The Chemical Structure of Double-Stranded DNA

 
Double-stranded DNA consists of two complementary polynucleotide chains where the bases on one strand form hydrogen-bonded associations with the bases on the other strand. There are only two pairs of bases that can form regular interactions where the edge of one base match the edge of another so that the two bases are joined by hydrogen bonds while lying in the same plane.

The A/T and G/C base pairs each have one purine (A or G) and one pyrimidine (T or C) which means that the size of each of the base pairs from one side to the other is almost the same. When two polynucleotide strands are laid side to side, as in the figure, the distance between the sugar residues on the two strands is the same for every base pair. What this means is that double-stranded DNA is a very regular structure in spite of the fact that the sequence of base pairs can be very different in different parts of the molecule.

The two strands are said to be complementary because all the bases in one strand are paired with the complementary bases on the other strand (A with T and G with C). This can only happen in a way that generates a regular structure if the two strands are antiparallel. If you look at the structure shown above you can determine the directionality of each strand by following the rules described in DNA Is a Polynucleotide. The left hand strand runs in the 5′→3′ direction from top to bottom while the right hand strand reads 3′→5′ from top to bottom.

The discovery of the structure of DNA by Watson & Crick was only made possible when they realized that the two strands of the helix had to be antiparallel.

There’s a convention for writing DNA sequences. They all have to be written in the same direction and that’s 5′→3′. Thus, the sequence of the bases on the left hand strand is AGTC and the sequence of the bases on the right hand strand is GACT. This may seem a bit confusing if you don’t understand the convention.

One of the classic questions on undergraduate exams is to give the sequence of one strand of double-stranded DNA (e.g., TAACTGGCGGA) and ask students to write down the sequence of the other strand. You’d be surprised at how many students haven’t paid attention when we discuss antiparallel strands in DNA and naming conventions.

©:Laurence A. Moran and Pearson/Prentice Hall 2007