Messages

1

General discussions (Q&As) / Re: Computing Stacking Interactions of Modified Bases

« on: August 11, 2017, 11:28:29 pm »

Hi Xiang-Jun,

Thanks a lot for your response and suggestion. I will look at the solvent accessible area calculations.

Regards,
Atul

2

General discussions (Q&As) / Re: Computing Stacking Interactions of Modified Bases

« on: August 11, 2017, 08:03:16 pm »

Hi Xiang-Jun,

I guess I did not attach the files correctly the last time. I've attached the files again.

Regards,
Atul

3

General discussions (Q&As) / Computing Stacking Interactions of Modified Bases

« on: August 11, 2017, 04:47:04 pm »

Hi all,

I have a question regarding the computing of stacking interactions of modified bases that contain different exocyclic groups than the canonical bases.

For example, the test_modified.pdb file contains a 3 base pair DNA duplex in which one of the bases (A16) has an exocyclic methyl group at the N6 atom of the Adenine. I would like to compute its stacking interactions (area of overlap) with its neighboring base pairs C15 and A17. Visually examining the structure indicates that the methyl group does overlap with the base moiety of C15. On computing the base pair overlap using 3DNA

Code: [Select]

find_pair test_modified.pdb test_modified.in
analyze test_modified.in

I get the following areas of overlap of the base pair step A16:T9
     step      i1-i2        i1-j2        j1-i2        j1-j2        sum
   1 TT/aA  5.60( 0.73)  0.00( 0.00)  0.00( 0.00)  1.45( 0.60)  7.05( 1.34)
   2 TG/Ca  3.99( 0.41)  0.00( 0.00)  0.01( 0.00)  0.00( 0.00)  4.00( 0.41)

In a similar structure lacking the methyl group test_modified_nomethyl.pdb, the areas of overlap computed using the protocol above are the same, indicating that 3DNA does not consider the methyl group while calculating the area of overlap.
    step      i1-i2        i1-j2        j1-i2        j1-j2        sum
   1 TT/AA  5.60( 0.73)  0.00( 0.00)  0.00( 0.00)  1.45( 0.60)  7.05( 1.34)
   2 TG/CA  3.99( 0.41)  0.00( 0.00)  0.01( 0.00)  0.00( 0.00)  4.00( 0.41)

I would like to know whether it is possible to explicitly define the base atoms (ring and exocyclic) over which the stacking/overlap calculation is performed.

Thanks a lot for your help.

Regards,
Atul