Types of DNA Structure

In this topic we will cover all types of DNA structure. According to Watson-Crick pairing the pairing occurs between A and T and between G and C which is said to be complementary. The base pairs lie almost flat, stacked on top of one another perpendicular to the long axis of double helix. Stacking adds to stability of DNA molecule by excluding water molecules from the spaces between the base pairs. While discussing a DNA molecule, biologists frequently refer to the individual strands as single stranded DNA and to the double helix as double stranded DNA or duplex DNA.

Types of DNA Structure / Forms of DNA

DNA can exist in other forms also like A, B, Z etc. Although only B- DNA and Z-DNA have been directly observed in functional organism. The conformation that DNA adopts depends on the following factors:-

The hydration level
DNA sequence
The amount and direction of supercoiling
Chemical modification of bases
Type and concentration of metal ions as well as the presence of polyamines in the solution
Conformational change involves the rotation around the glycosidic bond. . It changes the orientation of base in relation to the sugar.
Conformational changes around the bond between the 3’ and 4’ carbon can also take place.

Both the above (6,7) rotations result in changed positioning of two strands and certain alternate structure of DNA can be formed.

Types of DNA Structure / Forms of DNA

‘A’ DNA

It is very minor species of DNA that may or may not be present under normal physiological conditions.
A-DNA appears when the DNA fibre (B-DNA) is dehydrated, i.e., relative humidity is reduced from 92 to 75% and Na+, K+ and Cs+ ions are present in the medium.
In other words, in solution, DNA assumes the B form and under conditions of dehydration, the A form. This is because the phosphate groups in the A-DNA bind fewer water molecules than do phosphates in B-DNA.
The `A’ DNA is more compact than the `B’ DNA.
It has the diameter of 25.5 Å, distance between two adjacent bases is 2.9 Å and the pitch is 32 Å. Thus there are 11 bases/turn.
This form of DNA has high degree of resemblance with double stranded RNA.
It has much deeper major groove and the minor groove is very shallow.
The `A’ DNA is right handed in its helical turnings.

‘B’ DNA or Watson and Crick DNA double helix model

i. It consists of two antiparallel polynucleotide strands that wind about a common axis with a right handed twist to form a double helix.

ii. The ideal B-DNA helix has the diameter of 20 Å. The bases are 3.4 Å apart along the helix axis and the helix rotates 36° per base pair. Therefore, the helical structure repeats after 10 residues on each chain, i.e., at intervals of 34 Å. In other words, each turn of the helix contains 10 nucleotide residues.

iii. The phosphate and deoxyribose units are found on the periphery of the helix, whereas the purine and pyrimidine bases occur in the centre. The planes of the bases are perpendicular to the helix axis.

iv. Each base is hydrogen bonded to a base on opposite strand (A with T and G with C) to form a planar base pair. The planes of the sugars are almost at right angles to those of the bases.

v. The hydrogen bonding between the bases takes place either between the –NH₂ group of one base and =O of the other base or between =NH of one base and the –N of the other base. For stable bond formation, the distance between N-N is 0.30 nm and that between O-N is 0.28-0.29 nm.

vi. The double helix has major and minor grooves.

vii. When the ion such as Na⁺ and the relative humidity is >92%. Fibers of DNA assume the so called B- Conformation It is the most stable structure for a random sequence of DNA and is therefore the standard point of reference.

types-of-dna-structure — B-DNA-structure

‘C’ DNA

C-DNA is formed at 66% relative humidity in the presence of Li⁺ ions.
C-DNA is also right-handed, with an axial rise of 3.32 Å per base pair.
There are 9.33 base pair per turn of the helix ; the value of helix pitch is, therefore, 3.32 × 9.33 Å or 30.97 Å.
The rotation per base pair in C-DNA is approximately 360/9.33 or 38.58°.
The diameter of C-helix is 19 Å, which is smaller than that of both B- and A-helix.
The tilt of the base pairs is 7.8°.

‘D’ DNA

D-DNA consists of only 8 base pairs per helical turn.Therefore, is an extremely rare variant.
D- DNA is found in some of the DNA molecules which are devoid of guanine.
D-DNA has an axial rise of 3.03 Å per base pair, with a tilting of 16.7° from the axis of the helix.

By contrast, A-, B- and C forms of DNA are found in all DNA molecules, irrespective of their base sequence.

‘Z’ DNA

`Z’ DNA is left handed form of the DNA.
In Z DNA the turns in the DNA helix are in opposite direction than in other forms of DNA.
`Z’ DNA is slimmer and has a diameter of only 18.4 Å.
`Z’ DNA have about 12-bases/ turn.
`Z’ DNA have no major and minor grooves. There is only one groove and that too is narrow and deep.
`Z’ DNA named as such because the base conformation is more like a zig-zag arrangement.
Under experimental conditions the presence of `Z’ DNA has been shown in high salt condition or in presence of certain specific cations, such as spermine and spermidine.
Z’ DNA has high degree of negative supercoiling and has certain specific proteins attached to it.
Besides, relatively high methylation at 5- position of C residues has been found in `Z’ DNA.

Role of different forms

Though precise role of alternate forms of DNA is not very well understood, they may play some regulatory function. The possibility that some of these DNAs may be artifact of experimental conditions may not be completely ruled out. As discussed, the conformation of DNA plays an important biological function. Majority of the regulatory controls require binding of certain factors to DNA. Any change in the structure will affect the binding of these factors and will therefore regulate the biological activity.

Some Unusual Structures

Bent DNA

Bends occur in DNA helix wherever four or more adenosine residues appear sequentially in one strand.
Bent DNA may be important in binding of some proteins to DNA.

H DNA

H-DNA is usually found in polypyrimidine or polypurine segments that contain within themselves a mirror repeat.
One simple example is a long stretch of alternating T and C residues.
A striking feature of H-DNA is the pairing and interwinding of 3 strands of DNA to form a triple helix.
Triple-helical DNA is produced spontaneously only within long sequences containing only pyrimidines (or purines) in one strand.
Two of the three strands in the H-DNA triple helix contain pyrimidines and the third contains purines.

Hoogsteen Pairing

The N- 7, O6 and N6 of purines, the atoms that participate in hydrogen bonding of triplex DNA are often referred to as Hoogsteen position and the non Watson – Crick pairing is called Hoogsteen pairing.

The triplexes are most stable at low pH, and are readily formed within long sequences containing only purines in a given strand.

Tetraplex structures may also form in DNA sequences with a very high proportion of guanosine residues.

G-Quadruplex

Structure of a DNA quadruplex formed by telomere repeats.
The conformation of the DNA backbone diverges significantly from the typical helical structure.
Here, four guanine bases form a flat plate and these flat four-base units then stack on top of each other, to form a stable G-quadruplex structure.
The guanine-rich sequences may stabilize chromosome ends by forming very unusual structures of stacked sets of four-base units, rather than the usual base pairs found in other DNA molecules.
Telomeres and telomerase have recently received great attention because of their potential links to cancer, HIV and other diseases.
A unique G-rich DNA sequence in the telomeres was found to protect the chromosomes from recombination, end to end fusion, and degradation through forming G-quadruplexes with highly polymorphic structures in the presence of alkali metal cations.
This unusual structure and extensive cellular functions make G-quadruplex a very attractive target for drug design, which made it important for determination of G-quadruplex.