Elementary plant Biochemistry and Biotechnology (2+1)

Watson and Crick

• Watson and Crick combined chemical and physical data for DNA with a feature of the X-ray diffraction diagram that suggested that two helical strands are present in DNA and showed that the two strands are coiled about one another to form a double-stranded helix. The sugar phosphate backbones follow a helical path at the outer edge of the molecule and the bases are in a helical array in the central core. The bases of one strand are hydrogen bonded to those of other strand to form the purine-pyrimidine base pairs viz., A:T and G:C. Because each pair contains one two-ringed purine (A or G) and one single ringed pyrimidine (T or C, respectively), the length of each pair (in the sugar to sugar direction) is about the same and the helix can fit into a smooth cylinder.




• The two polynucleotide strands of the DNA double helix are antiparellel i.e. the 3’-OH terminus of one strand is adjacent to the 5’-P (5’ – phosphate) terminus of the other. The two bases in each base pair lie in the same plane and the plane of each pair is perpendicular to the helix axis. The base pairs are rotated 360 with respect to each adjacent pair, so there are 10 pairs per helical turn (Fig). The helix has two external helical grooves, a deep wide one (the major groove) and a shallow narrow one (the minor groove); both of these grooves are large enough to allow protein molecules to come in contact with the bases. Base pairing is one of the most important features of the DNA structure because it means that the base sequences of the two strands are complementary.




• In other words, purine in one strand is always pairs with pyrimidine in other strand i.e., if one strand has the base sequence AATGCT, the other strand has the sequence TTACGA, reading in the same direction. Specific pairing is achieved by reciprocal positioning of hydrogen bond acceptors and donors. Three hydrogen bonds form in G:C base pairs and two in A:T (or A:U) base pairs. This has deep implications for the mechanism of DNAreplication because in this way, the replica of each strand is given the base sequence of its complementary strand. This form of DNA double helix, known as B-form, is prevalent in vivo. However, other forms of the helix (such as A-form, Z-form) with distinct structures also exist (Table 2). The A-form of DNA (which is prevalent in vitro) is less soluble than the B-form. That is why DNA, which is over dried during plasmid preparation, for example, is difficult to dissolve.

Table 2. Comparison of morphological features and helical parameters of the three major types of DNA helix.

Morphological Characteristics	Conformation
	A	B	Z
Helical sense	Right	Right	Left
Pitch (base pairs per turn)	11	10	12
Major groove	Deep, narrow	Wide	Flat
Minor groove	Broad, shallow	Narrow	Narrow and very deep
Helix diameter	2.3 mm	1.9 mm	1.8 mm