Different forms of DNA generally exists in three common types, represented as B, A and Z forms. Inspite of B, A and Z forms, a DNA also exists as A, C and E forms which are not very common. Thus, a DNA can exist in different six forms either in a left or right-handed fashion, under appropriate physiological conditions.
Besides the above six forms, a DNA also forms some unusual structures like bent, triple-stranded, four-stranded DNA. The conformation of DNA strongly depends upon the pH and ionic strength of the solution. In certain viruses like bacteriophage ɸ x 174 consist of single stranded DNA. Some viruses and almost all prokaryotes consist of circular and superhelical DNA. So, in this content, we will discuss about all the possible forms of double-helical DNA.
Content: Different Forms of DNA
Different forms of DNA can define as the different structural configuration of DNA, which shows distinct change both in structure and physiology at relative pH and ionic strength of the solution. There are many different forms of DNA like B, A, C, D, E and Z have revealed after the X-ray diffraction analysis of DNA crystals at atomic resolution.
Forms of DNA
DNA, the hereditary material of the cell consist of a long polynucleotide chain which shows structural diversity by changing its structural configuration, based on various factors like:
- The hydration level
- Salt concentration
- DNA sequence
- Quantity and direction of supercoiling
- Presence of modified bases
- Presence of metal ions, polyamines in the solution
There are six types forms of DNA namely A, B, Z, C, D and E among which A, B and Z forms are most common and the other forms exist rarely.
It is the most common form of DNA, which exists as of right-handed double-helical DNA, given by Watson and Crick. This structure forms under the normal physiology conditions like 92% relative humidity and in low ionic strength and commonly refers as B-DNA. Based on X-ray diffraction studies, B-DNA represents an average conformation of DNA.
Majority of the cell comprises of B-DNA type and the coiling of B-form is in a right-handed pattern. In this, the nucleotide bases occupy at the core, whereas the sugar-phosphate bone occupies the peripheral region of the DNA-helix. In the solvent, the bases present at the edges of the B-form gets exposed. The width of each base pair is similar in both the polynucleotide chains of DNA.
The diameter of the B-form helix is 20Å and a single turn in B-form comprises of 10 base pairs are perpendicular to the helical axis. Bases show complementary base pairing in such a way like A=T and G≡C. In B-form, there is plectonemic coiling, where the two strands interwinds at the same helix.
The structure of B-form is “Asymmetric”, as the major and minor grooves are present alternatively. The major and minor groove is wider and narrow, respectively. In a B-type, the sugar pucker is at “C2” endoform. Width and depth of B-type major groove are 12Å and 8.5Å respectively, whereas width and depth of B-type minor groove are 6Å and 7.5Å, respectively.
It is the second most common form of DNA, which also refer to A-DNA and consists of right-helical sense. Its structure forms under the normal physiology conditions like 75% relative humidity and in the presence of sodium, potassium, caesium ions.
The coiling of A-form is in a right-handed fashion and it is metastable which can easily convert into D-form. In this, the nucleotide bases are displaced away from the core and found closer to the major groove. The conformation of bases in the A-form gives rise to the ribbon-like structure with an open cylindrical core.
A-DNA is considered to be more stable because of the presence of additional –OH group. The width of each base pair is similar in both the polynucleotide chains of DNA with the diameter of 23Å.
In A-form, base-pair tilt is higher than the B-form. A single turn in B-form comprises of 11 base pairs, which are perpendicular to the helical axis. In A-form also, both the strands are antiparallel and also having plectonemic coiling.
In A-form, the major groove becomes narrower and more profound, whereas the minor groove becomes wider and flattened. The sugar pucker or deoxyribose ring is present at “C3” endoconformation. A width of the B-type major groove is 2.7Å whereas a width of A-type minor groove is 11.0Å.
It is also a common form of DNA, which differs from both the B-DNA and A-DNA as it exists as left-handed double-helical DNA. This structure forms under very high salt concentration. Some of the cells, comprise of Z-DNA type and it was first introduced by three scientists, namely Rich, Northeim and Wang in 1984.
The coiling of Z-form is in a left-handed and zig-zag pattern. The conformation of Z-DNA is long and thin compared to the B-DNA. It shows an asymmetric structural configuration which gives rise to the zig-zag helical structure with no internal space.
