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 Jmol plugin to display three-dimensional structures (here, "PDB files", where PDB = protein data bank format).

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).
• A set of Jmol pages that enable molecular visualization of the four molecules below.
• B-DNA PDB file, and identical file tagged as a text file (.txt): B-DNA PDB text file. There us nothing magic about the PDB format. It is just text.
• A-RNA PDB file, and same as text file: A-RNA PDB text file.
• A real DNA molecule (PDB), illustrating that the molecule demonstrates substantial "microheterogeneity". Look for buckling, groove narrowing, and propeller twist.
• A real RNA molecule (PDB), including an extrahelical base and a loop at the end.
• A set of images illustrating the steric clashes that are believed to prevent the existence of B-form RNA.

Images

Here are gif images generated from the idealized A and B form PDB files used above, made using Rasmol, which is an earlier stand-alone incarnation of Jmol. The images in the left two columns emphasize the major and minor grooves of the DNA and RNA. The left column shows "wireframe" images. 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.