Tag Archives: DRAQ5

What our DNA looks like inside a living cell

Time to rewrite the textbooks.  DNA in the living cell looks nothing like the pictures that have appeared in textbooks for years. Gone are the 30 nanoMeter fiber and higher order structures.

Here is the old consensus of how DNA in the nucleus is organized.

There are two different structural models of the 30 nanoMeter fiber (1) solenoid — diameter 33 nanoMeters with 6 nucleosomes ever 11 nanoMeters along the axis (2) two start zigzag fiber — diameter 27 – 30 nanoMeters with 5 – 6 nucleosomes every 11 nanoMeters.
The 30 nanoMeter fiber is throught to assemble into helically folded 120 nanoMeter chromonema, 300  – 700 nanoMeter chromitids and mitotic chromosomes (1,400 nanoMeters).     The chromonema structures 9measured between 100 and 130 nanoMeters) are based on electron micrographic studies of permeabilized nuclei from which other components have been extracted with detergenes and high salt to visualize chromatin — hardly physiologic.

Got all that?  Good, now forget it.  It’s wrong.

First off, forget nanoMeters.  Organic chemists think in Angstroms — the diameter of the smallest atom Hydrogen is almost exactly 1 Angstrom, making it the perfect organic chemical yardstick.  If you must think in nanoMeters, just divide the number of Angstroms by 10.

First, a few numbers to get started.
 The classic form of DNA is B-DNA (this is still correct). https://en.wikipedia.org/wiki/Nucleic_acid_double_helix.  Each nucleotide pair is 3.4 Angstroms above the next and there are 10.4 nucleotides per turn of the helix  (so 1 full turn of B DNA is 35.36 Angstroms).  The diameter of B-DNA is 19 Angstroms.

The nucleosome consists of 147 bases of DNA wrapped around a central mass made of 8 histone proteins. The histone octamer is made of two copies each of histones H2A, H2B, H3 and H4.  The core particle in its entirety is 100 Angstroms in diameter and 57 Angstroms along the axis of the disk and possesses nearly dyadic symmetry.  There are 1.65 turns of DNA around the histone octamer, and during the trip there are 14 contact points between histones and DNA.

Now on to the actual paper [ Science vol. 357 pp. 354 – 355, 370, eaag0025 1 –> 13 ‘ 17 ]  The movies contained within alone are worth a year’s subscription to Science.

To visualize DNA in the living cells the authors invented a technique called  Chromatin Electron Microscopy Tomography (ChromEMT).

 DNA is transparent to electrons.  They use a fluorescent  DNA binding dye (Deep Red fluorescing AnthraQuinone Nr.5  ). For a structure see — http://onlinelibrary.wiley.com/doi/10.1002/1097-0320(20000801)40:4%3C280::AID-CYTO4%3E3.0.CO;2-7/full.  It has 3 probably aromatic rings fused together like anthracene, so it could easily intercalate between the bases of the double helix.   Then there are OH groups and amines to bind to the backbone.  The dye gets into cells easily.  Most importantly, DRAQ5 produces reactive oxygen species when hit by the right kind of light.  Somehow they get diaminobenzidine in the cells, which the reactive oxygen species polymerizes to polybenzimidazole.

 We’re not done yet.  The polymer is also transparent to electrons, but it can react with good old Osmium tetroxide (which is electron dense). permitting visualization of DNA on electron microscopy (at last)

  The technique is the first that can be used in living cells.  It shows that most chromatin in the nucleus is mostly organized as a disordered polymer of 50 to 240 Angstroms diameter.   This is consistent with beads on a string (with nucleosomes being the beads).  They found little evidence for higher order structures (the 300 to 1,200 Angstrom fibers of classic textbook models — which is in fact based on in vitro visualization of non-native chromatin. The 30 nanoMeter chromatin fiber (300 Angstroms) is nowhere to be seen.  However, they do find 300 Angstrom fibers using their new  method but only in nuclei purified from hypotonically lysed chicken RBCs treated with MgCl2 (hardly physiologic).

       They were able to make a movie of an electron micrograph in the nucleus using eight tilts of the stage There is more DNA at the nuclear rim (as that’s where the heterochromatin is mostly), but you still see the little 5 – 24  nanoMeter circles (just more of them the closer you get to the nuclear membrane).
      Another movie of a mitotic chromosome shows the same little circles (50 – 240 Angstroms) just packed together more closely.  You just see a lot of them, but there is no obvious bunching of them into higher structures.
     The technique (ChromEMT is amazing in that it allows the ultrastructure of individual chromatin chains, megabase domains and mitotitc chromosomes to be resolved and visualized as a continuum in serial slices.   The found that the 5 – 12 and 12 – 24 chromatin diameters were the same regardless of how heavily the chromatin was compacted.
      The paper is incredible and worth a year’s subscription to Science.  It likely is behind a paywall.
It’s hard to get your mind around the amount of compaction involved in getting the meter of DNA of the human genome into a nucleus.  Molecular Biology of the Cell 4th Edition p. 198 put it this way —  Compacting the meter of DNA into a 6 micron nucleus is like compacting 24 miles of very fine thread into a tennis ball.
I actually wrote a series of posts, trying to put the amount of compaction into human scale.  Here is the first post — follow the links at the end to the others.

