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Introduction to Heterocycles

Base Pairing

In the double-helical deoxyribonucleic acid (DNA) molecules, only two different base pairs are possible:

  • adenine with thymine and
  • guanine with cytosine.

The selective base pairing in double-helical DNA is a kind of molecular recognition.

Thus, in double-helical DNA, each purine base of one strand is always combined with a pyrimidine base of the other strand.

What is the structural reason behind the base pairing's selectivity? In order to answer this question, let us take a closer look of the bases' structures.


The selectivity of base pairing is the result of the alternatives that are offered in the formation of hydrogen bridge bonds between the heterocyclic purine and the pyrimidine bases of DNA. The strength of a hydrogen bridge bond depends on the distance and the spatial orientation of the atoms involved. Therefore, it is determined by the three-dimensional structure of the bases. Even small deviations from the most appropiate distance and orientation of the respective atoms lead to a considerable reduction of the strength of the hydrogen bridge bond. As a result, only base pairings of appropiate bases yield connections that are stable enough in enabling the double-helical DNA structure. If only a few inappropiate base pairings appear in a double-helical DNA, the two strands would not be able to hold together.

In the adenine-thymine base pair (AT), the bases are connected by two hydrogen bridge bonds, while in the GC base pair guanine and cytosine are held together by three hydrogen bridge bonds.

Hydrogen bridge bonds in AT and GC base pairs.
Hydrogen bridge bonds in the AT base pair Hydrogen bridge bonds in the GC base pair

As a result of the selective base pairing, the base sequences of the two strands of a double-helical DNA are complementary. The selective base pairing and the complementarity are the basis of DNA replication and the translation of the DNA's genetic information into the protein structures.

Base pairing in DNA (3D representation)
This 3D molecule is from a DNA-Tutorial.
Selectable variants of the 3D representation
Adenine-thymine base pair Guanine-cytosine base pair
Reset Spacefill

The genetic information is saved in the sequence of the purine and pyrimidine bases in the DNA and RNA chains. The base sequence of the DNA is transferred to a RNA molecule with a complementary base sequence (messenger RNA, mRNA). This process is known as transcription. The mRNA's base sequence is then transmitted to the amino-acid sequence of a protein. This process is called translation. In translation, three consecutive bases of the RNA are each translated into one amino acid of the protein. Thus, four different bases can code the twenty naturally occuring amino acids, as four different bases can even produce 43 = 64 different combinations of three bases each. A base triplet is also called a codon. During DNA replication and transcription, the two DNA strands of the double-helical DNA must be partially separated in the region that is being red.

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