Different Forms of DNA

The basic structural and functional unit of life i.e., cell consists of the nucleus. The nucleus holds the constituents of every living organism and the generations that would come later. Inside the nucleus is the chromosome which in turn consists of the genetic equation i.e., Deoxyribonucleic acid (DNA).

All cellular organisms have double-stranded DNA genomes. DNA can be considered as a modified form of RNA since the normal ribose sugar in RNA is reduced into deoxyribose in DNA, whereas the simple base uracil is methylated into thymidine.

In modern cells, the DNA precursors (the four deoxyribonucleotides, dNTPs) are produced by reduction of ribonucleotides di- or triphosphate by ribonucleotide reductase. The synthesis of DNA building blocks from RNA precursors is a major process. Based on the structure and certain characters, there are different forms of DNA namely A-DNA, B-DNA, and Z-DNA

Formation of A, B & Z Forms of DNA

Whether the DNA sequence will be A, B or Z depends on the three most important factors.

  • There must be anionic or hydrating environment that can facilitate the conversion between different helical forms of the DNA. Z DNA can be favored by a high concentration of chloride molecules as well.
  • A-DNA is favored by certain stretches of purines or pyrimidines, whereas Z facilitates more readily into alternating purine pyrimidine combinations.
  • The final factor is that there should be the presence of proteins that can bind to DNA in one helical conformation and force the DNA to adopt a different conformation.
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In living cells, B-DNA is among the most common forms of DNA found.

1. A-DNA

The major difference in this form of DNA over other forms is that the conformation of its deoxyribose sugar ring. A-DNA is present in the third carbon (C3 endo conformation). It has its base pairs displaced away from the central axis and appears much closer to the groove. This results in a ribbon-like helical structure with a more open cylindrical core.

There are eleven base pairs and an axial rise of 0.26 nm. It possesses a twist angle of 33 degrees and is 2.3 nm in helix diameter. A-DNA appears more compressed along its axis than B-DNA. Dehydration of DNA drives it into the A form, and this protects DNA under conditions such as the extreme desiccation of bacteria.

Protein binding can also strip solvent off of DNA and convert it to the A form, as revealed by the structure of several hyperthermophilic archaeal viruses, including rod-shaped SIRV2 and SSRV1, enveloped filamentous lipotrim viruses AFV1, SFV1, and SIFV, tristromavirus PFV2 as well as icosahedral portoglobovirus SPV1.

A-form DNA is believed to be one of the adaptations of hyperthermophilic archaeal viruses to harsh environmental conditions in which these viruses thrive.

The motors that package double-stranded DNA in bacteriophages exploit the fact that A-DNA is shorter than B-DNA during conformational changes. In A-DNA, ATP hydrolysis is used to drive protein conformational changes that dehydrate and rehydrate the DNA in the shortening/lengthening cycle.

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2. B-DNA

It is the most common form of DNA which we all possess, the model proposed by Watson and Crick. They are double-stranded, each in a right-hand helix wound around the same axis. Both the strands are held together by H-bonding between the bases, referred to as anti-conformation.

The strands run anti-parallel and coiled. The nucleotides are arrayed in a 5’-3’ (read as five prime to three prime) on one strand aligning with the complementary opposite strand as 3’-5’.

The bases are paired as per Chargaff’s rule of pyridine of one with the purine of the other. This pairs a keto base with an amino base. Two hydrogen bonds can be formed between adenine and thymine and three between guanine and cytosine.

Consists of 34 nm space between each base pair and are about 9 nm in diameter. It consists of a twist angle of 36 degrees.

3. Z-DNA

Z-DNA is a radically different structure, with the two strands coiling in left-handed helices and a pronounced zig-zag pattern in the phosphodiester backbone. Z-DNA can form when the DNA is in an alternating purine-pyrimidine sequence such as GCGCGC, and with G and C in different conformations.

The big difference is at the G nucleotide. It has the sugar in the C3′ endo conformation (like A-form nucleic acid, and in contrast to B-form DNA) and the guanine base is in the syn conformation. This places the guanine back over the sugar ring, in contrast to the usual anti-conformation seen in A and B-form nucleic acid.

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The duplex in Z-DNA has to accommodate the distortion of this G nucleotide in the syn conformation. The cytosine in the adjacent nucleotide of Z-DNA is in the “normal” C2′ endo, anti-conformation.

It was discovered by Rich, Nordheim & Wang in 1984. It consists of antiparallel strands as B-DNA and has 12 bp per turn, 0.45 nm axial rise, 45o helix pitch, and 7o base-pair tilt.

Difference & Comparison Between A, B, & Z Forms of DNA

The most intricate fact is that A-DNA is formed from B-DNA under dehydrating conditions. It appears much wider and flatter than B-DNA. Both the forms share a similar feature of being a right-handed helix. A-DNA is 20-25% shorter than B-DNA due to the smaller rise it constitutes per turn. Unlike B-DNA, A-DNA has a hollow central core, which is an axial hole at the exact center. 

On the other hand, Z-DNA is completely different from both A and B, mainly due to its physical structure. Z-DNA is completely left-handed in terms of its twists. The pattern of Z-DNA is more of a zig-zag helix, unlike A and B. The helical turns would consist of 12 nucleotides. It possesses a much more flat major grove than A-DNA and B-DNA. 

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