Hydrogen Bonding and Stability
Hydrogen bonding is the chemical interaction that underlies the base-pairing rules described above. Appropriate geometrical correspondence of hydrogen bond donors and acceptors allows only the "right" pairs to form stably. DNA with high GC-content is more stable than DNA with low GC-content, but, contrary to popular belief, the hydrogen bonds do not stabilize the DNA significantly, and stabilization is mainly due to stacking interactions.
The larger nucleobases, adenine and guanine, are members of a class of double-ringed chemical structures called purines; the smaller nucleobases, cytosine and thymine (and uracil), are members of a class of single-ringed chemical structures called pyrimidines. Purines are complementary only with pyrimidines: pyrimidine-pyrimidine pairings are energetically unfavorable because the molecules are too far apart for hydrogen bonding to be established; purine-purine pairings are energetically unfavorable because the molecules are too close, leading to overlap repulsion. Purine-pyrimidine base pairing of AT or GC results in proper duplex structure. The only other purine-pyrimidine pairings would be AC and GT and UA (in RNA); these pairings are mismatches because the pattern of hydrogen donors and acceptors do not correspond. The GU pairing, with two hydrogen bonds, does occur fairly often in RNA (see wobble base pair).
Paired DNA and RNA molecules are comparatively stable at room temperature but the two nucleotide strands will separate above a melting point that is determined by the length of the molecules, the extent of mispairing (if any), and the GC content. Higher GC content results in higher melting temperatures; it is, therefore, unsurprising that the genomes of extremophile organisms such as Thermus thermophilus are particularly GC-rich. On the converse, regions of a genome that need to separate frequently — for example, the promoter regions for often-transcribed genes — are comparatively GC-poor (for example, see TATA box). GC content and melting temperature must also be taken into account when designing primers for PCR reactions.
Read more about this topic: Base Pair
Famous quotes containing the words hydrogen, bonding and/or stability:
“All you of Earth are idiots!... First was your firecracker, a harmless explosive. Then your hand grenade. They begin to kill your own people a few at a time. Then the bomb. Then a larger bomb, many people are killed at one time. Then your scientists stumbled upon the atom bomb—split the atom. Then the hydrogen bomb, where you actually explode the air itself.”
—Edward D. Wood, Jr. (1922–1978)
“At the heart of male bonding is this experience of boys in early puberty: they know they must break free from their mothers and the civilized world of women, but they are not ready yet for the world of men, so they are only at home with other boys, equally outcast, equally frightened, and equally involved in posturing what they believe to be manhood.”
—Frank Pittman (20th century)
“Every nation ... whose affairs betray a want of wisdom and stability may calculate on every loss which can be sustained from the more systematic policy of its wiser neighbors.”
—James Madison (1751–1836)