Skip to comments.Ultra-sensitive microscope reveals DNA processes
Posted on 11/16/2005 3:40:35 AM PST by snarks_when_bored
* 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.
Its 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. Its pretty incredible. You would never have believed it could be possible 10 years ago.
Journal reference: Nature (DOI: 10.1038/nature04268)
As an aside, note that the RNA polymerase, once brought into contact with the DNA strand, simply begins its replicative journey, moving along the strand one base pair at a time (as the experiment apparently demonstrates for the very first time). Now why does the RNA do this? Nobody (in their right mind) would suggest that it has a will and is acting intentionally, or that some unseen deity's hand is continually pushing it along, so it must be acting as its chemical structure compels it to act. This base-pair by base-pair copying motion must simply be what the chemical structure of RNA does. So why this chemical structure and not some other? This is a question that doesn't appear to lend itself to a scientific answer. Perhaps an ID'er would suggest that a higher intelligence designed the chemical structure of RNA to do just what it does. That may or may not be, but, clearly, it's not an hypothesis of empirical science. As a consequence, prolonged examination of such a hypothesisas if it were a scientific hypothesishas absolutely no place in a science classroom.
The more we learn about the microscopic world, the less likely it seems that non-physical (or non-mathematical) principles are needed to explain its behavior.
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God built the RNA-DNA engine. A very beautiful thing.
Holy Cow! That is awesome!
Do I see cloning as a common reality coming?
Me thinks so ... .
I'm not convinced knowing how this works will lead to good things considering the mindset of MANY in the field of science.
God built the RNA-DNA engine.
You may be right, of course, but the notion isn't scientific and oughtn't to be taught as such (which, of course, was the point of my little aside).
A very beautiful thing.
Dang, Junior! Hadn't seen that.
What concerns me is how the godless will use this information. There is no honor amongst them ... . Ethics are not present either.
This is far from true, as some thought and some attention to history would show. And (by way of anecdote) don't forget that the BTK monster was a well-respected Lutheran congregant...
Slick, indeed. A kind of Glasperlenspiel. Hesse might have been pleased.
I hear that often. Is it true?
For since the creation of the world God's invisible qualitieshis eternal power and divine naturehave been clearly seen, being understood from what has been made, so that men are without excuse. (Romans 1:20)
Perhaps an ID'er would suggest that a higher intelligence designed the chemical structure of RNA to do just what it does.
Perhaps a scientist will be able to show how something OTHER than a copy manages to get into the strand.
Since this is the very essence of Evolution, THAT is what is needed now to blast the IDer's out of the water.
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