B-DNA: structure and direction
Predict firstDo the bases sit inside the double helix, or do they form the outermost backbone?
Recognize base complementarity, antiparallel direction, and the spatial structure of the double helix.
Prerequisites: A nucleotide is made of a phosphate, a deoxyribose sugar, and a base; 5′ and 3′ label the chemical direction of a strand.Meet the structural units
Predict firstDo the bases sit inside the double helix, or do they form the outermost backbone?
The outside is the sugar phosphate backbone: the pentagons stand for the sugar and the ochre spheres for the phosphate, while the blocks inside stand for a whole base rather than a single atom. Connections along the backbone and hydrogen bonds across the strands are different kinds of relationship.
How to observe
- Pick one base pair and look at the complementary pairing
- Compare the 5′→3′ directions of the two backbones
- Rotate to the side and look at the grooves of unequal width
Model notes
The measured mode uses the atomic coordinates of the 12 base pairs of RCSB PDB 1BNA (a 1.90 Å X-ray structure), with crystal waters removed; the original file contains no hydrogen atoms, and bonds are inferred from distance without bond orders. The teaching mode uses an ideal right-handed B-DNA sketch: 22 base pairs, about 10.5 bp per turn and a rise of 0.34 nm per layer. Backbones and base blocks mark structural units, not atomic coordinates; the unequal grooves are a qualitative layout. Replication, thermal motion and protein binding are not simulated, and the real conformation changes with sequence and environment.