DNA Structure
In DNA there are four bases: adenine (A) Cytosine (C) Guanine (G) and Thymine(T). Adenine and guanine are purines, both of which have two joined carbon rings but have different side chains. Thymine and cytosine are pyrimidines, with only one ring but also having different side chains:
- Thymine
- Adenine
- Cytosine
- Guanine
A nucleoside consists if a base covalently bonded to a sugar. In DNA the sugar is deoxyribose so this is a deoxynucleoside. There are 4 types of these in DNA; deoxyadenosine, deoxyguanosine, deoxythymidine and deoxycytidine. A nucleotide is base + sugar +phosphate covalently bonded together. In DNA this is a deoxynucleotide. In DNA the nucleotides are covalently joined together by 3´5´ phosphodiester bonds to form a repetitive sugar-phosphate chain which is the backbone to which the bases are attached.
The phosphoric acid groups are both ionised at physiological pH, since the have pKas of 2 and 7. This makes them highly hydrophilic. DNA is strongly negatively charged. The sugar with its hydroxyl group is also highly hydrophilic. The bases are different in that they are almost water- insoluble. Their flat faces are essentially hydrophobic but at the edge they can form H-bonds.
Ribose is used in RNA but not in DNA. The difference here is that the 2´- OH group of ribose makes the polyribonucleotide less stable than the deoxyribose version. This is because in the presence of OH- ions the 2´OH group is well placed for a nucleophilic attack on the phosphorous atom, breaking the phosphodiester link.
In a DNA double helix, the two strands are wound round each other with the bases on the inside and the sugar-phosphate backbones on the outside.
The 2 chains are held together by complementary pairing between the bases, joining by H-bonds; A forming 2 H-bonds with T, C and G forming 3. It is the sequence of the bases that codes for the genetic information. Because A-T is only held by 2 bonds a piece rich in A+T will be less strongly held together. There is also a similar trend caused by reduced van der Waals forces in stacks of A+T pairs.
The hydrophobic interactions in the stacks contribute to the stability of the DNA molecule, (in fact they cause the increase in free energy of the helical structure relative to the flat ladder-like structure), but as in proteins the H-bonds have little contribution since they are replaced by H-bonds with water in the denatured protein. Input of temperature breaks the bonds in the molecule and causes denaturation, forming a random configuration. Eventually this renatures if the temperature is kept low enough.
The helix is right-handed and the strands are anti-parallel, meaning that they run in opposite directions. The structure is such that there is a major groove and a minor groove. The major groove provides easier access for proteins to recognize the edges of the base pairs. Structural proteins fit into the major groove.
This is the description of B-DNA, as proposed by Watson and Crick and this is the normal form for DNA to exist in cells, but it can adopt different conformations in special circumstances. When dehydrated, the helix becomes more squat and the bases are tilted; this is the A-DNA form, which may occur in spores. Z-DNA has a zigzag backbone with a left-handed helix. The significance of these is unknown. Real DNA differs from the ideal structures, as revealed by X-ray; eg the helical twist per base pair may range from 28 to 42 degrees. Each base pair may also roll or twist. However the backbone is conformationally constrained because of noncovalent interactions between the ribose ring and the phosphate groups and in polynucleotides there is steric interference between the nucleotides.
|