## Saturday, June 5, 2010

### How is a base-pair rectangular block defined in 3DNA?

One of 3DNA's unique features is the base-pair (and base) rectangular blocks, as shown in the figure below. Since such a schematic was initialized by Calladine and Drew in their Understanding DNA book, I normally refer it as the Calladine-Drew style representation.

By default, a base-pair [BP, (a)] has a dimension of 10x4.5x0.5 Å; a purine [R, (b) left] 4.5x4.5x0.5 Å; a pyrimidine [Y, (b) right] 3x4.5x0.5 Å; and a mean base [M, (c)], which is exactly half of the base-pair, 5x4.5x0.5 Å.

The blocks are put into specific files: Block_BP.alc, Block_R.alc, and Block_Y.alc respectively. To use M for R and Y, one just needs to copy file Block_M.alc to overwrite Block_R.alc and Block_Y.alc in the current directory or the system directory (\$X3DNA/config/). These blocks are used in the rebuilding and visualization components of 3DNA (see my blog post "blocview: a simple, effective visualization tool for nucleic acid structures").

The blocks are stored in the ALCHEMY format for easy specification of the nodes and edges, and since ALCHEMY is a format supported by RasMol (and Jmol). As an example, Block_BP.alc has the following content:
`   12 ATOMS,    12 BONDS    1 N      -2.2500   5.0000   0.2500    2 N      -2.2500   0.5000   0.2500    3 N      -2.2500   0.5000  -0.2500    4 N      -2.2500   5.0000  -0.2500    5 C       2.2500   3.5000   0.2500    6 C       2.2500   0.5000   0.2500    7 C       2.2500   0.5000  -0.2500    8 C       2.2500   3.5000  -0.2500    9 C      -2.2500   5.0000   0.2500   10 C      -2.2500   0.5000   0.2500   11 C      -2.2500   0.5000  -0.2500   12 C      -2.2500   5.0000  -0.2500    1     1     2    2     2     3    3     3     4    4     4     1    5     5     6    6     6     7    7     7     8    8     5     8    9     9     5   10    10     6   11    11     7   12    12     8`
Astute viewers may observe that nodes 1-4 are identified as N (nitrogen) and have exactly the same coordinates as 9-12 (C, carbon). This is a trick so RasMol can display the the minor groove edge in a different color than the other five sides of the rectangular, as shown in the following figure:

Note that the rectangular is preset in the standard base reference frame. Thus the nodes have y-coordinates of +5 Å and -5 Å along the long edge of the base pair, and x-coordinates of +2.25 Å and -2.25 Å along the short edge.

As an extra bonus of storing the blocks in external ALCHEMY text files, the dimensions of the blocks are be readily changed. For example, the depth of a block (z-coordinates) can be easily increased from 0.5 to 1.0 Å to make it thicker (see \$X3DNA/config/Block_BP1.alc). Moreover, the blocks do not need to be rectangular either – see \$X3DNA/config/block/Block_R_nr.alc for an example.