Opening Image: A-, B- and Z-DNA. Each double-stranded structure contains 14 Watson-Crick base pairs.
backbone traces. Both the A- and B-DNA are right-handed helices. Remember the sense of a helix is intrinsic (it does not depend on the end from which it is viewed). For a right-handed helix, the strands rotate in a clockwise direction as they move away from you. alternate views.
base stacking in the different helices.
Besides the right-handed double helix (B-DNA) first proposed by Watson and Crick, DNA can adopt other biologically relevant structures. Four-stranded Holliday junctions and left-handed duplexes (Z-DNA) are two important examples. Here, we compare the structure of B-DNA with the A- and Z-forms.
A- vs. B- DNA
The B-form of the DNA double helix is the typical conformation of DNA in cells. The A-form is wider and more compressed than the B-DNA helix. The A-form has a very deep major groove that is narrower than the major groove in B-DNA. The minor groove in A-DNA is shallow. DNA fibers adopt the A-form when hydration of the helix is very low. However, the natural helical form for DNA-RNA and RNA-RNA is the A-form helix, not the B-form helix. This is due to the fact that the –OH group in the 2′ position of ribose would be sterically hindered in the B-form helix.
A- vs. B- DNA
Crystal structure of DNA-RNA chimeric decamerd(CCGGC)r(G)d(CCGG).
DNA-RNA and RNA-RNA complexes have the A conformation. The introduction of a single 2′-hydroxyl group on the sugar-phosphate backbone of the B-DNA decamer d(CCGGCGCCGG) transforms it to A-DNA.
backbone trace. The chimeric duplex exhibits typical A-DNA geometry, with all the base pairs inclined from the helix axis and displaced to the outside.
ball-and-stick model of the backbone. All the sugars are in the C3′-endo conformation (see next tutorial).
Z-DNA: The Left-handed Double Helix
Left-handed Z-DNA can be formed by certain sequences containing alternating purine and pyrimidine bases and is a higher energy form of the double helix. It is stabilized by negative supercoiling generated either by transcription or by unwrapping nucleosomes. Z-DNA is also stabilized by proteins which bind specifically to Z-DNA.
Sequences favoring Z-DNA formation are found frequently near the promoter region of genes. This places them in a position where they can trap negative supercoiling, which accumulates behind a moving polymerase. Z-DNA is dynamic, flipping back and forth between the left- and right-handed forms.