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Ultra-sensitive microscope reveals DNA processes
New Scientist ^ | November 15, 2005 | Gaia [sic] Vince

Posted on 11/16/2005 3:40:35 AM PST by 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)


TOPICS: Culture/Society; Extended News; Miscellaneous
KEYWORDS: biology; chemistry; crevolist; dna; microscopy; rna; rnap; science
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To: Dimensio
No, geometry and mathematics are not science.

Really? Einstein, the mathematician, was not a scientist?

You are an idiot...

921 posted on 11/17/2005 6:21:09 PM PST by Sir Francis Dashwood (LET'S ROLL!)
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To: Sir Francis Dashwood
Einstein, the mathematician, was not a scientist?

Einstein was a mathematician?

BWAHAHAHAHAHAHAHA!

Okay, you've revealed yourself. No one would willingly make statements this rooted in ignorance who wasn't trolling.
922 posted on 11/17/2005 6:22:27 PM PST by Dimensio (http://angryflower.com/bobsqu.gif <-- required reading before you use your next apostrophe!)
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To: Sir Francis Dashwood

Really? Einstein, the mathematician, was not a scientist?

IIRC, Einstein admitted that math was not one his strengths.

923 posted on 11/17/2005 6:24:21 PM PST by ml1954 (NOT the disruptive troll seen frequently on CREVO threads)
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To: Sir Francis Dashwood
"It was not axiomatic before Pythagoras..."

And we can be thankful that Pythagoras (or one of his students, it isn't possible to know who actually came up with it) figured out the theorem. That doesn't make it science. Mathematics is a subset of logic, not science. It is an integral tool of science, but science is a different thing. It's possible to prove a mathematical theorem only because you can set the premises as true. When a formula is used to describe the real world, the math may be correct, but the relationship of that formula to reality will always be approximate. Newton's theory of gravity is an excellent example. It works for most objects in our normal experience but breaks down when you are dealing with very massive objects or very tiny objects. It has not been proved, nor can it be. It's still useful.
924 posted on 11/17/2005 6:24:30 PM PST by CarolinaGuitarman ("There is a grandeur in this view of life...")
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To: ml1954

I'm pretty sure that any good high-school Physics teacher would mention this.


925 posted on 11/17/2005 6:25:16 PM PST by Dimensio (http://angryflower.com/bobsqu.gif <-- required reading before you use your next apostrophe!)
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To: ml1954
E = mc2 is not science, but simply a deluded creationist's theory???

Albert Einstein was not a scientist???

Get over it...

926 posted on 11/17/2005 6:26:21 PM PST by Sir Francis Dashwood (LET'S ROLL!)
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To: ml1954
It may be creative but it doesn't explore the unknown or add to our knowledge of the universe.

The chip sets in your computer don't add to your knowledge of the universe?

In your case, maybe not....

927 posted on 11/17/2005 6:28:39 PM PST by Sir Francis Dashwood (LET'S ROLL!)
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To: Dimensio

I'm pretty sure that any good high-school Physics teacher would mention this.

But, but, but how important are facts and details, like really, when you are trying to do God's work and change the world for the better for everyone?

928 posted on 11/17/2005 6:28:58 PM PST by ml1954 (NOT the disruptive troll seen frequently on CREVO threads)
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To: longshadow
Internet abuse placemarker.
929 posted on 11/17/2005 6:29:09 PM PST by PatrickHenry (Expect no response if you're a troll, lunatic, retard, or incurable ignoramus.)
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To: Kelly_2000
Molecule and cell factories are applications in their infancy at present but the 4th and 5th generation technologies according to some of the roadmaps I have seem are nothing short of breathtaking

See if you can get in with "founder's shares" before the IPO :-P

Cheers!

930 posted on 11/17/2005 6:30:48 PM PST by grey_whiskers (The opinions are solely those of the author and are subject to change without notice.)
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To: PatrickHenry
Wake-up DarwinCentral™!

