little circles of DNA have
different biochemical

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properties than the long, linear
chromosomes or the big

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chunks of DNA.

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And you can use biochemistry to
separate little circles of

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DNA from big chunks of DNA.

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So no problem.

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You can purify the plasmids.

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Purify the plasmid,
and there it is.

36
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It's back again.

37
00:01:32,100 --> 00:01:35,230
And now, you've got
your Arg1 gene.

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How do I study it?

39
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Well, the first thing I might
want to find out about my Arg1

40
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gene, is how big
is that insert.

41
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How can I find out how
big that insert is?

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00:01:47,445 --> 00:01:48,355
AUDIENCE: Electrophoresis.

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ERIC LANDER: Electrophoresis.

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I first have to cut
out the insert.

45
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How do I do that?

46
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AUDIENCE: The restriction
enzyme.

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ERIC LANDER: My restriction
enzyme, EcoRI.

48
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I cut with EcoRI and it
liberates the insert.

49
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And then I take a gel, which can
be made out of different

50
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substances, and I put
my DNA there.

51
00:02:10,470 --> 00:02:13,510
Agarose is particularly nice
stuff, which is basically

52
00:02:13,510 --> 00:02:17,980
Jell-O. And I turn on
an electric field.

53
00:02:17,980 --> 00:02:20,260
DNA is what, positively charged
or negatively charged?

54
00:02:20,260 --> 00:02:21,180
AUDIENCE: Negative.

55
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ERIC LANDER: So what kind of
charge do I want to put here?

56
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AUDIENCE: Positive.

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00:02:24,290 --> 00:02:25,550
ERIC LANDER: What charge
do I put here?

58
00:02:25,550 --> 00:02:26,265
AUDIENCE: Negative.

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00:02:26,265 --> 00:02:28,780
ERIC LANDER: What happens
if I do it backwards?

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Bad.

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Everybody does it backwards
in the lab at some point.

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So then you do this.

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The DNA goes this way and it
turns out that agarose is this

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matrix of cross links
and all that.

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And DNA molecules wiggle through
like a snake, through

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00:02:46,660 --> 00:02:50,430
this matrix, and little ones go
much faster than big ones.

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So what happens is, little DNA
molecules move faster than big

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00:02:56,930 --> 00:02:58,660
DNA molecules.

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And if I stop at some point, and
I add a dye that sticks to

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DNA, and look at it with a
fluorescent light, I can

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00:03:05,850 --> 00:03:08,520
actually see where the
DNA molecules are.

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So I've grown up a ton of this
plasmid, lots of it, couple of

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00:03:11,850 --> 00:03:13,050
micrograms of it.

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I cut it, I add it to the top of
my well here, I turn on the

75
00:03:16,260 --> 00:03:20,330
electricity, and it wiggle,
wiggle, wiggles through.

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00:03:20,330 --> 00:03:26,180
This is the vector, and
this is the insert.

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It might be actually, that I
found another plasmid that

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could do this too, that
rescued yeast.

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It had a vector and maybe
at a different insert.

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00:03:33,870 --> 00:03:36,455
Maybe I had one, I don't know
why, that had the same insert

81
00:03:36,455 --> 00:03:37,490
right there.

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00:03:37,490 --> 00:03:39,810
In any case, the first
characterization that I would

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00:03:39,810 --> 00:03:43,470
do is look at the size
of my insert.

84
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How big is that insert?

85
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I might find out that the insert
is one kilobase, 1,000

86
00:03:59,450 --> 00:04:06,740
bases, or one KB, or 2 KB
or something like that.

87
00:04:06,740 --> 00:04:08,975
That's a first order of
characterization.

88
00:04:08,975 --> 00:04:10,580
Now, of course, what I
really want to know

89
00:04:10,580 --> 00:04:13,950
about the insert, sequence.

90
00:04:13,950 --> 00:04:15,910
I want the DNA sequencing
insert, right?

91
00:04:15,910 --> 00:04:18,050
Let's not just mess around with,
it's got 1,000 bases, I

92
00:04:18,050 --> 00:04:20,110
want to know what are those
bases in what order.

