The hydrophobic effect. While the edges of the base pairs can make hydrogen bond contacts, the planar surfaces are relatively hydrophobic. Therefore, water is less ordered with the bases outside the helix (no base-paired) than when they are inside (base-paired). The hydrophobic effect that produces this arrangement is calledbase stacking.
2. The two strands are antiparallel.
That is one strand goes in the 3' to 5' direction, while its complementary strand goes in the opposite direction. This is shown in Figure 2.14, above.
3. The helix has three distinct forms:
Properties of DNA helices A Form B Form Z Form RNA-DNA Hybrid Direction of helix rotation rightright left right Residues per turn 11 1012 11Rotation per residue 33 deg. 36 deg. –30 deg. 33 deg. Rise 0.255 nm0.34 nm 0.37 nm 0.255 nm Pitch 2.8 nm3.4 nm 4.5 nm 2.8 nm
A- form DNA occurs when the amount of water in the surrounding medium is about 75%. The B- form occurs at much higher moisture content, 92%. Z-DNA, or left-handed DNA occurs in regioins of high GC content. Notice that anRNA/DNA hybrid has the same structural parameters as A form DNA.
Here's a side-by-side comparison of A-form and B-form DNA, using wire-frame models: