Sunday, December 23, 2007

A-DNA

The A-DNA structure.
The A-DNA structure.

A-DNA is one of the many possible double helical structures of DNA.
It is a right-handed double helix fairly similar to the more common and well-known B-DNA form, but with a shorter more compact helical structure. A-DNA is thought to be one of three biologically active double helical structures along with B- and Z-DNA. It appears likely that it occurs only in dehydrated samples of DNA, such as those used in crystallographic experiments, and possibly in hybrid pairings of DNA and RNA strands.

Structure

A-DNA is fairly similar to B-DNA given that it is a right-handed double helix with major and minor grooves. However, as shown in the comparison table below, there is a slight increase in the number of base pairs per rotation (resulting in a tighter rotation angle), and smaller rise/turn. This results in a deepening of the major groove and a shallowing of the minor.

Predicting A-DNA structure

An algorithm for predicting the propensity of a sequence to flip from B-DNA to A-DNA was developed by Beth Basham, Gary Schroth, and P. Shing Ho at Oregon State University.[1]

The abstract of their work describes this algorithm:

The ability to predict macromolecular conformations from sequence and thermodynamic principles has long been coveted but generally has not been achieved. We show that differences in the hydration of DNA surfaces can be used to distinguish between sequences that form A- and B-DNA. From this, a "triplet code" of A-DNA propensities was derived as energetic rules for predicting A-DNA formation. This code correctly predicted > 90% of A- and B-DNA sequences in crystals and correlates with A-DNA formation in solution. Thus, with our previous studies on Z-DNA, we now have a single method to predict the relative stability of sequences in the three standard DNA duplex conformations.[1]

Comparison Geometries of the Most Common DNA Forms

Side view of A-, B-, and Z-DNA.
Side view of A-, B-, and Z-DNA.
The helix axis of A-, B-, and Z-DNA.
The helix axis of A-, B-, and Z-DNA.
Geometry attribute A-form B-form Z-form
Helix sense right-handed right-handed left-handed
Repeating unit 1 bp 1 bp 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 2.3 Å (0.23 nm) 3.32 Å (0.332 nm) 3.8 Å (0.38 nm)
Rise/turn of helix 24.6 Å (2.46 nm) 33.2 Å (3.32 nm) 45.6 Å (4.56 nm)
Mean propeller twist +18° +16°
Glycosyl angle anti anti pyrimidine: anti,
purine: syn
Sugar pucker C3'-endo C2'-endo C: C2'-endo,
G: C2'-exo
Diameter 26 Å (2.6 nm) 20 Å (2.0 nm) 18 Å (1.8 nm)


http://en.wikipedia.org/wiki/A-DNA

2 comments:

Panhandle Poet said...

You have a very interesting site. Excellent graphic on the A-DNA.

Professor Howdy said...

Wow that's great...