The cell nucleus and its DNA on a human scale – I

The nucleus is a very crowded place, filled with DNA, proteins packing up DNA, proteins patching up DNA, proteins opening up DNA to transcribe it etc. Statements like this produce no physical intuition of the sizes of the various players (to me at least).  How do you go from the 1 Angstrom hydrogen atom, the 3.4 Angstrom thickness per nucleotide (base) of DNA, the roughly 20 Angstrom diameter of the DNA double helix, to any intuition of what it’s like inside a spherical nucleus with a diameter of 10 microns?

How many bases are in the human genome?  It depends on who you read — but 3 billion (3 * 10^9) is a lowball estimate — Wikipedia has 3.08, some sources have 3.4 billion.  3 billion is a nice round number.  How physically long is the genome?  Put the DNA into the form seen in most textbooks — e.g. the double helix.  Well, an Angstrom is one ten billionth (10^-10) of a meter, and multiplying it out we get

3 * 10^9 (bases/genome) * 3.4 * 10^-10 (meters/base) = 1 (meter).

The diameter of a typical nucleus is 10 microns (10 one millionths of a meter == 10 * 10^-6 = 10^-5 meter.   So we’ve got fit the textbook picture of our genome into something 1/100,000 smaller. We’ll definitely have to bend it like Beckham.

As a chemist I think in Angstroms, as a biologist in microns and millimeters, but as an American I think in feet and inches.  To make this stuff comprehensible, think of driving from New York City to Seattle.  It’s 2840 miles or 14,995,200 feet (according to one source on the internet). Now we’re getting somewhere.  I know what a foot is, and I’ve driven most of those miles at one time or other.  Call it 15 million feet, and pack this length down by a factor of 100,000.  It’s 150 feet, half the size of a (US) football field.

Next, consider how thick DNA is relative to its length.  20 Angstroms is 20 * 10^-10 meters or 2 nanoMeters (2 * 10^-9 meters), so our DNA is 500 million times longer than it is thick.  What is 1/500,000,000 of 15,000,000 feet?  Well, it’s 3% of a foot which is .36  of an inch, very close to 3/8 of an inch.   At least in my refrigerator that’s a pair of cooked linguini twisted around each other (the double helix in edible form).  The twisting is pretty tight, a complete turn of the two strands every 35.36 angstroms, or about 1 complete turn every 1.5 thicknesses, more reminiscent of fusilli than linguini, but fusilli is too thick.  Well, no analogy is perfect.  If it were, it would be a description.   One more thing before moving on.

How thinly should the linguini be sliced to split it apart into the constituent bases?  There are roughly 6 bases/thickness, and since the thickness is 3/8 of an inch, about 1/16 of an inch.  So relative to driving from NYC to Seattle, just throw a base out the window every 1/16th of an inch, and you’ll be up to 3 billion before you know it.

You’ve been so good following to this point that you get tickets for 50 yardline seats in the superdome.  You’re sitting far enough back so that you’re 75 feet above the field, placing you right at the equator of our 150 foot sphere. The north and south poles of the sphere are over the 50 yard line. halfway between the two sides.  You are about to the watch the grounds crew pump 15,000,000 feet of linguini into the sphere. Will it burst?  We know it won’t (or we wouldn’t exist).  But how much of the sphere will the linguini take up?

The volume of any sphere is 4/3 * pi * radius^3.  So the volume of our sphere of 10 microns diameter is 4/3 * 3.14 * 5 * 5 * 5 *  = 523 cubic microns. There are 10^18 cubic microns in a meter.  So our spherical nucleus has a volume of 523 * 10^-18 cubic meters.  What is the volume of the DNA cylinder? Its radius is 10 Angstroms or 1 nanoMeter.  So its volume is 1 meter (length of the stretched out DNA) * pi * 10^-9 * 10^-9 meters 3.14 * 10^-18 cubic meters (or 3.14 cubic microns == 3.14 * 10^-6 * 10^-6 * 10^-6

Even though it’s 15,000,000 feet long, the volume of the linguini is only 3.14/523 of the sphere.  Plenty of room for the grounds crew who begin reeling it in at 60 miles an hour.  Since they have 2840 miles of the stuff to reel in, we’ll have to come back in a few days to watch the show.  While we’re waiting, we might think of how anything can be accurately located in 2840 miles of linguini in a 150 foot sphere.

Here’s a link to the next paper in the series