How intimately can we observe DNA replication?

[Cody Richeson]

I found this interesting computer animation representing DNA functions in cells.



My questions:
1) How precisely can we actually magnify cell functions, and what is preventing us from peering in as closely as depicted in the video (keeping in mind that I know it's probably technologically infeasible to construct an atomic sized camera that can zip around and record what's going on)?

2)I've seen photographs of individual atoms, so why is it that when I search for magnified images of cells, it's never at the atomic level?

3)Have florescent dyeing techniques been able to resolve any of these functions at the atomic scale?

4) Would high speed video from a powerful microscope (shooting at perhaps 10,000-50,000 frames per second) be able to provide useful temporal information about the process of DNA replication?

 

[jedishrfu]

This may answer your questions on the limits of cellular process observation:

http://www.ncbi.nlm.nih.gov/books/NBK26880/

and this discussion on cell microscopy:

http://www3.delta.edu/cmurbano/brandnew/171/files/labs/lab 4_cells_observing_the_.pdf

 

[jim mcnamara]

A simple answer using a homey analogy -
Brownian motion. Molecules in a liquid "bump"around at high "speeds", and chemical reactions happen VERY quickly. So if we could actually look at what is going on, we would see something like this:
Imagine a movie of Grand Central station, showing what happens there over a five hour period. Now play it back - in one second. You will note that virtually everything moves off the screen, as filmed in real time, in about one minute. So where is the bus hours later?

Now pretend the bus was a large molecule. You could not say where it will be in the next few milliseconds in the fast playback version. You would be hard pressed to track anything.

Look closely at the video, we are interested the black dots (small molecule sized things) Image tracking one of them with an electron microscope.
https://en.wikipedia.org/wiki/Brownian_motion

 

[Ygggdrasil]

Visible light microscopy is ultimately constrained by the diffraction limit of light. Because of the quantum nature of light, you cannot focus a light beam down to below ~ half the wavelenght of the light you are using. Therefore, visible light (~400-600 nm) has a resolution limit of ~ 200 nm (atoms are on the scale of ~0.1 nm). There are some trick you can play with optics to perform super-resolution imaging, which now can routinely image with ~ 10-20 nm resolution, and has been reported to get to the 0.1-1 nm scale under optimal conditions. However, many of these higher-resolution techniques are slow, posing challenges for imaging fast processes in live cells.

It is possible to image at higher resolutions using shorter wavelenghts of light (x-rays) or electrons, but these are damaging to biological tissue and cannot be used on live samples. Atomic force microscopy has been used to image atoms and molecules, but this technique cannot see inside of cells (though you can use it to watch purified motor proteins move in the laboaratory).

Indeed, using purified components, scientists have developed a number of single-molecule techniques to track the motion of motor proteins like DNA polymerase in real time. Techniques such as optical tweezers, fluorescence, and AFM can be used to watch the movement of these proteins along their tracks (e.g. DNA polymerase moving along DNA, kinesin walking along microtubules).

 

[jim mcnamara]

While @Ygggdrasil is completely correct, please do not take his reply to mean 'Yes, we can see individual DNA strands (DNA is a polymer) in a live cell.'
We cannot do that right now. My post was predicated on what I thought was your apparent level of understanding. Sorry if that's wrong.

This is what you have to do to be able to do that -- with a DNA strand from a dead cell. It is really cool.
https://www.physicsforums.com/insights/whats-application-polymer-physics-genetic-sequencing/
DNA is folded into a glob in live cells during most of a cell cycle, for starters.

 

[Asteropaeus]

We can do different measurements, using different techniques. Then we can use computer models and simulations and our knowledge of chemistry to make these animations.

At the lab I work they do measurements using fluorescence labeled polymerases and nucleotides (FRET). This allows measuring how distances between these fluorescent labels change. When combined with crystal structures, you can greatly limit the number of theoretically possible conformations the molecules truly pass through as DNA is being copied, narrowing down on the 'true way'.