The Structure of DNA

DNA, is a polymer of deoxyribonucleotides
All living cells (both prokaryotic and eukaryotic) contain double stranded DNA as their genetic material.
 

   Chemical Structure of DNA Monomers

 Individual monomers - deoxyribonucleotides (nucleotides)
Components:
1) deoxyribose (5 carbon sugar, pentose sugar) (Fig. 1).

 2) phosphate group (1 phosphorus and 4 oxygens) (Fig. 2).

 At pH 7.0 the phosphate group has a net negative charge. The phosphate group is attached to deoxyribose at the 5' carbon position and the 3' carbon position.

 The alternation of deoxyribose-phophate-deoxyribose, etc. is referred to as the phosphate sugar backbone of DNA (Fig. 5). The type of chemical bond that holds the backbone together is called a phosphodiester bond. It is a very strong covalent bond (oxygen from phosphate group forms an ester linkage with either the 3' or 5' carbon).

 3) Nitrogenous Base - attached to deoxyribose at the first carbon. Four types are found in DNA: (Note: to view these bases interactively on your Web browser, the free Chemscape Chime plug-in viewer must be installed in your browser's plug-in folder.)
adenine, guanine, thymine, cytosine

 Two structural families:
purines - double ring structure (adenine and guanine) (Fig. 3).
pyrimidines - single ring (thymine and cytosine) (Fig. 4)
 

 Base + Sugar = nucleoside

 Base + Sugar + Phosphate Group = nucleotide

 A DNA molecule is a long polymer of subunits called deoxyribonucleotides.

The backbone of the polymer is composed of phosphate groups alternating with a sugar (deoxyribose) to form a covalently linked chain. (Fig. 5)

Just like with proteins N-----> C the chain has directionality 5'P--------->3'OH .

Attached to the sugar ring is one of 4 nitrogenous bases. The bases project out from the sugar-phosphate backbone toward the center of the structure. (Sort of like the R groups of the proteins projecting out).

 *The order of nucleotide bases along the polymer chain, provides the information that specifies the composition of a cell's protein molecules.

Chargoff examined base ratios from bacteria, animals, and plants. Whenever he determined the ratio of the two purines (adenine / guanine) the A:G ratio was found to vary dramatically.
0.4 for bacteria 1.72 for yeast

 Interestingly, the ratio of the two pyrimidines (thymine to cytosine) also varied
However, from such data, a common theme emerged: the ratio of purines to pyrimidines was always 1:1.

 Chargoff's Rule A+G = T+C

 Out of these observations the idea of base pairing between purines and pyrimidines emerged (Fig. 6).

 You may often hear reference to G:C content

 G+C
G+C+A+T relative amount of G+C to total number of bases

 Some evidence was also coming in concerning the physical structure of DNA. X-ray diffraction revealed that DNA was a very long, thin structure - stacking of bases periodicity.

 Watson - Crick

Compiled available data to propose a model for the structure of DNA. They themselves contributed no data to the model, they simply interpreted other people's findings into an hypothesis.
Nature 1953 171:737-738 The structure of deoxyribonucleic acid.

 So...DNA consists of two strands held together by hydrogen bonding between adjacent base pairs. The two strands are then twisted to the right to form a helix (Fig. 6).

 *10 base pairs per turn
*each base pair is 0.34 nm thick
*10 base pairs would be 0.34 nm X 10 = 3.4 nm length
If you are given the length of a segment of DNA you can calculate the number of base pairs. If a DNA molecule is 1 um

 1u = 1000nm
1000 nm/0.34 nm/bp = 2941 base pairs

A 3-D interactive  DNA model.  (Note: to view these bases interactively on your Web browser, the free Chemscape Chime plug-in viewer must be installed in your browser's plug-in folder.)

B -DNA has major and minor grooves because of the helix (Fig. 7).

Very importantly, it is these grooves which allow DNA binding proteins access to the bases. Sequence specific proteins, must make contact with base pairs. Major groove is most accessible.

 DNA is anti-parallel
One strand runs from 5' ------>3' while the opposite strand runs 3'----->5' (Fig. 5). Both DNA replication and transcription occur from the 5' end toward the 3' end. In other words new nucleotides are always added onto the 3' hydroxyl group.

 Two DNA strands are complementary due to specific base-pairing (Fig. 6).
adenine is always hydrogen bonded to thymine (2 hydrogen bonds)
cytosine is always hydrogen bonded to guanine (3 hyrdrogen bonds)

The structure of DNA we have described today is designated B-DNA (Fig. 7).

Other forms are known to exist. i.e. A-DNA (Fig. 8) and Z-DNA (Fig. 9) which is a left handed DNA in a zig zag pattern.

Comparison of the A-, B-, and Z-forms of DNA show differenced in width, handedness, and number of bases/turn (Fig. 10).

Comparison of the two right handed forms, A- and B-, show differences in the accessability of the major and minor grooves (Fig. 11)as well as the orientation around the central axis (Fig. 12).

 Probably exerts a regulatory activity when in Z conformation (Fig. 10).