93
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So that means I have to
invent DNA sequencing.

94
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All right.

95
00:04:33,790 --> 00:04:36,350
So how am I going to invent
DNA sequencing?

96
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This is a little tough.

97
00:04:38,550 --> 00:04:40,265
I have my piece of DNA.

98
00:04:40,265 --> 00:04:42,280
I cut it out.

99
00:04:42,280 --> 00:04:48,772
Here's my piece of DNA,
5 prime to 3 prime,

100
00:04:48,772 --> 00:04:50,090
5 prime to 3 prime.

101
00:04:52,900 --> 00:05:03,330
Let's give it a sequence
ATTAAGAATGCAT, et cetera.

102
00:05:07,370 --> 00:05:11,620
DNA sequencing is actually
remarkably cute.

103
00:05:11,620 --> 00:05:16,370
I take a primer just like
Kornberg did back when he was

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00:05:16,370 --> 00:05:18,880
discovering polymerase.

105
00:05:18,880 --> 00:05:21,450
Here's my primer, let's say.

106
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Here's my primer.

107
00:05:25,730 --> 00:05:26,980
Here's the matching template.

108
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And what did Kornberg
teaches us?

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He taught us that if we add
polymerase, what will

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00:05:35,110 --> 00:05:38,040
polymerase do?

111
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It'll add the right
bases, right?

112
00:05:39,910 --> 00:05:46,910
TACGTA onward.

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If we could look really fast,
maybe we could just

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see it going by.

115
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But we can't look really fast.

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If we just add polymerase,
it'll just zip up

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and add all the bases.

118
00:06:03,500 --> 00:06:06,590
But someone had a
clever trick.

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The clever trick is this.

120
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Suppose I threw in a smidgen
of defective Ts, Ts that

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00:06:16,860 --> 00:06:18,550
couldn't be extended
for some reason?

122
00:06:21,060 --> 00:06:22,310
I'll call that T star.

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00:06:28,480 --> 00:06:30,640
What happens if a defective
T goes in there?

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00:06:33,700 --> 00:06:34,950
Can't be extended anymore.

125
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And what happens then
to my reaction?

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It comes to a halt.

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00:06:43,560 --> 00:06:47,520
Ah, but what happened if
I put in a good T?

128
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Then instead, what would
the next base be?

129
00:06:55,232 --> 00:06:59,780
A. Then what would happen?

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00:06:59,780 --> 00:07:05,470
C, G. Then what's next?

131
00:07:05,470 --> 00:07:10,460
T. And what would happen if
I put in a defective T?

132
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It would stop.

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Now, maybe instead the defective
T didn't go in.

134
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And it would go on, and the
next T that it encounters,

135
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maybe it would put a
defective T there.

136
00:07:42,480 --> 00:07:46,750
Or maybe it would put
a defective T there.

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00:07:49,830 --> 00:07:51,520
Now, of course, I just have
a little smidgen of

138
00:07:51,520 --> 00:07:54,020
defective T, right?

139
00:07:54,020 --> 00:07:55,650
So which of these will happen?

140
00:07:55,650 --> 00:07:58,920
Will it sometimes stop
at the first T?

141
00:07:58,920 --> 00:08:01,160
Sometimes at the second?

142
00:08:01,160 --> 00:08:02,410
Sometimes at the third?

143
00:08:05,190 --> 00:08:08,260
I'll actually get a series
of molecules.

144
00:08:08,260 --> 00:08:12,350
What will the lengths of those
molecules tell me?

145
00:08:12,350 --> 00:08:13,820
Where the Ts are.

146
00:08:17,960 --> 00:08:19,710
Kind of cute.

147
00:08:19,710 --> 00:08:21,890
This is very cute.

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00:08:21,890 --> 00:08:29,340
So if I do that reaction, I'll
call that the defective Ts, I

149
00:08:29,340 --> 00:08:33,260
could see that there is some
molecules, stop here at this

150
00:08:33,260 --> 00:08:36,150
very small size, some stop here,
some stop here, some

151
00:08:36,150 --> 00:08:37,890
stop there, some stop there.

