Base-pairing in DNA

(Download basepair.pdb)

The following skill will be taught here:

• Identification of bases in DNA
• Display the hydrogen bond pattern
• Measuring the distance between two atoms

Open the file basepair.pdb:

The structure represents a short fragment of DNA consisting of 2 base- pairs. One of them is an A-T pair and the other one is a G-C pair.

To identify which is which, we can following the following steps:

• First of all, identify which is a purine (A or G) - double rings, and which is a pyrimidines (C or T, NEVER find U in DNA!)- single ring.
• As we know, there are 2 hydrogen bonds in A-T bond and 3 hydrogen bonds in G-C bond. Bear this in mind because we will use this fact in the identification process.
• Activate the command line interface of RasMol by clicking the "RasMol Command Line Button" on the Toolbar:

• The command line interface allows you to access the more advanced features of RasMol. One of them is to show hydrogen bonding pattern. Try to type the following command in the command window:

RasMol>hbond on

• The dotted lines represent hydrogen bonds between the bases. So we can have the following predictions:

• If you want to turn off the hydrogen bond display, just type the following in the command window:

RasMol>hbond off

Measuring the distance between two atoms

To turn on distance monitor:

RasMol>set picking monitor

Then pick any two atoms in the Main Window of RasMol:

The distance's unit is Angstrom (1 Angstrom= 0.1nm)

To turn off the distance monitor and set the picking mode back to default:

RasMol>monitor off

RasMol>set picking ident