Forms of the DNA molecules
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A, B and Z forms of the DNA molecule In the deoxyribonucleic acid (DNA) molecule different combinations of monomeric compounds — nucleotides — linked together in a long chain are used to encode the information about the structure of proteins. Two chains of deoxyribonucleotides interact with each other following a certain rule — the principle of complementarity (adenine forms hydrogen bonds and pairs with thymine and guanine with cytosine) to form a double helix. The resulting molecule can be extremely long. At the human cells nuclei 2 meters of DNA is stored in a volume of 40 cubic micrometers (1).

DNA structure in different forms

The DNA molecule exists in different forms under different conditions. The ordinary form of DNA, the B form, predominates in the cell. B-DNA nitrogenous bases are almost perpendicular to the helical axis, and each base pair is twisted 36 degrees relative to the adjacent bases. Each complete turn of the helix encompasses 3.4 nm or 10 base pairs (9.7 and 10.6 in different crystals) (2).

The diameter of the B-DNA helix (the distance between phosphorus atoms of one complementary base pair) equals 2 nm, and purine and pyrimidine bases occupy 3/5 and 2/5 of this distance, respectively. The depths of the minor and major grooves are 0.85 nm and 0.75 nm, respectively. At the same time, the major groove is approximately two times wider (1.2 nm) than the minor groove (3).

It has been shown that in the higher salt concentrations or with the addition of non-electrolytes (e.g., ethanol), the DNA structure may change from the B to the A form. The deoxyribose ring changes its conformation from the C2-endo to the C3-endo form. The bases incline toward the axis by approximately 13o. In this form, there are 11 base pairs per turn (4).

  • A-form DNA molecule (A-DNA) - side view

    A-DNA side view

  • A-form DNA molecule (A-DNA) - end-view

    A-DNA end view

The A-DNA and B-DNA structures differ significantly in that in the B-form, the base pairs are tilted with respect to the helix axis by almost half of its radius. As a result, a cavity appears along the axis of the molecule, the major groove becomes deeper and more narrow, whereas the minor groove becomes wider and flatter (5). The B to A transformation occurs not only when the relative humidity of the sample is lowered but also when the heteroduplex with RNA is formed. A-DNA appears more stable due to the additional OH group in the ribose; thus, in the process of replication, A-DNA always exists in the cell during transcription, reverse transcription, and RNA-primer annealing.

In addition to the A and B forms of DNA, a Z form of double-stranded DNA has also been reported. Unlike the A and B forms, Z-DNA is a left-handed double helical structure with a 4.4-nm turn length and 12 base pairs per turn. Under conditions of low humidity and in the presence of certain salts, some parts of the DNA molecule rich in purine-pyrimidine sequences (stretches of alternating G and C sequences) are especially prone to conversion into the Z form. The presence of Z-DNA is characteristic of some enhancers (6, 7). This form may follow the action of RNA polymerase because of the negative super coiling of the DNA molecule.

  • Z-form DNA molecule (Z-DNA) - side view

    Z-DNA side view

  • Z-form DNA molecule (Z-DNA) - end view

    Z-DNA end view

Other forms of the DNA double helix, such as H, B`, ะก, and D forms, have also been described. However, these forms of DNA are rare and are not as physiologically relevant as the forms described above.

  • 3D-visualization:
    Ivan Konstantinov
  • Text:
    Yury Stefanov, (PhD)
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