152
00:08:37,890 --> 00:08:40,010
And what have I just learned?

153
00:08:40,010 --> 00:08:43,950
The sizes, the lengths of the
fragments that end in T.

154
00:08:43,950 --> 00:08:44,700
But that's not good.

155
00:08:44,700 --> 00:08:47,352
I also want to know the As.

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00:08:47,352 --> 00:08:49,090
AUDIENCE: Do it with
defective As.

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00:08:49,090 --> 00:08:50,910
ERIC LANDER: Do it will
defective As, right?

158
00:08:50,910 --> 00:08:54,180
I'll just use defective As.

159
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And then I'll see the
As stop there.

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00:08:58,520 --> 00:09:00,540
And then I'll do it with
defective Cs, and I'll do it

161
00:09:00,540 --> 00:09:02,540
with defective Gs.

162
00:09:02,540 --> 00:09:06,570
And I'll see exactly where the
molecules are, the lengths of

163
00:09:06,570 --> 00:09:14,090
the molecules that end
in A, T, C, and G.

164
00:09:14,090 --> 00:09:17,620
And I've just read the
sequence, haven't I?

165
00:09:17,620 --> 00:09:19,180
Pretty cool.

166
00:09:19,180 --> 00:09:21,010
This actually is so cool,
it won a Nobel Prize.

167
00:09:23,730 --> 00:09:26,152
I mean cool usually means won
a Nobel Prize or something

168
00:09:26,152 --> 00:09:27,980
like that in this class.

169
00:09:27,980 --> 00:09:30,300
So actually, how do
I visualize the

170
00:09:30,300 --> 00:09:32,520
little letters there?

171
00:09:32,520 --> 00:09:35,780
So the little fragments
on the gel?

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00:09:35,780 --> 00:09:37,480
I visualize the little
fragments back in

173
00:09:37,480 --> 00:09:39,076
ancient days, yes?

174
00:09:39,076 --> 00:09:41,992
AUDIENCE: How do you
know [INAUDIBLE]

175
00:09:45,394 --> 00:09:47,518
necessarily be inserted
in every place

176
00:09:47,518 --> 00:09:48,768
where there is a letter?

177
00:09:50,740 --> 00:09:52,500
ERIC LANDER: I'd make
the right ratio.

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00:09:52,500 --> 00:09:55,290
I'd choose a ratio of defective
to good Ts.

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00:09:55,290 --> 00:09:58,510
Like if I choose 1% defective
T's, then about 1% of the

180
00:09:58,510 --> 00:10:00,920
time, I put in the defective
T it turns out.

181
00:10:00,920 --> 00:10:02,560
It turns out to work OK.

182
00:10:02,560 --> 00:10:06,020
I just put in a smidgen of
defective Ts, like 1%, and 1%

183
00:10:06,020 --> 00:10:09,260
of the time it stops here, and
1% here, and 1% there.

184
00:10:09,260 --> 00:10:13,670
So and then, of course, to see
them in old days, what people

185
00:10:13,670 --> 00:10:17,540
did was they made these primers
radioactive, and these

186
00:10:17,540 --> 00:10:22,050
radioactive primers here within
the gel would be held

187
00:10:22,050 --> 00:10:25,380
up against a piece of x-ray
film, and you would see where

188
00:10:25,380 --> 00:10:27,660
little radioactive bands were.

189
00:10:27,660 --> 00:10:29,690
That's how you could visualize
the primers, because it turns

190
00:10:29,690 --> 00:10:31,460
out you have too little primer
to see it even with my

191
00:10:31,460 --> 00:10:32,620
fluorescent dye.

192
00:10:32,620 --> 00:10:36,430
But a little radioactivity,
you add radioactivity, you

193
00:10:36,430 --> 00:10:39,480
take the gel off, you put on a
piece of, I guess you've got

194
00:10:39,480 --> 00:10:40,690
to wrap it with Saran.