The Z-DNA forms by the alternating stretching of purines and pyrimidines bases. The diameter of the Z-form helix is 18Å and the base-pair tilt is 7 Å, which is lower than the B and A-form. A single turn in B-form comprises of 12 base pairs, which are perpendicular to the helical axis.
In Z-form also, there is zig-zag plectonemic coiling and consist of antiparallel strands like B-DNA. In Z-type, the sugar pucker or deoxyribose ring is present at “C3” endoform for the purine bases and “C2” endoform for the pyrimidine bases. A width of the Z-type major groove is 2Å whereas a width of Z-type minor groove is 8.8Å.
In the cell, C-DNA is found in minimal quantity and its configuration exists at 66% relative humidity with low ionic strength. The helix of C-DNA is twisted in a right-handed fashion with a helix pitch of 30.97Å. It consists of 9.33 base pairs per turn.
Both the strands of C-DNA are antiparallel to each other, unlike Z-DNA. C-DNA has a helix diameter of 19.0 Å. The rotation per base pair is 38.6 Degrees, with a base pair tilt of 7.8 Degrees. The size and shape of the C-DNA are smaller than the B-DNA and A-DNA.
In the cell, D-DNA is found very rarely. The helix of D-DNA is twisted in a right-handed fashion and also refers as poly (dA-dT) and poly (dG-dC) form. D-form consists of 8 base pairs per turn which are displaced backwardly with respect to the DNA-helix. Both the strands of D-DNA are antiparallel to each other. The base pair tilt of D-DNA shows a negative tilt -16.7 Degrees with an axial rise is 3.03Å per base pair.
In the cell, E-DNA is found very rarely and is having an extended or eccentric DNA. The helix of E-DNA is long, and the bases are perpendicular to the helical axis. E-DNA consists of the deep major axis and shallow minor axis. After the X-ray crystallographic study, E-DNA is found intermediate between the B-DNA to A-DNA.
|Helical sense||Right handed coiling||Right handed coiling||Left handed coiling||Right handed coiling||Right handed coiling||-|
|Occurrence conditions||75% relative humidity with the presence of ions like sodium, potassium, cesium.||92% relative humidity with the low ion concentration||Occur at very high salt concentration with alternating purine and pyrimidine base sequence||66% relative humidity with the presence of lithium and magnesium ions.||-||-|
|Plane of the base||Perpendicular to the helical axis||Perpendicular to the helical axis||Perpendicular to the helical axis||Perpendicular to the helical axis||Perpendicular to the helical axis||-|
|Rotation per base pair||33 Degrees||36 Degrees||30 Degrees||38.6 Degrees||-||-|
|Axial rise per base pair||2.56 Å||3.38 Å||3.71 Å||3.32 Å||3.03 Å||-|
|Helix diameter||25.5 Å||20 Å||18 Å||19.0 Å||-||-|
|Base pairs per turn||11bp||10bp||12bp||9.33bp||8bp||7.5bp|
|Sugar phosphate backbone||Normal||Normal||Zig-Zag||Normal||Normal||-|
|Base pair tilt||19 Degrees||6.3 Degrees||7 Degrees||-7.8 Degrees||-16.7 Degrees||-|
|Helix pitch||25.5 Å||35.5 Å||45.6 Å||30.9 Å||-||-|
|Major groove||Narrow and deep major groove||Wide and deep major groove||Flat major groove||-||-||-|
|Minor groove||Wide and deep minor groove||Narrow and deep minor groove||Narrow and deep minor groove||-||-||-|
|Sugar puckering||C3 – endoconformation||C2 – endoconformation||C3 – endoconformation for purines and C2 – endoconformation for pyrimidines||-||-||-|
Factors Influencing Conformational Change
The conformational change of the double-helical DNA into different forms mainly depends upon the three factors like:
Physiological conditions: Humidity and the ionic or hydration environment favours the conformation change in the DNA.
DNA base sequence: It is the most crucial factor, which decides the shape, size, coiling and other structural properties of DNA.
Presence and binding of protein: A protein binds with the one helical conformation of the DNA and allows it to change its structure into different forms.
For example, a protein can bind to the B-DNA and change its conformation into either A or Z forms.
Thus, the above three factors mainly influence the DNA and make it structurally variant. Therefore, we can conclude that the double-helical structure of the DNA is not uniform and can vary under different physiological conditions provided.