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Why does DNA contain the base thymine and not uracil?



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Why does DNA contain the base thymine and not uracil?

One reason is that the methyl group on the thymine is exposed in the major groove of DNA. This adds a hydrophobic hydrocarbon group on one side of the major groove (left or right) and helps an enzyme to distinguish an A:T base pair from a T:A base pair(‘looking’ into the groove from the side). The methyl group present on one side adds another molecular recognition point for certain more hydrophobic amino acids present in the active site of nucleic acid binding enzymes. Without the methyl group an enzyme ‘looking’ at uracil would ‘see’ just a hydrogen bond acceptor (the O-4 carbonyl from the uracil) and a hydrogen bond donor (the N–H group of the adenine amino group).Another reason for the presence of uracil is that there is a very slight increase in the thermal stability of the double helix itself, which may be due to a number of structural features; for example, better base pair stacking within the double helix. Despite the structural differences between thymine and uracil, they both base pair with adenine. There a son for the methyl-containing thymine base in DNA is based on the fact that conversion of the uridine mono phosphate (UMP) nucleosides to thymidine monophosphate (TMP) (via methylation – addition of a methyl group –CH3) is energetically expensive to the cell and the presence of a repair system to correct the slow spontaneous conversion (via de-amination –loss of an amine group –NH2) of cytosine in DNA touracil. This process of de-amination can also occur due to the presence of chemicals, for example, bisulfites (hydrogen sulfites).The effect of this reaction is potentially mutagenic and leads to a point mutation (transition), since uracil base pairs with adenine and so after replication one daughter strand would contain an AU base pair rather than the original GC base pair, i.e.:G–C → G–U → G–C and A–U This mutation is prevented by the presence of a repair enzyme (uracil DNA glycosylase) which recognizes uracil to be ‘foreign’ to DNA. The uracil is removed and replaced with cytosine. Thus the methyl group on thymine is a ‘marker’ which distinguishes thymine from de-aminated cytosine; otherwise there would be no means of identifying uracil in its correct place from uracil formed by the de-amination of cytosine. Consequently, it is hypothesised that thymine is used instead of uracil in DNA to enhance the fidelityof the genetic message. RNA is not repaired in the same way and so contains uracil, a less ‘expensive building block’. Presumably, very strong selective pressures lead to the evolution of an enzyme that removes uracils from DNA. This is perhaps the most important reason for having thymine in the place of uracil in DNA.


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