195
00:10:40,690 --> 00:10:42,045
You'd better be standing
behind a shield.

196
00:10:42,045 --> 00:10:44,060
So you're standing behind a
plastic shield, you reach

197
00:10:44,060 --> 00:10:46,510
around the shield, you wrap
it with Saran Wrap.

198
00:10:46,510 --> 00:10:48,340
You then put x-ray film on.

199
00:10:48,340 --> 00:10:49,760
You are you doing this
in a dark room.

200
00:10:49,760 --> 00:10:50,980
You then seal it up.

201
00:10:50,980 --> 00:10:52,600
You put it in the freezer
for two weeks.

202
00:10:52,600 --> 00:10:53,210
You take it out.

203
00:10:53,210 --> 00:10:54,050
You develop it.

204
00:10:54,050 --> 00:10:56,380
You get your magic marker, and
you follow where all the

205
00:10:56,380 --> 00:10:58,160
little bands are.

206
00:10:58,160 --> 00:10:59,410
And that's DNA sequencing.

207
00:11:03,300 --> 00:11:03,660
It's cool.

208
00:11:03,660 --> 00:11:04,355
It won a Nobel Prize.

209
00:11:04,355 --> 00:11:07,160
It's also like really tedious.

210
00:11:07,160 --> 00:11:13,490
So little tricks were done to
speed it up, some nice pieces

211
00:11:13,490 --> 00:11:15,910
of engineering.

212
00:11:15,910 --> 00:11:30,620
Instead of visualizing our DNA,
faster DNA sequencing,

213
00:11:30,620 --> 00:11:31,870
what happens instead?

214
00:11:35,270 --> 00:11:38,640
What people did, which was very
cool, was they simply

215
00:11:38,640 --> 00:11:43,390
took the As, Ts, Cs and Gs,
the defective ones, they

216
00:11:43,390 --> 00:11:47,150
attached a colored
dye to each one.

217
00:11:47,150 --> 00:11:51,810
The As were green, and the Ts
were blue and the Gs were red.

218
00:11:51,810 --> 00:11:56,900
Now, when I run it out, I can
do it with fluorescence.

219
00:11:56,900 --> 00:12:00,900
And I can see the Ts all glow
one color, and the As glow

220
00:12:00,900 --> 00:12:02,750
another color.

221
00:12:02,750 --> 00:12:06,340
Now, it turns out, of course,
if they're glowing four

222
00:12:06,340 --> 00:12:10,090
different colors, I don't
actually need to run them in

223
00:12:10,090 --> 00:12:12,330
separate lanes.

224
00:12:12,330 --> 00:12:14,780
I could run them in the
same lane, right?

225
00:12:14,780 --> 00:12:29,950
So I could run them all in a
single lane, and I'd see Ts

226
00:12:29,950 --> 00:12:33,753
and As, and Gs.

227
00:12:37,560 --> 00:12:43,500
And now, instead of putting this
up against the piece of

228
00:12:43,500 --> 00:12:45,800
x-ray film, I could do
this in a very thin

229
00:12:45,800 --> 00:12:47,050
tube called a capillary.

230
00:12:53,810 --> 00:12:57,960
And instead of holding it up to
an x-ray film, I could just

231
00:12:57,960 --> 00:12:59,210
put a laser detector.

232
00:13:03,170 --> 00:13:06,975
I can turn on the electricity
and watch the fragments go by

233
00:13:06,975 --> 00:13:09,200
and just look at it with
my laser detector.

234
00:13:09,200 --> 00:13:09,890
Shines a light.

235
00:13:09,890 --> 00:13:12,900
I say, oh yeah, green,
red, blue.

236
00:13:12,900 --> 00:13:15,440
That's the sequence.

237
00:13:15,440 --> 00:13:18,020
This made it a lot
easier than that.

238
00:13:18,020 --> 00:13:20,070
I actually got involved in
molecular biology when it was

239
00:13:20,070 --> 00:13:22,680
still that.

