The DNA molecule is known to exist in different forms under different conditions. The ordinary form of DNA called B form predominates in the cell. B-DNA bases are nearly perpendicular to the helical axis, and each base pair is twisted 36 degrees relative to the adjacent bases. Each complete rotation of the molecule encompasses 3.4 nm that is 10 base pairs (9.7 and 10.6 in different crystals) [1].
The diameter of the B-DNA helix is 2 nm (the distance between phosphorus atoms of one complementary base pair), purine and pyrimidine bases occupy 3/5 and 2/5 of this distance respectively. The depths of 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 one [2].
It has been shown that with less water present (higher salt concentrations), or with non-electrolytes (e.g. ethanol) added DNA structure may change from B to A form (upper picture). Desoxyribose ring changes its conformation from C2-endo to C3-endo form. The bases incline to axis by approximately 13º. In this form there are 11 base pairs per turn [3].
A significant difference between A-DNA and B-DNA consists in the fact that in the latter form base pairs are tilted with respect to the helix axis by almost half of its radius. As a result there appears cavity along the axis of the molecule. The major groove becomes deeper and narrower, whereas the minor groove becomes wider and flatter [4].
The B->A transformation occurs not only when the relative humidity of the sample is lowered but also when heteroduplex with RNA molecules is formed. A-DNA appears more stable due to the additional OH group of the ribose. Thus A-DNA always exists in the cell during transcription, reverse transcription, and RNA-primers annealing in the process of replication.
Alongside with A and B forms, Z form of double-stranded DNA was reported (the lower picture). Unlike the first two forms it is a left-handed double helical structure with turn length 4.4 nm and 12 base pairs per turn. Under low humidity and some salts added some parts of the molecule rich in purine-pyrimidine sequences (stretches of alternating G and C sequences) are especially prone to the conversion into Z form. The presence of Z-DNA is characteristic for some enhancers [5]. This form may follow RNA-polymerase at work as a result of negative superspiralization of the DNA molecule.
Other forms of DNA double helix are also known: H, B`, Ñ, and D forms. But they are found rarely, and are not as physiologically relevant as forms described above.
More:
Ultraviolet light-induced DNA damage: DNA-photolyase.
Molecular visualization of DNA-polymerase IV.
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 DNA images distributed with the licence. End user licence agreement.
The pictures was repeatedly used in press and in online resources, including:
News portal Lenta.ru (December 18, 2008); Lenta.ru (November 6, 2008);
Cast:
Project director, 3D vizualizator: Konstantinov Ivan
Web-technologist: Grishanin Kirill
Article author: Stephanov Yuri (translated from the Russian by Varvara Melikhova)
1. Baikalov I., Grzeskowiak K., Yanagi K., Quintana J., Dickerson R. E. The crystal structure of the trigonal decamer C-G-A-T-C-G-6meA-T-C-G: a B-DNA helix with 10.6 base-pairs per turn. J. Mol. Biol., 231; 768-784 (1993) 
2. Lipanov A., Kopka M. L., Kaczor-Grzeskowiak M., Quintana J., Dickerson R. E. Structure of the B-DNA decamer C-C-A-A-C-I-T-T-G-G in two different space groups: conformational flexibility of B-DNA. Biochemistry, 32; 1373-1389 (1993)
3. Auffinger P., Westhoff E. Water and ion binding around RNA and DNA (C,G) oligomers. J. Mol. Biol., 300; 1113-1131 (2000)
4. Eisenstein M., Shakked Z. Hydration patterns and intermolecular interactions in A-DNA crystal structures. Implications for DNA recognition. J. Mol. Biol., 248; 662-678 (1995)
5. Jaworski A., Hseih W.-T., Blaho J. A., Larson J. E., Wells R. D.Left-handed DNA in vivo. Science, 238; 773-777 (1987) |
