DNA conformation

Nucleic acids can adopt different conformations.

  • B-DNA is found at low salt concentrations. It is believed to be the native conformation occurring in chromatin.In the cell nucleus DNA is complexed with about an equivalent mass of protein to form a structure known as chromatin. Chromatin is a periodic structure made up of repeating, regularly spaced subunits, the subunit being the nucleosome. Within the nucleosomes the major part of DNA is wrapped around histones. The remaning DNA joining each nucleosome is known as linker DNA.

    Recently, the X-ray crystal structure of the nucleosome core particle of chromatin has been determined. It shows in atomic detail how the histone protein octamer is assembled and how 146 base pairs of DNA are organized into a superhelix around it (Luger et al., Nature 1997, 389, 251-260). The PDB code of this structure is 1aoi.

  • In solutions with higher salt concentrations or with alcohol added A-DNA is found.
  • Z-DNA occurs for alternating poly(dG-dC) sequences in solutions with high salt concentrations or alcohol.
  • RNA occurs (contrary to DNA) almost exclusively in the A-conformation (or in a related A’-form).
  • There are further nucleic acid conformations like C-DNA, H-DNA or others which are not discussed here.

Geometrical features:

The distance between two subsequent base pairs along the helical axis is called helical rise (h).The pitch (p) is the length of the helix axis for one complete helix turn. The turn angle per nucleotide or twist angle (t) is given by 360° / number of nucleotides per turn. C2′-endo and C3′-endo are descriptions of sugar conformations.

The most frequently occurring nucleic acid model conformations are characterized by the following geometrical parameters :

  • A-DNA
    • right-handed helix; sugar pucker: C3′-endo; number of nucleotides per pitch: 11; h: 2.56 Å; t: +32.7°.
  • B-DNA
    • right-handed helix; sugar pucker: C2′-endo; number of nucleotides per pitch: 10; h: 3.38 Å; t: +36° .
  • Z-DNA
    • left-handed helix; G: syn conformation; sugar pucker: C3′-endo; C: anti conformation, sugar pucker: C2′ endo; number of nucleotides per pitch: 6×2; h: 3.7×2 Å; t= -30°x2 (for Z-DNA the repeat unit is the dimer (G-C).

These geometrical features lead to different widths and depths of the minor and major grooves of the nucleic acid double helix (data from Jeffrey, Saenger, Hydrogen Bonding in Biological Structures, Springer-Verlag, 1991, Table 20.1, p. 401).

Groove Width Groove Depth
Major Minor Major Minor
A-DNA 2.7 Å 11.0 Å 13.5 Å 2.8 Å
Z-DNA 11.7 Å 5.7 Å 8.5 Å 7.5 Å

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