>> OK, so, hopefully that wasn't too painful.

I realize it might have been--

if you even put your name on the piece of paper,

you will get some points that I promise you.

In addition, next time I say that there's something I'd

like you go look up, I hope you take I mores [phonetic]--

you take it seriously.

But don't panic.

Hopefully, that's not too painful.

Let me just tell you very quickly the answers, OK?

So, last time we saw that half life of DNA was

on the order of 220 million years.

And I challenge you to go out and find

out what it-- had to measure it.

And at least one person came to my office hour with the solution

which is to heat the DNA so you can heat it up

and to the high temperature, measure the half life

at the higher temperature and extrapolate back

to the lower temperature.

And you don't have to provide me with a lot of equations

to show that that's true.

But if you just write heat on probably--

number two, I will accept it, OK?

But again, if you have your name on a sheet of paper

with your UCI ID number, we'll give--

you'd get at least some points, OK?

OK. All right, we're back to normal stuff now.

I want to pick up where we left off last time.

We were talking about structure of DNA and reactivity of DNA,

and we saw last time-- oh gees.

What happened here?

One moment.

I just [inaudible] this.

OK, we saw last time a lot about Watson-Crick based-pairing

and structures of DNA.

And it's B-DNA form.

Now, one thing I got asked about immediately

after the lecture was, you know,

ethidium bromide is commonly considered to be a carcinogen.

This molecule over here that we discussed as an interculator

of DNA is also a carcinogen.

It's a molecule that causes cancer and that's the reason why

when we work with it in the laboratory, over here,

we're exceptionally careful to keep it off of our skin, OK?

Now, yeah, it's a-- it articulates into DNA

and DNA interculators can caused,

can help to initiate carcinogesis, can--

it helps initiate cancer in the following ways.

Number one, it distorts the structure of DNA.

I showed you that on the previous slide over here

where I showed you how the structure of the DNA has

to unwind to accept interculator.

So it distorts the structure of DNA.

Number two, it places a hydrophobic functionality

in the center of the DNA.

This hydrophobic functionality can inappropriately attract

transcription factors to the DNA setting off incorrect

transcription, OK?

So those are two possible modes that this can start to cause--

this can start to initiate improper self responses

that will eventually lead to cancer.

And I want to talk about cancer today.

It's one of the prime topics in this class.

It's something we've already spend quite a bit

of time discussing in many different context

and we'll certainly be talking about it

in the context of DNA, OK?

So, any other questions about what we saw last time.

That was a really good question.

OK, last thought about ethidium bromide,

although it is definitely-- it is a cancer causing agent

and it's something you definitely do not want to ingest

or you definitely want to keep it off your hands.

I don't want to exaggerate its carcinogenic potential.

It's also used as an antibiotic in sheep.

I don't know if it's still is, but it was for a while.

It is-- It does have some other--

and so it's actually fed to sheep.

I don't know why sheep.

But in any case, as a tumor forming agent,

its activity is rather modest specially compared

to the other cancer causing small molecules that we're going

to see very shortly, OK?

All right, well let's dive right in this.

So last time, I was showing you that DNA likes

to form Watson-Crick based-pairing.

This is C binding to Gs.

A is binding to Ts and we saw that GCs,

Watson-Crick based-pairings have three hydrogen bonds

and ATs has only have two, OK?

Now, if we know that AT based-pairs are weaker than GCs,

there's a very simple that we can use to estimate the strength

of any two DNA strands taking together.

This rule is called the Wallace Rule and I'd

like you to memorize it, OK.

The Wallace Rule tells us

that the approximate melting temperature

for DNA sequence is equal to 2 times the number

of AT base pairs plus 4 times the number of GC base pairs

in degree C. This melting temperature is where 50 percent

of the DNA is no longer forming a double-stranded structure.

Let me explain.

So0 when you do a UV/Vis scan of DNA, this is what--

here's what you find, OK?

So this is absorbance on the Y axis and wave length,

the nanometers on the X axis.

And this is single-stranded DNA

and then this is double-stranded DNA in blue.

And to get this, you simply add higher temperature.

So at higher temperature, the DNA stands melt apart.

In other words, they separate out into the two single strands

and so at 82 degrees, this is the single-stranded

and 25 degrees, this is the double-stranded DNA.

Notice that the absorbance at 260 nanometers is higher

for the single-stranded DNA than the double-stranded DNA.

So you can use that change in absorbance to follow whether

or not your DNA is single-stranded

versus double-stranded.

And so, you can do this while at the same time,

you ramp up the temperature and at

about 50 percent-- and so here it is.

