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Chapter: Biochemistry: Nucleic Acids: How Structure Conveys Information

What is the nature of the DNA double helix?

What is the nature of the DNA double helix?
The determination of the double-helical structure was based primarily on model building and X-ray diffraction patterns.

What is the nature of the DNA double helix?

The determination of the double-helical structure was based primarily on model building and X-ray diffraction patterns. Information from X-ray patterns was added to information from chemical analyses that showed that the amount of A was always the same as the amount of T, and that the amount of G always equaled the amount of C. Both of these lines of evidence were used to conclude that DNA consists of two polynucleotide chains wrapped around each other to form a helix. Hydrogen bonds between bases on opposite chains determine the alignment of the helix, with the paired bases lying in planes perpendicular to the helix axis. The sugar– phosphate backbone is the outer part of the helix (Figure 9.7). The chains run in antiparallel directions, one 3' to 5' and the other 5' to 3.'


The X-ray diffraction pattern of DNA demonstrated the helical structure and the diameter. The combination of evidence from X-ray diffraction and chemi-cal analysis led to the conclusion that the base pairing is complementary, meaning that adenine pairs with thymine and that guanine pairs with cytosine. Because complementary base pairing occurs along the entire double helix, the two chains are also referred to as complementary strands. 

By 1953, studies of the base composi-tion of DNA from many species had already shown that, to within experimental error, the mole percentages of adenine and thymine (moles of these substances as percentages of the total) were equal; the same was found to be the case with gua-nine and cytosine. An adenine–thymine (A–T) base pair has two hydrogen bonds between the bases; a guanine–cytosine (G–C) base pair has three (Figure 9.8).


The inside diameter of the sugar–phosphate backbone of the double helix is about 11 Å (1.1 nm). The distance between the points of attachment of the bases to the two strands of the sugar–phosphate backbone is the same for the two base pairs (A–T and G–C), about 11 Å (1.1 nm), which allows for a double helix with a smooth backbone and no overt bulges. Base pairs other than A–T and G–C are possible, but they do not have the correct hydrogen bonding pattern (A–C or G–T pairs) or the right dimensions (purine–purine or pyrimidine–pyrimidine pairs) to allow for a smooth double helix (Figure 9.8). The outside diameter of the helix is 20 Å (2 nm). The length of one complete turn of the helix along its axis is 34 Å (3.4 nm) and contains 10 base pairs. The atoms that make up the two polynucleotide chains of the double helix do not completely fill an imaginary cylinder around the double helix; they leave empty spaces known as grooves. There is a large majorgroove and a smaller minor groove in the double helix; both can be sites at whichdrugs or polypeptides bind to DNA (see Figure 9.7). At neutral, physiological pH, each phosphate group of the backbone carries a negative charge. Positively charged ions, such as Na+ or Mg2+, and polypeptides with positively charged side chains must be associated with DNA in order to neutralize the negative charges. Eukaryotic DNA, for example, is complexed with histones, which are positively charged proteins, in the cell nucleus.


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