Biotechnology and Bioinformatics (1+1)

1.2.2.1.The Double helix

Polynucleotides

DNA molecules form chains of building blocks called nucleotides. Each nucleotide consists of a sugar molecule called deoxyribose that bonds to a phosphate molecule and to a nitrogen-containing compound, known as a base. DNA uses four bases in its structure: adenine (A), cytosine (C), guanine (G), and thymine (T).

The order of the bases in a DNA molecule—the genetic code —determines the amino acid sequence of a protein .

In the cells of most organisms, two long strands of DNA join in a single molecule that resembles a spiraling ladder, commonly called a double helix.

• Alternating phosphate and sugar molecules form each side of this ladder.
• Bases from one DNA strand join with bases from another strand to form the rungs of the ladder, holding the double helix together.
• The pairing of bases in the DNA double helix is highly specific—adenine always joins with thymine, and guanine always links to cytosine.
• These base combinations play a fundamental role in DNA’s function by aiding in the replication and storage of gene tic information. Complementary base pairing enables to predict the sequence of bases on one strand of a DNA molecule if the order on the corresponding or complementary DNA strand is known.
• Watson and Crick found that the best model that satisfied all the X-ray data was a double helix with the sugar phosphate chain on the outside and the bases on the inside.
• The two chains run in an anti parallel fashion with one chain having a 5'→3' orientation and the other having a 3'→ 5' orientation.
• The width of the helix was found to be 2 nm. The purine and pyrimidine bases were stacked 0.34 nm apart in a ladder.
• The helix made one full turn every 3.4 nm and, therefore, there should be 10 layers of bases stacked in one turn.
• Since the width of the helix is 2 nm it can accommodate only 2 strands.
• Each step would contribute a pair of bases, with each base attached to one of the sugar-phosphate backbone.
• In a given DNA, adenine is equal to thymine and guanine to cytosine.
• The two strands of DNA are held together by hydrogen bonds. There are two hydrogen bonds for A = T pairing and three bonds for C º G pairing. C º G pairing is stronger than A = T pairing.
• Helical structure is right handed.
• The fifth (5- prime, of 5') carbon of the pentose ring is connected to the third (3 - prime, of 3 ') carbon of the next pentose ring via a phosphate group, and the nitrogenous bases stick out from this sugar-phosphate back bone.
• By convention, DNA sequence s are read from 5'→3' with respect to the polarity of the strand.

Watson and Crick model suggested a copying mechanism for DNA. Since one strand is the complement of the other, the two strands can be separated, and each can serve as the template for building a new strand.

Watson and Crick were aware of this potential and they wrote in the Journal Nature, "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material".