Ultra-sensitive microscope reveals DNA processes

New Scientist ^ | November 15, 2005 | Gaia [sic] Vince

[snarks_when_bored]

Ultra-sensitive microscope reveals DNA processes

    * 14:02 15 November 2005
    * NewScientist.com news service
    * Gaia Vince

A new microscope sensitive enough to track the real-time motion of a single protein, right down to the scale of its individual atoms, has revealed how genes are copied from DNA – a process essential to life.

The novel device allows users to achieve the highest-resolution measurements ever, equivalent to the diameter of a single hydrogen atom, says Steven Block, who designed it with colleagues at Stanford University in California.

Block was able to use the microscope to track a molecule of DNA from an E.coli bacterium, settling a long-standing scientific debate about the precise method in which genetic material is copied for use.

The molecular double-helix of DNA resembles a twisted ladder consisting of two strands connected by “rungs” called bases. The bases, which are known by the abbreviations A, T, G and C, encode genetic information, and the sequence in which they appear “spell out” different genes.

Every time a new protein is made, the genetic information for that protein must first be transcribed from its DNA blueprint. The transcriber, an enzyme called RNA polymerase (RNAP), latches on to the DNA ladder and pulls a small section apart lengthwise. As it works its way down the section of DNA, RNAP copies the sequence of bases and builds a complementary strand of RNA – the first step in a new protein.

“For years, people have known that RNA is made up one base at a time,” Block says. “But that has left open the question of whether the RNAP enzyme actually climbs up the DNA ladder one rung at a time, or does it move instead in chunks – for example, does it add three bases, then jump along and add another three bases.

Light and helium

In order to settle the question, the researchers designed equipment that was able to very accurately monitor the movements of a single DNA molecule.

Block chemically bonded one end of the DNA length to a glass bead. The bead was just 1 micrometre across, a thousand times the length of the DNA molecule and, crucially, a billion times its volume. He then bonded the RNAP enzyme to another bead. Both beads were placed in a watery substrate on a microscope slide.

Using mirrors, he then focused two infrared laser beams down onto each bead. Because the glass bead was in water, there was a refractive (optical density) difference between the glass and water, which caused the laser to bend and focus the light so that Block knew exactly where each bead was.

But in dealing with such small objects, he could not afford any of the normal wobbles in the light that occur when the photons have to pass through different densities of air at differing temperatures. So, he encased the whole microscope in a box containing helium. Helium has a very low refractive index so, even if temperature fluctuations occurred, the effect would be too small to matter.

One by one

The group then manipulated one of the glass beads until the RNAP latched on to a rung on the DNA molecule. As the enzyme moved along the bases, it tugged the glass bead it was bonded too, moving the two beads toward each together. The RNAP jerked along the DNA, pausing between jerks to churn out RNA transcribed bases. It was by precisely measuring the lengths of the jerks that Block determined how many bases it transcribed each time.

“The RNAP climbs the DNA ladder one base pair at a time – that is probably the right answer,” he says.

“It’s a very neat system – amazing to be able see molecular details and work out how DNA is transcribed for the first time,” said Justin Molloy, who has pioneered similar work at the National Institute for Medical Research, London. “It’s pretty incredible. You would never have believed it could be possible 10 years ago.”

Journal reference: Nature (DOI: 10.1038/nature04268)

[Kelly_2000]

"It appears I have struck a nerve with you"

No I just am a little unsure why you seem to be pointedly ignoring my previous posts? Why is that?

again it's in post 677 :-)

[Kelly_2000]

"So since it is obvious that you don't want to answer any of the questions"

Bizarre? I again mention for the 5th time now that I have responded to you in post 677 can you please take a look.

[b_sharp]

Thanks for the reply and the compliment.

Now if Darwin Central would notice my work...

[P-Marlowe]

OK thats fine please proceed to post 677 where I presented my views and perspectives unambiguously and in crystal clarity. I look forward to hearing your informed opinions after that :-)

So it appears that you do believe that God wrote the 10 Commandments (as found in Exodus Chapter 20) on the Tablets of Stone with his own hand?

If so, then do you accept God's own word as recorded on those stone tablets as to how he created the heavens and the earth and all that in them is?

If so, how do you reconcile that with your denial of intelligent design?

[P-Marlowe]

Bizarre? I again mention for the 5th time now that I have responded to you in post 677 can you please take a look.

