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

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..

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 Å2) :

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°
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)
• Thanks for your answer though! You suggest taking cross sectional area of a circle for DNA? Commented Jul 29 at 7:39
• As I said, I'm not sure what you're asking, so I don't know if cross-sectional area would be appropriate. I don't know if (for example) electron density matters.
– gringer
Commented Jul 29 at 19:58