Biology Strange

First Direct Imaging of DNA Fibers' Double Helix

Isn’t it strange that you are made up of perhaps 37.2 trillion cells, almost all of which have a copy of your complete DNA? Here is a first direct image of DNA, the physical structure that holds the instructions used to make you. That dark line in the image is stretched out DNA. The double helix cork screw spiral can be seen in the lower right image.

Direct imaging becomes important when the knowledge at few/single molecule level is requested and where the diffraction does not allow to get structural and functional information….  The experimental breakthrough is the production of robust and highly ordered paired DNA nanofibers that allowed its direct TEM imaging and the double helix structure revealing.
via Direct Imaging of DNA Fibers: The Visage of Double Helix – Nano Letters (ACS Publications).
… now, for the first time ever, scientists have actually snapped a real image of DNA using an electron microscope — spiraling corkscrew and all.
The image was taken by Enzo di Fabrizio from the University of Genoa, Italy. He choreographed the scene by pulling a small strand of DNA from a diluted solution and then propping it up like a clothesline between two nanoscopic silicon pillars.
The trick to the technique was in acquiring a discrete strand of DNA that could be stretched out and ready to view with an electron microscope. Di Fabrizio managed this by creating a pattern of pillars that repelled water — which resulted in quick moisture evaporation and a residual strand of DNA all ready to go.
Then, in order to create a high-resolution image, di Fabrizio drilled tiny holes in the base of the nanopillar bed and shone beams of electrons. Aside from creating a cool image, the technique will allow the researchers to investigate DNA in greater detail, as well as seeing how it interacts with proteins and RNA.
via io9

I’m not sure how much it stretches dynamically, but you can see that real DNA has much tighter the twists than all the illustrations we’ve seen of DNA.

Most of the 37.2 trillion of your cells has a full copy of your genome. That is 22 paired chromosomes, plus the X chromosome (one in males, two in females) and, in males only, one Y chromosome. Exceptions are red blood cells which have no nucleus and thus no DNA and except for egg or sperm cells which have only a randomly assigned 1/2 of your DNA, but most of your cells contain a total of over over 3 billion base pairs, lengths of which are your genes. Genes provides the instructions to create proteins to carry out cellular functions.

There are an estimated 19,000-20,000 human protein-coding genes.[7] The estimate of the number of human genes has been repeatedly revised down from initial predictions of 100,000 or more as genome sequence quality and gene finding methods have improved, and could continue to drop further. Protein-coding sequences account for only a very small fraction of the genome (approximately 1.5%), and the rest is associated with non-coding RNA molecules, regulatory DNA sequences, LINEs, SINEs, introns, and sequences for which as yet no function has been determined.

It seems a strange design, all of your cells having their own full copy of your DNA. Given that, how does any given cell know which genes to use?
It can be thought of as an intricate micro-mechanical system:

There are a huge number of proteins that protrude through the cell membrane, such that they have one piece outside the cell and one piece inside. Some of these proteins, known as receptors, can bind to one or more specific types of chemical that’s sometimes found outside the cells – hormones, sugars and other small molecules, other proteins, viruses, you name it, there’s probably a receptor for it. When the receptor finds and binds its partner, the part of the receptor protein that’s inside the cell changes its shape, and this is what triggers changes in gene activity.
The change in the receptor protein’s shape can cause another protein that was previously attached to it to detach, float away, and bind to an inactive protein; that protein then becomes activated, changes shape, detaches, and floats away to bind another inactive protein; etc etc etc. Ultimately, the signal being carried by all these small changes in protein shapes ends up in the nucleus, where it instructs an enzyme called a transcription factor to interact with specific pieces of DNA, which changes the activity level of those genes.

via Quora

In terms of seeing the reality of DNA, a glimpse at the micro-mechanical reality, there is this amazing video which changed many of our pre-existing ideas.

The researchers watched replicating DNA from E. coli bacteria….
Until now, scientists believed that the polymerases on the two strands coordinated their movement somehow to ensure that one didn’t get too far ahead of the other. However, this video shows that this isn’t the case.
Stop And Go
Instead, the progress of the “lagging strand” polymerase looks a lot like stop and go traffic, stopping unpredictably and starting up again at random speeds that can vary tenfold. What seemed like coordination is really just the average outcome over time of this random process of variable speeds and starting and stopping. …
via Futurism
You may recall from watching an animation in some science documentary the elegant way in which the double helix DNA molecule supposedly duplicates itself. An enzyme called helicase makes the helix unwind and unzip. Primers are added by a second enzyme. And then DNA polymerase moves in and rebuilds the matching half of each strand, leaving two molecules, each with one old backbone and one new.
via ScienceFriday

This shows us that the blueprint for life on our planet operates more randomly that we thought since there is no coordination between DNA strands as a cell reproduces. The strands of DNA appear to operate more like independent organisms, achieving a common goal, but completely autonomously.
I find this reality, what happens at the molecular level in each of us, as mind blowing as the vastness of space. It is easy to just ignore, of course. What can you do about it? Nothing. So what’s the point of knowing it? I don’t know. Some people live their entire lives never giving DNA a second thought, and yet there it is, the whole time, doing stuff that makes us do stuff. Wild.

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