Pure double-stranded DNA, lower absorbance and then here it is

at a higher temperature

where it's entirely single-stranded DNA.

And the approximate 50 percent part

where 50 percent is melted is called the melting temperature.

And again, you can estimate what this melting temperature is

using this Wallace rule formula.

People in chemical biology laboratories uses Wallace rule

formula on a daily basis, OK, certainly in my laboratory

and certainly and probably five

or six other laboratories here at UCI Irvine.

So, I'd like you to memorize this rule.

It's incredibly useful.

Now, you're probably wondering, big deal.

So I know whether or not something melts, whether

or not it forms double stranded DNA.

If you know the temperatures

that it forms double-stranded DNA, you can start

to design structures made out of DNA.

Let me show you.

OK. So here are structures of DNA where it's single-strands

of DNA that are now hybridizing against each other

and forming elaborate patterns such as this pattern here.

And here's an atomic force microscope image

of this double-stranded DNA and you could see it's all--

it's forming this exact costly pattern

that was designed using something just a little bit more

complicated than the Wallace rule

which I asked you to memorize, OK?

It gets even better.

Check this out.

OK. So this is worked done by Paul Rothemund and colleagues

and coworkers at Caltech.

And he's using the Wallace rule to design DNA that folds

up into happy faces over here or check out this map

of the world written out of DNA that's been folded

up with itself.

OK. So that Wallace rule that I asked you

to memorize is actually pretty powerful.

You can develop whole structures of that stuff.

Now, exactly what the structures of DNA are going to be useful

for is not a hundred percent known at this point.

There are sort of a frontier

in chemical biology building structures out of DNA

and then trying to do something useful with them.

I've only seen one paper in 20 years of staring

at these beautiful pictures that has convinced me

that maybe there might be something useful about this.

And in that paper this DNA-- a DNA structure like this one,

not the happy face but something elaborate was used

as a delivery vehicle that bound to the surface of cells

and then dislodged drug therapeutic.

And it's possible that our future might feature many more

of these sort of examples of nanometer scale structures

that are designed by you, by the people on this room

to have specific properties such as binding

to specific cell types, unloading cargos

at specific times, et cetera.

This is a really exciting frontier and I encourage you

to think about it in your proposal preparation

because it's an area that's kind of wide open

for creative-- for creativity.

OK, so in addition to those sort of macro structures of DNA

that we saw, short stretches of DNA can also fold

and there's a couple of canonical structures

that we're going to see time and again.

One of these for example is called-- are called hairpins.

One of these is called the hairpin.

And so, these consist of a sequence

that folds back on itself.

Notice that it satisfies all

of the Watson-Crick base pairing requirements, G is to Cs.

A is to Ts and it forms something that looks kind

of like an old-fashioned hairpin.

OK. And it looks structurally like this.

This is the x-ray crystal structure of what it looks like.

And again, we're going to see this quite a bit.

OK. So DNA has a propensity to fold on itself.

It wants to form Watson-Crick base pairs.

It wants to form Watson-Crick base pairs with other sequences.

It wants to form base pairs with itself.

And so for this reason, DNA is rarely found.

It's sort of an unwound

which rarely found a single-stranded DNA

for one thing.

And furthermore, it's rarely found in the sort

of canonical B-DNA conformation that I've been showing you

where it says nice right-handed coiled double helix.

Rather, in cells, we typically find DNA in a wound

up configuration called a supercoil.

So a supercoil is where you take a coil

such as this old-fashioned telephone cord

which I'm sure is unfamiliar to everyone in this room.

But back in my day kids, we used to have this

and it would form the sort of supercoils

and it drove you nuts.

You know, you constantly be on the phone trying

to untangle the darn thing.

In fact, she [phonetic] was kind of a nice thing to do

because if you're on the phone with the tense conversation

or something, it gave you a task to take your mind off

of the annoyances that you're dealing with on the phone.

But anyway, so this is called supercoiling

and this is an example of a DNA plasmid which is a sequence

of DNA that forms a circle.

OK. So this is a nice plasmid DNA and again we rarely find it

in this sort of B-DNA where it's completely unwounded

configuration, rather it likes to twist up.

So here's a little twistiness.

Here's more twistiness, even more twistiness

and then finally even-- the most twistiness.

OK. So that's really the structures of DNA that we find.

For short sequences, we find it wound

up with itself to form hairpins.

I showed you that structure first.

For larger sequences like plasmids,

we find it supercoiling and twisting itself up.

And then for even larger sequences like you carry

out at genomes which I'll show you on the next slide,