Introduction to CHIME: Tutorial on 3D Structure of DNA


barnes@mail.clarion.edu             Send questions or comments to Dr. Barnes!
 
 









CHIME is an application which allows you to view an organic chemical or biochemical in 3-dimensions, from any angle.  It also allows you to display it in various ways and in different color schemes.
 

To see what CHIME can do, go to the CHIME site at the University of Massachusetts.
Click on:  " DNA. An introductory level nonlinear self-paced tutorial."
 
 

The Sugar-Phosphate backbone
Explore the sugar-phosphate backbone by clicking on   "5. Strands and helical backbone"   Now you should see a model  of the double stranded DNA molecule. Each strand is presented in a different color.  Below the model is a control panel with "X" buttons.
  1. Click on the "Y spin" button
  2. Click on the "Side" button"
  3. Click on "X spin"
  1. Click on "Bases" and "H bonds" to erase the nitrogenous bases and hydrogen bonds between the bases.  Now we see only the sugar-phosphate backbones of the gold and brown single strands of DNA.
  2. Click on "Phosphorus".  This  emphasizes how the dexoxyribose sugars are linked together by phosphate molecules.
  3. Click on "X spin".
  4. Click on "Reset"
  1. Click on "Bases" and "H bonds" to erase the nitrogenous bases and hydrogen bonds between the bases.
  2. Click on "Y spin".  From an end view, note how the 2 strands twist around each other to form a hollow tube.
  3. Click on "Reset"


The Nitrogenous Base Pairs
  1. Click on "Sugars" to erase the deoxyribose sugars.  Now you can see the pairs of nitrogenous bases which are held together by hydrogen bonds ( white dotted lines).
  2. Simultaneously move your mouse and click on the left key.  You will find that you can now manipulate the molecule in any way you choose.  Move it around so you can get a good idea of what the base pairs look like.

 
The image can be translated X or Y (moved left or right; up or down)  with the mouse by holding down the control key and the right button on the mouse.

The image can be yawed (rotated left and right about the Y axis ) or pitched (rotated up or down about the X axis)  with the mouse by holding down the left button on the mouse.

The image can be rolled about the Z axis with the mouse by holding down the shift key and the right button of the mouse.

The image can be resized with the mouse by holding down the shift key and the left button on the mouse.

  1. Click on "Reset"
  2. Click on "End"
  3. Click on "Sugars" to erase the deoxyribose sugars.  Now you can see how the base pairs (held together by hydrogen bonds), form a core which fills up the hollow center of the tube created by the sugar-phosphate backbone.
  4. Click on "Reset"

 
A single strand of DNA.
  1. Erase the brown strand by clicking on the far left button.  Now you will see only one of the two strands of the DNA molecule.
  2. Click on the buttons to erase the H bonds.
With the commands which follow, the mouse cursor should be positioned over the black window which contains the image. You may not get the CHIME menu otherwise.
  1. Hold down the right  mouse button.  On the menu which appears, go to "Select".  This brings up a sub-menu.  Go to "Nucleic".  This brings up a sub-menu. Go to "DNA.  We have now selected our molecule.
  2. Hold down the right  mouse button.  On the menu which appears, go to "Color".  On the sub-menu, go to "Monochrome".  The single strand should now appear in white.
  3. Hold down the right mouse button.  Choose "Select" ---> "Nucleic" --->  "Backbone"
  4. Hold down the right  mouse button.  On the menu which appears, go to "Color" --->  "Chain".  The sugar-phosphate backbone should now appear in blue, with the nitrogenous bases in white.
  5. Click on "Phosphorus" to emphasize the links holding the deoxyribose sugars together.  Use the mouse to manipulate the model, until you have a good idea of the way it is put together.

 
The Double Stranded DNA molecule
  1. Click on "Reset".  Now you should see 2 strands - a blue strand and a red strand, with the base pairs in white.
  2. Click on "X spin"
  3. Click on "Y spin".  Now you see an end view of the molecule. Note how the sugar-phosphate backbones form a hollow tube while the nitrogenous base pairs fill up the core.
  4. Click on "Side".
  5. Use the mouse to manipulate the molecule.
  6. Click on "Reset"
  1. Hold down the right mouse button.  Choose "Display" ---> "Spacefill" ---> "Van der Waals Radii".
  2. Resize the molecule by holding down the shift key and the left mouse button.  Move the mouse up or down to zoom in or out.  Reduce the molecule to the height of your window.
  3. Manipulate the molecule with your mouse to stand it up vertically.
  4. Hold down the right mouse button.  Choose "Options" ---> "Rotation".
  5. Click on "X  Spin".
  6. Hold down the right mouse button.  Choose "Options" ---> "Stereo Display".
To properly see the model in stereo, put your nose to the screen so that you can't focus on it.  Slowly move back - but do not allow your eyes to focus!  If you are doing it right, you will first see 4 spinning molecules.  Concentrate on the middle two; they will get closer together as you move farther away.  When they come together you will see the molecule in stereo!

The Genetic Code
Return to the DNA Index page.  This time click on the link:   "4.  The Code"

This will bring up a model of double stranded DNA with the sugar-phosphate backbones in brown, and each nucleic acid displayed in a different color.

Starting with the guanosine (green) in the lower left of the screen, and reading toward the right ..........


Length of Double Stranded  DNA
In living organisms, DNA is a very long molecule.
Watson and Crick
A double stranded DNA molecule is not actually shaped like a ladder as shown in the diagram above.  It is really twisted into a helix.  Imagine holding a toy ladder in your right hand. Then pointing it away from you, twist the top with your left hand in a clockwise manner.  This produces what is known as a right-handed helix.

The B-form of DNA is a right handed helix.  It is the classical structure first described by James Watson and Francis Crick.
 


 
 
 

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