B-form DNA and A-form RNA

This page is a skeletal tutorial on the structures of A and B form nucleic acids and on the use of the Rasmol program to display three-dimensional structures (here, "PDB files", where PDB = protein data bank format).

NEW:

Key concepts

• Understand what a protein or other ligand "sees" when it approaches a DNA or RNA molecule.
• Understand the biologically relevant differences between A and B form.
• Appreciate that real DNA and RNA have much more conformational variability than the idealized versions.

Contents

• This page: directions and sample views (these can be enjoyed without running the viewer program, but you could look at a book instead).
• B-DNA PDB file, and same thing as a text file: B-DNA PDB text file
  A-RNA PDB file, and same as text file: A-RNA PDB text file.
  
• Command list for manipulation of DNA and RNA. Note that this is different from a Rasmol "script", which is a set of internally-generated commands for regenerating a given view. Scripts are useful for regenerating views, but not for learning how to use the program.
• A real DNA molecule, illustrating that the molecule demonstrates substantial "microheterogeneity". Look for buckling, groove narrowing, and propeller twist.
• A set of images illustrating the steric clashes that presumably prevent the existence of B-form RNA.

Directions

1. If you haven't worked out how to use Rasmol, see the Installation Page.
2. Load the molecule of your choice into RasMol (either automatically within Netscape or by hand). The command list includes a line on how to do this but doesn't do it automatically (because of path issues on the Mac).
3. Open the the command list. It might be best to open it as a separate window, which should happen automagically (if not, on the Mac, hold the mouse button down until the menu pops up).
4. Copy and paste from command list file to Rasmol window, or download the file and do it from a text editor (any word processor will do). On Windows, pasting doesn't work and you need to save parts of the file and run them as scripts (use the Notepad). You may need to give a full path for the script name.

Results

Here are gif images generated from the PDB file and scripts above. The images in the left two columns emphasize the major and minor grooves of the DNA and RNA. The left column shows "wireframe" images, much faster to display in RasMol. The center column shows spacefilling images. The color coding is as follows:
Major groove -- red Minor groove -- yellow Watson-Crick H-bonding face -- blue major groove and WC face -- purple major groove and WC face -- green backbone -- white, with orange P atoms other atoms -- brown. Sugar protons not shown. imino protons -- pink
B-DNA. The helix backbone is in cyan.	B-DNA. Note the large, accessible major groove and narrow minor groove.	The top view shows the base pairs in the center of the helix.
A-form RNA. Note the inclined base pairs.	A-RNA. Note the deep, inaccessible major groove and shallow minor groove.	A-RNA. Note the base pairs are offset toward the outside of the helix.