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)

[Elsie]

Can I run my car on this?

[b_sharp]

"When physical matter demonstrates patterns of organization and can be categorized into a table of elements that is rarely appended or modified "

I'm sorry, I don't understand what this means. Could you restate it in simpler terms please?

[Elsie]

Maybe snowflakes are so we can make snowmen. :-)

It is obvious to any observer:

Snowflakes Prove that GOD exists and interacts with His creation.

Proof:

---

1. Snow falls in winter

2. Winter is when kids are in school, learning about Evolution is Science classes.

3. God sends the snow (Job 37:6 He says to the snow, 'Fall on the earth,' and to the rain shower, 'Be a mighty downpour.')

4. Whiny liberal twerps fear for our children, and call a snow day.

5. No more Science classes: Evolution is foiled.

Ergo.....

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(Then there are the metaphors..........)

 

 

Psalm 51:7
Cleanse me with hyssop, and I will be clean; wash me, and I will be whiter than snow.

 

Isaiah 1:18
"Come now, let us reason together," says the LORD. "Though your sins are like scarlet, they shall be as white as snow; though they are red as crimson, they shall be like wool.

[BlueStateDepression]

primary determinant of a person's religion was what religion they were "raised as" from childhood.

That is so true and I'll tell ya, my mother still has not come to terms with how I strayed away from that very process. She nails me every holiday calling on me to say prayer before dinner! Really puts me on the spot.

Until then, it looks pretty 'relative' after all

Sure does to me.

He might be an alien from an alternate plane of existence working on his Cosmology 101 term project

I find that valid as an Idea worth exploration. I would need some evidence to discount it.

I would indeed be interested in watching this movie rapture. Thanks for the tip. Ill let you know what i think of it after I see it.

Don't they have any basic ethics of their own?

They may even have them but they need some reason to excercise them other than.....well, it's the RIGHT thing to do. It astounds me how common it is for that simple bit of common sense is so often overlooked. Could it be that common sense is not so common after all?

methods which could be used to build and refine a body of knowledge which was reliable, usable, and effective.

(from the post you linked me too)

I would suggest that any method aside from the one taught to em (ie their religion) is deemed by them to be something less than the one they subscribe to. When a person TRULY believes in something as real, they would allow it to stand up against any method of truthful scrutiny. I would think a true beliver whould attempt to use these methods developed to prove their position.

I'll be drawing conclusions from the evidence and using them to achieve real-world results

Progress! Something we all should be embracing.

Contact was a great flick! And no, not just cuz jodi foster is a hottie either! :)

When you speak of the overwhelming size of the Universe and how people overlook that. It occurs to me that when you say "opportunity" or "spirit" or "Hubble" to most people they will have no clue as to what they are, much less what knowlege they have contributed to mankind.

I've at various times been presumed (or accused) to be: an atheist, a fundamentalist, a Jew, a Christian, a "Muslim-lover", a materialist, a mystic, a conservative, a neo-conservative, a liberal, a moderate, a socialist, etc. etc. etc.

Ha Ha HA I have been there too! But you forgot one...TROLL! LMAO Attempting to conserve the realistic view of we do know and what we do not know as provable fact, often draws fire from those that will rely on assumption and general ideology as their view of proof required for belief.

I'm *still* waiting for that transporter, dangit...

The movie the FLY made me content to let them work out the bugs before they hit the market.

[dread78645]

> It is obvious to any observer:

Snowflakes Prove that GOD exists and interacts with His creation.

"Beer is proof that God loves us and wants us to be happy."
- Ben Franklin

(Smart fellow, that Benjamin ... )

[Elsie]

Indeed it is forced thru intimidation and not by my own accord at all.

I urge you to quit playing in the street. BIG trucks are coming!

[Elsie]

"Double Plus Ungood" ??

AHhh...

A c++ programmer!

[Elsie]

Evolution can be observed.

Where?

[Elsie]

A red light whore.....

HMmmmm.... I didn't know they had BOARDS!!!!

[Elsie]

Oh, I *definitely* believe in the existence of asses.

We have PROOF!

Congress

[editor-surveyor]

Tired of the circular reasoning; try something more logical.

[BMCDA]

Do you deny that the long ages obtained through C14 dating are used to support the theory that earth is very old? I see your point, but you would agree that there is a correlation between the two issues wouldn't you?

The dates obtained through C14 dating can be used to show that the earth is older than YECs claim.
To determine the true age of the earth they are pretty irrelevant since C14 dating is only accurate up to 50000 years.

[Kelly_2000]

Hi GOPPachyderm :-)

I have an undergraduate physics background only :-) I am actually a virologist, sorry my intent was not to intimidate but to present some scientific rebuttal to the debate. The anti-chaos theory has a huge wealth of corroborative research as well as being observable within many biological systems. Anti-chaos theory has a large body of credible empirical support. It is germane to my field of microbiology. For the record I consider myself a Christian so i do think I have the benefit of a credibility and objectivity when I make these points.

"String theory and chaos are very interesting fields of study but not incontrovertible facts "

This is an established aspect of nonlinear math not string theory.

Also the rest of the thermodynamics points such as energy within closed and open systems where erroneous. I don't think they where written by a physicist.

[Elsie]

I guess your creationist sources sort of "forgot" to inform you about the vast amounts of scientific evidence for evolution, eh?

 

Ah yes:  the ever changing eyesocket size and shape drawing.

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http://www.gcssepm.org/images/fossil_a.gif

[b_sharp]

"If intelligence is considered natural, then there is nothing above nature "

This creates another logical problem. Why would all else be natural because intelligence is natural? Spell it out a little more fully and tie them together.

[Elsie]

I admit that I'm impressed that they attached a glass bead to each end of a DNA strand.

(Heavy Sigh)

Today's youth!

They'll put wires and studs ANYWHERE!!

[Fester Chugabrew]

Two things are needed for science to take place. Can you name them?

[Elsie]

Must be awfully dsutned in that sbrtl;ijbELE.

Your KEYBOARD just Evolved!!!!

[Fester Chugabrew]

The dictionary definition of design suits me fine. No need for science to give it a special meaning of its own.

[BlueStateDepression]

Islam is a threat of man against man in the name of and by the direction of allah. While christians of today aren't perpatrating such a thing, I would offer that the christian bible shows a God to man aggression, threat, punishment for lack of compliance in the area of worship.

At least christians have enough sense to know that doling out such punishment isn't theirs to dole out and they refrain from doing so. Maybe the Muslims will learn that someday.