What is the cross sectional area of DNA? Can we find persistence length using oxDNA?

Question

i wish to determine the persistence length of double strand DNA with different bases (10 to 150). i found an equation: P= B_s/ K T where B_s is the bending stiffness and B_s= E * I where I is the cross sectional area

The persistence length qualifies the bending stiffness of a polymer. If the pieces of the polymer is less than persistence length, then the molecule behaves like a rigid rod. however, if it's longer, the polymer can bend. Such is the case of double strand DNA.

So, I just need to determine cross section of double strand DNA.

Also, has anyone ever used oxDNA on Python before? i want to determine the persistence length on oxDNA as well to be able to compare the values

Well, i am currently exploring oxDNA. And for the cross section, i wonder if i should take that of a cylinder or circle..

Answer 1

Not quite sure what you're asking, but I have found the Wikipedia page on Nucleic acid double helix to be quite informative for modeling DNA for 3D printing and as flavour graphics. Here's the table of structural features (averaged, because they differ from base to base), which gives a value for the diameter of B-DNA of 20 Å (2.0 nm). That means that if you were to treat it as a full circle in cross section (not quite accurate), then the cross-sectional area would be (on average) π nm² (or 100 Ų) :

Geometry attribute	A-DNA	B-DNA	Z-DNA
Helix sense	right-handed	right-handed	left-handed
Repeating unit	1 bp	1 bp	2 bp
Rotation/bp	32.7°	34.3°	60°/2
bp/turn	11	10.5	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)
Pitch/turn of helix	28.2 Å (2.82 nm)	33.2 Å (3.32 nm)	45.6 Å (4.56 nm)
Mean propeller twist	+18°	+16°	0°
Glycosyl angle	anti	anti	C: anti, G: syn
Sugar pucker	C3'-endo	C2'-endo	C: C2'-endo, G: C2'-exo
Diameter	23 Å (2.3 nm)	20 Å (2.0 nm)	18 Å (1.8 nm)