Table of Contents
Biomolecules Gateway Page
Jmol Tutorial

In this module:

Polymerization of Nucleotides
Base Pairing 1
Base Pairing 2
Complementary Sequences

Complementary Base Pairing: Hydrogen Bonding

Nucleotides are full of groups that can participate in hydrogen bonds. The hydrogen-bonding capability of the bases are especially important for specific base pairing.

What is hydrogen bonding?

The structures of adenine and cytosine are shown below. Move your mouse over the structure of adenine to see its potential hydrogen bond donors and acceptors. Then click on the hydrogen bond donors and acceptors on the structure of cytosine.

Find 1 H-bond donor in C.
Now find 4 H-bond acceptors in C.



Hydrogen Bond Donor
Hydrogen Bond Acceptor
Correct! The amine group on cytosine can act as a hydrogen bond donor.
Remember, to be a hydrogen bond donor the hydrogen atom must be bound to an electronegative atom. That hydrogen is bonded to carbon, which is not very electronegative.
Correct! That is one of cytosine's four hydrogen bond acceptors.
Remember, a hydrogen bond acceptor is an electronegative atom with a nonbonding electron pair that can form a partial bond to a hydrogen atom. A hydrogen bond donor is an electronegative atom bonded to a hydrogen atom.
You have already identified that hydrogen bond acceptor. Please try again.

As asked on the previous page, since the DNA double helix has enough space to allow four base combinations, A-C, G-T, A-T, and G-C, why are only the second two and not the first two seen? The answer is that A-T and G-C pairs maximize the number of hydrogen bonds across the shared helical axis. A's hydrogen donors can pair up with T's hydrogen bond acceptors, and G's hydrogen bond acceptors can pair up with C's hydrogen bond donors. A-T and G-C are called complementary base pairs .

Click on the test tube at left to practice finding complementary base pairs.

Shown at lower right are a paper structure and a ball and stick model of uracil (U), another nucleotide which sometimes fits into the DNA double helix. Move your mouse over the structures to see their patterns of hydrogen bond donors and acceptors. Which of the four nucleotides of DNA do you think uracil will pair with? Make your selections and click on the Check button to find out.

Hydrogen Bond Donor
Hydrogen Bond Acceptor
As you can see, A and G can form base pairs with U. The most common pairing is with A, and this is what is found in the process of transcription, but G often forms base pairs with U in RNA molecules (See the DNA 2 module for descriptions of RNA and transcription).
Remember, the one-ring bases are too small to form base pairs with each other.
Please make your selection from the boxes at left above.

Use the structure below to see the hydrogen bonding patterns between A-T and G-C in more detail.

Base Pairing 2