Sorry, when I ask a yes or no question I usually look to see whether there is a yes or no answer. :-)

[Fester Chugabrew]

No, that IS your view . . .

On the contrary, it is you who maintains the known universe cannot be explained in terms of intelligent design and yet remain "scientific." Do you really think intelligence is beyond the realm of scientific inquiry? Your view of science is both warped and truncated. As I said, must be awfully dsutned in that sbrtl;ijbELE.

[Kelly_2000]

"If so, then do you accept God's own word as recorded on those stone tablets as to how he created the heavens and the earth and all that in them is?"

The account of Genesis and creation was not on the stone tablets the 10 commandments where.

Intelligent Design is not a theory from the Bible it is a theory from men.

[js1138]

TRVTH or consequenses; that is the question.

[Kelly_2000]

"Sorry, when I ask a yes or no question I usually look to see whether there is a yes or no answer. :-)"

OK we made progress so there is hope for us yet ;-)

[js1138]

Now if Darwin Central would notice my work...

Everything was pine fresh this morning.

[CarolinaGuitarman]

"On the contrary, it is you who maintains the known universe cannot be explained in terms of intelligent design and yet remain "scientific."

That's not the argument from incredulity, which you have explicitly accepted as valid. I said that all such claims are outside of science. They are.

" Do you really think intelligence is beyond the realm of scientific inquiry? "

You are switching the argument. We are talking about the existence of God, not intelligence.

Now, are you going to enlighten us with YOUR definition of what design is? If you can't even define it, how can you detect it from an entity whose motives and capabilities are inscrutable?

"Your view of science is both warped and truncated."

You're view is mystical and subjective and includes anything and everything into science, including your feelings, hallucinations, feverish delusions, and logical fallacies. I'll stick with my view, which is what has been accepted and used in science for centuries now.

"As I said, must be awfully dsutned in that sbrtl;ijbELE."

Time to put down that drink and answer my question about the definition of design which I have asked you over and over. I'll have to assume you have none if you refuse again.

[b_sharp]

I have a good idea of what it takes to practice science. I asked you what your definition of science is and what methodology you would use because your definition appears to be different than that used by scientists. I would appreciate if you would tell me/us what your vision of science is so that I can better understand your posts.

"Also, once you do, please elaborate upon how they can exist apart from either intelligence or design.

Again, let me point out we are concerned with the current version of ID which claims to be able to differentiate between designed and naturally(undesigned) formed events and objects. It does not refer to the intelligence or design inherent in procedures used by either science or ID. You seem to be either confusing or conflating the two.

[BlueStateDepression]

(("Don't you see the beauty of it all? ))"

Sir I see no beauty in being threatened into compliance with anothers will while being told that bowing to that threat of punishment is done by my own accord.

If the path to take is right and proper I need no threat to follow it. When a path is threatening I will do one of two things, I will seek another path, or I will stand tall in directly opposing that threat.

Threat in order to impose will is agression. I do not bow to agression and threat nor do I consider doing so to be a 'beautiful thing'.

[Vinnie]

Amazing how this was initiated by millions, maybe tens, hundreds of millions of chance encounters before it finally got it right.

[Kelly_2000]

WELL said the path of threat or compliance is that of Islam not Christianity

[BlueStateDepression]

(("Once He shows His face "in no uncertain terms," it's over. Good news for those who know He's been on our side all along. Bad news for those who deny His existence or think they can earn His favor by good works."))

Do you mean the Game is over? I would offer that is a very GOOD thing. If good works do not earn favor then so be it. That , to me, is just another reason why worship is unfounded. For those that do good works are the ones that i find honorable. Those that care not about good works are those I find dishonorable.

[BlueStateDepression]

Absolutely look for truth. When it comes to the subject of God, it seems some of the truth found so far is a bit less than honorable.

[airborne]

Next time I'll no better than to read a science thread here.

What a dummy I turned out to be. 8^(

[Kelly_2000]

"If good works do not earn favor then so be it."

this accounting you are being given is wrong, the bible is full of examples of people with good hearts and honorable existences that where NOT Christian becoming friends or saved by Jesus.

The criminal on the cross for example also see the parable of the Good Samaritan

Churches or religions that preach convert or die messages are false in my opinion and revolting

[BlueStateDepression]

WOW, thanks for that tidbit, I find that most exciting.

It gives me hope that one day we might just be able to in the scale required. Sounds as if it is really just a matter of time. A guy can have hope right? :)