A-DNA
DNA model conformation

Images

Structures

A-DNA

InsightII

• decamer, spacefill (mono,stereo)
• decamer, ribbon, balls and sticks (mono, stereo)
• decamer, spacefill, topview (mono, stereo)

MIDAS

• decamer, ribbon, plates (mono, stereo)
• decamer, ribbon, plates, top view (mono, stereo)
• 21-mer, ribbon, plates (mono, stereo)
• 21-mer, spacefill (mono, stereo)
• 21-mer, sticks (mono, stereo)
• 30 base pairs, spacefill (mono, stereo)

WEBLAB

• 21-mer, lines, top view (mono, stereo, VRML)
• 21-mer, sticks, top view (mono, stereo)
• 21-mer, ribbon, lines (mono, stereo, VRML)

Location of the helix axis

In A-DNA the helix axis is located in the major groove side of the base pairs.

This is shown for the decamer D( GCACGCGTGC) structure (PDB/NDB code: 260d/adj075). The mono, stereo and VRML representations display in orange the helix axis calculated with the CURVES algorithm and in grey axes corresponding to the related principal axes of inertia. Only two base pairs are shown. More detailed information on the double helix geometry of this structure can be found on the helix analysis and bending pages.

Comparing A- and B-DNA

InsightII

• A-DNA and B-DNA on one image, balls and sticks (mono, stereo)
• A-DNA and B-DNA on one image, balls and sticks, top view (mono)
• A-DNA and B-DNA on one image, spacefill (mono, stereo)
• A-DNA and B-DNA superimposed, ribbon, sticks (mono, stereo)

Distance Plots

A-DNA

• dodecamer, representative atom: O3* (GIF, PDF)

Comparing A- and B-DNA

• difference distance plots A-DNA - B-DNA:representative atom: O3* (GIF, PDF)

COMMENTS

The coordinates were generated using INSIGHTII.

For the dodecamer the sequence is the same as for the Okazaki fragment (1ofx_ahj040, 169d).

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