240
00:13:22,680 --> 00:13:24,120
That is a lot better.

241
00:13:29,540 --> 00:13:31,750
By the way, I didn't tell
you what the defective

242
00:13:31,750 --> 00:13:33,148
Ts were, did I?

243
00:13:33,148 --> 00:13:36,284
AUDIENCE: [INAUDIBLE].

244
00:13:36,284 --> 00:13:37,230
ERIC LANDER: Sorry?

245
00:13:37,230 --> 00:13:38,565
AUDIENCE: [INAUDIBLE].

246
00:13:38,565 --> 00:13:40,490
ERIC LANDER: Well, they gotta
have something that prevents

247
00:13:40,490 --> 00:13:43,380
them from being extended,
right?

248
00:13:43,380 --> 00:13:44,920
What prevents them from
being extended?

249
00:13:44,920 --> 00:13:50,710
Do we remember how
DNA is extended?

250
00:13:50,710 --> 00:13:53,390
We have a sugar phosphate
backbone, right?

251
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Phosphate, base, 5 prime.

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Where do we extend, what base?

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3 prime.

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00:14:08,300 --> 00:14:11,400
And what do we use
to extend on?

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The 3 prime hydroxyl.

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00:14:13,670 --> 00:14:16,970
Remember, DNA has no hydroxyl
at its 2 prime position.

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Its normal DNA is
2 prime deoxy.

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How do you think we prevent
it from being extended?

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00:14:30,536 --> 00:14:32,410
AUDIENCE: 2 prime [INAUDIBLE].

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ERIC LANDER: 2 prime,
3 prime dideoxy.

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Defective just means 2 prime,
3 prime dideoxy.

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00:14:47,220 --> 00:14:49,140
See, we tell you about these
structure not just so you

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00:14:49,140 --> 00:14:51,430
memorize structures, but because
those are the tricks

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00:14:51,430 --> 00:14:52,580
we use in the trade.

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00:14:52,580 --> 00:15:01,260
Now, you get yourself some 2
prime, 3 prime dideoxies.

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You put in a smidgen,
maybe 1%.

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You run your reaction.

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00:15:05,020 --> 00:15:09,120
Those dideoxies have dyes,
spelled differently, D-Y-E

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00:15:09,120 --> 00:15:11,250
color dyes attached to them.

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00:15:11,250 --> 00:15:14,190
And you sit there with
your laser detector.

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Turns out to be even better.

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If you have one capillary,
you could have two.

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00:15:20,270 --> 00:15:22,670
If you have two, you could have
three, and the machines

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that were built around 1999
had 96 capillaries.

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I'll call it 100.

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00:15:37,620 --> 00:15:45,060
You could sit there and read
700 bases every hour.

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00:15:48,480 --> 00:15:51,640
You can do this maybe
20 hours in the day

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00:15:51,640 --> 00:15:52,890
because it's automated.

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You could do this
360 days a year.

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And at MIT, we had 100 machines
during the Human

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Genome Project.

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And if you do the arithmetic, we
could read about 60 billion

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bases a year, 60 billion bases
a year during the height of

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00:16:27,610 --> 00:16:28,860
the Human Genome Project.

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00:16:35,900 --> 00:16:52,650
Now, this is pretty cool, but
it ain't nothing compared to

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what we're doing
10 years later.

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00:16:56,490 --> 00:17:12,250
Currently, we are doing
60 billion bases every

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00:17:12,250 --> 00:17:17,039
10 minutes at MIT.

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00:17:20,819 --> 00:17:25,010
There's a little trick that I'll
tell you about next time

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of how DNA sequencing went from
that, where you could do

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00:17:29,500 --> 00:17:34,110
about 250 letters a day, when I
first got involved in this,

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00:17:34,110 --> 00:17:37,420
to that, where at a large
facility like MIT, you could

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00:17:37,420 --> 00:17:41,330
do 60 billion letters a day, to
today when you can do about

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00:17:41,330 --> 00:17:43,750
60 billion letters
in 10 minutes.

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We'll touch on that next time.