Different Forms of DNA

DNA generally exists in three common types (represented as B, A and Z forms). Besides B, A and Z forms, DNA may rarely exist as A, C and E forms. Therefore, DNA possesses six different forms that are either in a left or right-handed fashion, under appropriate physiological conditions.

Inspite of the above six forms, DNA may form some unusual structures like bent, triple-stranded and four-stranded DNA. The conformation of DNA strongly depends upon the pH and ionic strength of the solution. Certain viruses like bacteriophage ɸ x 174 comprise a single stranded DNA.

Some viruses and almost all prokaryotes possess circular and superhelical DNA. In this context, we will discuss all the possible forms of double-helical DNA.

Content: Different Forms of DNA

    1. Definition
    2. Forms of DNA
    3. Factors Influencing Conformational Change

Definition

Different forms of DNA can define as the different structural configuration of DNA that shows a distinct change in structure and physiology at relative pH and ionic strength of the solution. 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 (hereditary material of the cell) consists of a long polynucleotide chain and 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

forms of DNA

Common Forms

Among six different forms of DNA, B, A and Z forms are the most common:

B-form

It is the most common form of DNA, which exists as a right-handed double-helical DNA. It was pioneered by Watson and Crick. B-DNA structure forms under normal physiological conditions like 92% relative humidity and low ionic strength.

Based on the X-ray diffraction studies, B-DNA represents an average conformation of DNA. The majority of the cell comprises a B-DNA type, and the coiling of B-form is in a right-handed pattern.

The nucleotide bases occupy 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 10 base pairs (perpendicular to the helical axis). Bases show complementary base pairing in such a way as A=T and G≡C. There is plectonemic coiling in the B-form, where the two strands interwind at the same helix.

The B-form structure is “Asymmetric”, as the major and minor grooves are present alternatively. The major and minor grooves are wider and narrow, respectively. In a B-type, the sugar pucker is at “C2” endoform.

The width and depth of the B-type major grooves are 12Å and 8.5Å, respectively. Oppositely, the width and depth of the B-type minor grooves are and 7.5Å, respectively.

A-form

It is the second most common form of DNA, also called A-DNA. It has DNA of right-helical sense. A-DNA structure forms under normal physiological conditions like 75% relative humidity and the presence of sodium, potassium, and caesium ions.

The coiling of A-DNA is in a right-handed fashion. It is metastable, i.e. easily turns into a D-form. 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 an additional –OH group. The width of each base pair is similar in both the polynucleotide chains of DNA with a diameter of  23Å.

In A-form, base-pair tilt is higher than the B-form. A single turn in B-form comprises 11 base pairs (perpendicular to the helical axis). In A-form also, both the strands are antiparallel, or they have 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. The B-type major groove’s width is 2.7Å, while the width of the A-type minor groove is 11.0Å.

Z-form

It is another form of DNA, which differs from both the B-DNA and A-DNA. It exists as left-handed double-helical DNA. This structure forms under very high salt concentration. Some of the cells comprise the Z-DNA type, and it was first introduced by the three scientists Rich, Northeim and Wang in 1984.

The coiling of the 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 Z-form helix’s diameter 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 12 base pairs, which are perpendicular to the helical axis.

In Z-form also, there is zig-zag plectonemic coiling. It possesses antiparallel strands like B-DNA. In Z-type, the sugar pucker or deoxyribose ring is present at the “C3” endoform for the purine bases and the “C2” endoform for the pyrimidine bases. The Z-type major groove’s width is , whereas the width of the Z-type minor groove is 8.8Å.

Different types of DNA

Other Forms

Besides A, B and Z forms of DNA, few other types rarely occur:

C-form

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.

D-form

In the cell, D-DNA is found very rarely. The helix of D-DNA is twisted in a right-handed fashion and called the 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 of -16.7 degrees with an axial rise of 3.03Å per base pair.

E-form

In the cell, E-DNA is found very rarely and having 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.

PropertiesA-DNAB-DNAZ-DNAC-DNAD-DNAE-DNA
Helical senseRight handed coilingRight handed coilingLeft handed coilingRight handed coilingRight handed coiling-
Occurrence conditions75% relative humidity with the presence of ions like sodium, potassium, cesium.92% relative humidity with the low ion concentrationOccur at very high salt concentration with alternating purine and pyrimidine base sequence66% relative humidity with the presence of lithium and magnesium ions.--
Plane of the basePerpendicular to the helical axisPerpendicular to the helical axisPerpendicular to the helical axisPerpendicular to the helical axisPerpendicular to the helical axis-
Rotation per base pair33 Degrees36 Degrees30 Degrees38.6 Degrees--
Axial rise per base pair2.56 Å3.38 Å3.71 Å3.32 Å3.03 Å-
Helix diameter25.5 Å20 Å18 Å19.0 Å--
Base pairs per turn11bp10bp12bp9.33bp8bp7.5bp
Sugar phosphate backboneNormalNormalZig-ZagNormalNormal-
Base pair tilt19 Degrees6.3 Degrees7 Degrees-7.8 Degrees-16.7 Degrees-
Helix pitch25.5 Å35.5 Å45.6 Å30.9 Å--
Major grooveNarrow and deep major grooveWide and deep major grooveFlat major groove---
Minor grooveWide and deep minor grooveNarrow and deep minor grooveNarrow and deep minor groove---
Sugar puckeringC3 – endoconformationC2 – endoconformationC3 – 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 following three factors:

Factors influencing DNA to change its conformation

  1. Physiological conditions: Humidity and the ionic or hydration environment favours the conformation change in the DNA.
  2. DNA base sequence: It is the most crucial factor, which decides the shape, size, coiling and other structural properties of the DNA.
  3. Presence and binding of protein: A protein binds with the one helical conformation of the DNA and changes its structure into different forms. For example, a protein can bind to the B-DNA and change the conformation into A or Z forms.

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.

1 thought on “Different Forms of DNA”

Leave a Comment

Your email address will not be published. Required fields are marked *