We have a new nominee for tha all-time most unintentionally funny post in the history of FR:

"It [a2 + b2 = c2] was a theory Pythagoras proved..."

[see post #913]

This is the first serious contender for dislodging the reigning champion of intended irony:

"Wildly elliptical planetary orbits"

931 posted on 11/17/2005 6:31:07 PM PST by longshadow
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To: Sir Francis Dashwood

If you had attempted to converse about what I wrote I might respond in kind. But you didn't.


932 posted on 11/17/2005 6:33:02 PM PST by ml1954 (NOT the disruptive troll seen frequently on CREVO threads)
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To: Sir Francis Dashwood
The chip sets in your computer don't add to your knowledge of the universe?

Keep in mind that the original statement was 'our' knowledge, referring to the universal body of knowledge shared by humanity. And in that respect, no, an already existing computer chip does not, by itself, do that. Are you really incapable of admitting that you're not fully up to snuff with respect to what exactly science is? Your attempts to lump the mere tools of science as fields of science in themselves is starting to look rather desperate.
933 posted on 11/17/2005 6:33:17 PM PST by Dimensio (http://angryflower.com/bobsqu.gif <-- required reading before you use your next apostrophe!)
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To: longshadow

make that: "UNintended" irony....


934 posted on 11/17/2005 6:33:23 PM PST by longshadow
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To: Dimensio
Keep in mind that the original statement was 'our' knowledge, referring to the universal body of knowledge shared by humanity...

Oh, you are a collectivist... that explains everything...

935 posted on 11/17/2005 6:35:32 PM PST by Sir Francis Dashwood (LET'S ROLL!)
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To: Sir Francis Dashwood
E = mc2 is not science, but simply a deluded creationist's theory???

E = mc2 is simply a mathematical formula. Without definitions for E, m and c it has no meaning. With E, m and c defined it isn't a theory, but a definition of the relationship between them.
936 posted on 11/17/2005 6:35:35 PM PST by Dimensio (http://angryflower.com/bobsqu.gif <-- required reading before you use your next apostrophe!)
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To: PatrickHenry
Internet abuse placemarker.

drinking problem, most likely.

937 posted on 11/17/2005 6:35:38 PM PST by longshadow
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To: Sir Francis Dashwood
Oh, you are a collectivist... that explains everything...

Are you so utterly devoid of rational arguments of your own that you have to take to dishonest misrepresntation of the statements of others?

You made a mistake about what is and is not science. Admit it and move on.
938 posted on 11/17/2005 6:36:31 PM PST by Dimensio (http://angryflower.com/bobsqu.gif <-- required reading before you use your next apostrophe!)
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To: longshadow
This is the first serious contender for dislodging the reigning champion of intended irony

It's a winner, no doubt about it. But the other guy was good for frequent laughs. The current situation just isn't interesting at all.

939 posted on 11/17/2005 6:36:31 PM PST by PatrickHenry (Expect no response if you're a troll, lunatic, retard, or incurable ignoramus.)
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To: b_sharp
No sir, that is not what is meant by supernatural in the case of God or in these discussions about science. What is meant by supernatural is a phenomena or cause that not only is exempt from the physical laws we utilize in testing science but can willfully change or circumvent those laws. This potential inconsistency in physical laws makes any result of tests we perform useless.

Useless for what? A good "99.9% of the time" rule of thumb is pretty useful for lots of stuff. :-)

Why don't you spell out your underlying assumptions a little more clearly for those of your disputants who were not trained in science? A little pinch of "mutually exclusive, collectively exhaustive" here, a smidgeon of "uniformity of causes within a closed system" there, and, ...presto!

Full Disclosure: Mutually exclusive, collectively exhausting is a pretty good description of many of the flame wars on these threads, too ;-)

940 posted on 11/17/2005 6:36:34 PM PST by grey_whiskers (The opinions are solely those of the author and are subject to change without notice.)
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