Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · Reproduce DSSR · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Author Topic: Quantifying base stacking interactions  (Read 100 times)

Offline chubetty

  • regular
  • *
  • Posts: 1
    • View Profile
Quantifying base stacking interactions
« on: August 17, 2017, 03:07:53 pm »
Hi Xiang-Jun,

I am analyzing the base stacking interactions, which I generated using the --non-pair option, in my DNA model. If I were to quantify the amount of base stacking interactions by using the numbers in and out of parentheses, would the units just be Angstroms^2? And would you define these numbers as area of overlap of the bases?

Thank you!

Betty Chu

Offline xiangjun

  • Administrator
  • regular
  • *****
  • Posts: 1193
    • View Profile
    • 3DNA homepage
Re: Quantifying base stacking interactions
« Reply #1 on: August 17, 2017, 03:30:03 pm »
Hi Betty,

Quote
If I were to quantify the amount of base stacking interactions by using the numbers in and out of parentheses, would the units just be Angstroms^2?

Yes, the unit is in Å2. The numbers outside () take consideration of the exocyclic atoms, while those within () use only the 6- (pyrimidines) or 9- (purines) membered base rings (polygons). You may use a Jmol/PyMOL or other molecular viewer to see how the numbers match intuitive observations.

Quote
And would you define these numbers as area of overlap of the bases?

Yes. The reported area is the overlapped polygon of the two corresponding rings projected onto the mean plane of the base normals.

Here is the relevant portion excerpt from the 2003 3DNA NAR paper:

Quote
The stacking interactions are quantified in 3DNA by the shared overlap area, in Å2, of closely associated base rings, i.e. the nine-membered ring of a purine R (A or G) and the six- membered ring of a pyrimidine Y (C, T or U), projected in the mean base pair plane. ... To account for the stacking interactions (overlap areas) of exocyclic atoms over base rings, ... an extended polygon, which includes exocyclic atoms, is used. For cytosine, the extended polygon is defined by the C1'-O2-N3-N4-C5-C6-C1' atomic sequence.

HTH,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.