Base Pairing And Hybridization Of Dna Strands

In its natural state in the cell, DNA is actually composed of two strands that are linked together through a process known as hybridization. Individual nucleotides pair up with their 'complementary base' through hydrogen bonds that form between the bases. The base pairing rules are such that adenine can only hybridize to thymine and cytosine can only hybridize to guanine (Figure 2.2).

Figure 2.2

Base pairing of DNA strands to form double-helix structure.

There are two hydrogen bonds between the adenine-thymine base pair and three hydrogen bonds between the guanine-cytosine base pair. Thus, GC base pairs are stuck together a little stronger than AT base pairs. The two DNA strands form a double helix due to this 'base-pairing' phenomenon (Figure 2.2).

The two strands of DNA are 'anti-parallel', that is one strand is in the 5' to 3' orientation and the other strand lines up in the 3' to 5' direction relative to the first strand. By knowing the sequence of one DNA strand, its complementary sequence can easily be determined based on the base pairing rules of A with T and G with C. These combinations are sometimes referred to as Watson-Crick base pairs for James Watson and Francis Crick who discovered this structural relationship in 1953.

Hybridization of the two strands is a fundamental property of DNA. However, the hydrogen bonds holding the two strands of DNA together through base pairing may be broken by elevated temperature or by chemical treatment, a process known as denaturation. A common method for denaturing double-stranded DNA is to heat it to near boiling temperatures. The DNA double helix can also be denatured by placing it in a salt solution of low ionic strength or by exposing it to chemical denaturants such as urea or formamide, which destabilize DNA by forming hydrogen bonds with the nucleotides and preventing their association with a complementary DNA strand.

Denaturation is a reversible process. If a double-stranded piece of DNA is heated up, it will separate into its two single strands. As the DNA sample cools, the single DNA strands will find their complementary sequence and rehybridize or anneal to each other. The process of the two complementary DNA strands coming back together is referred to as renaturation or reannealing.

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