DNA Structure

Reference: Dickerson, et al., 1982 Science, v216, p 475-483. (Also good: Meth. Enz. v.211, 67-111).
Be sure to see the interactive tutorial on DNA structure. Links to other tutorials can be found at my Nucleic Acids Tutorial page.

A, B and Z forms, depending upon salt and water concentrations and sequence.

Original Xray studies of DNA done using fiber of bulk DNA (B-DNA) or simple copolymer DNA (A-DNA). The molecules were not aligned in a three-dimensional lattice, like true crystals, so the resultant pattern could not be resolved to atomic level detail. Models were built to fit the available data.

DNA structures are now determined using crystals of synthetic oligonucletides. This has improved the precision of the description of DNA structure, but we will see there is still some ambiguity about the structure of Z-DNA

 


 

The geometry of the DNA forms can be used to describe the differences seen.
  A B Z
Helix sense Right handed Right-handed Left handed
Repeating unit 1 bp 1bp 2 bp
Rotation/bp 33.6° 35.9° 60°/2
Mean bp/turn 10.7 10.0 12
Inclination of bp to axis +19° -1.2° -9°
Rise/bp along axis 2.3Å 3.32Å 3.8Å
Pitch/turn of helix 24.6Å 33.2Å 45.6Å
Mean propeller twist +18° +16°
Glycosyl angle anti anti C: anti, G: syn
Sugar pucker C3'-endo C2'-endo C: C2'-endo, G: C2'-exo
Diameter 26Å 20Å 18Å

Grooves and stacking of bases:

Major and minor groove definition:

Sugars are on minor groove side of the base pair
 
A B Z
RNA and low humidity DNA

Bp displaced from axis-> deep major groove

Hydrated DNA

Bp on axis, both major and minor grooves available

High salt DNA (Pu-p-Py polymers) bp stick out into major groove.

 

Sugar pucker:

Differences --> differences in forms of helices
 
A B Z
C3'-endo (favored in RNA due to steric problems with 2'OH) C2'-endo C: C2'-exo

G: C2'-endo

Glycosyl (c) ant Glycosyl (c) anti C: Glycosyl (c) anti

G: Glycosyl (c) syn

Most of variations in conformation come from variations in d and c. Can plot them like Ramachandran plots for proteins.
 
A-form: mostly clustered in one region B-form: continuum of values, but d related to c. Z-form: tight clusters of values, but differ for purine and pyrimidine.

Notes from web tutorial:

B-form

Note that the major groove (at the top, when you have just clicked the button) is wide and easily accessible.

Now the bases are easier to see. Notice how they are stacked upon each other and are nearly perpendicular to the axis of the double helix. Note also that the backbone forms a smooth, continuous curve.

Zoom in on a few base pairs with this button. Hydrogen bonds between the bases are shown in white. You are looking into the major groove. Each base pair stacks on the next similarly, as shown from this view. A-form DNA also stacks in this way, but compare this with Z-DNA, which behaves much differently. DNA is usually found in the B form under physiological conditions. Sometimes kinks are found in the B helix at transcriptional control regions. These kinks can either be intrinsic to the DNA sequence or caused by transcription factor binding.
 
 

A-form

Note that the major groove (at the top, when you have just clicked the button) is very deep.

Notice how they are stacked upon each other but not perpendicular to the axis of the double helix. They are also displaced to the side of the axis. The result is a wide, short helix. Note also that the backbone forms a smooth, continuous curve.

Zoom in on a few base pairs with this button Hydrogen bonds between the bases are shown in white. You are looking into the major groove. Each base pair stacks on the next similarly, as shown from this view. B-DNA also stacks in this way, but compare this with Z-DNA, which behaves much differently. Essentially all helical RNA is in A form, but DNA can also be found in A form under certain conditions (particularly in RNA-DNA hybrids). The 2'-OH of ribose (shown in white in this view) favors the C3'-endo sugar pucker necessary for A-form geometry. The O2' stericly disfavors the C2'-endo conformation favored in B-DNA.
 
 
 
 

Z-form

Note that the major groove (at the top, when you have just clicked the button) is so wide that it is not really a groove any more.
Now the bases are easier to see. Notice how they are stacked upon each other and are nearly perpendicular to the axis of the double helix. But notice that the base pairs do not stack upon each other equivalently. The backbone also is not a continuous curve, it "zig-zags" back and forth (hence "Z"-DNA)

Notice how the blue bases stack well on the adjacent blue ones, but not on adjacent red ones, and vice versa. So it is the dinucleotide unit, rather than mononucleotide that is the repeating unit of the structure. This explains the need for alternating purines and pyrimidines to form Z-DNA. You can see the same view without the backbone. Going 5' to 3', there is good stacking within the GpC dinucleotide, but not between them (CpG). A top view also illustrates the stacking arrangement. . You can also see this view without the backbone.