Computing Stacking Interactions of Modified Bases

[rala.atulk]

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

[xiangjun]

Hi Atul,

Thanks for using 3DNA and for posting such a clearly defined question!

Your two attachments are identical: specifically, test_modified.pdb does not have a methyl group on A16. Could you please verify, and re-attach an updated file with a methyl-modified A16?

Best regards,

Xiang-Jun

[rala.atulk]

Hi Xiang-Jun,

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

Regards,
Atul

[xiangjun]

Thanks for updating the test_modified.pdb file. Now I can see that the methylation is on atom N6 of A16. By design, 3DNA only includes the first layer of exocyclic base atoms for stacking interactions. That explains why you did not see any difference in the two output files on test_modified.pdb and test_modified_nomethyl.pdb, i.e., the methyl carbon is not considered for the calculation of overlap area.

For the record, here is the abbreviated portion from the 2003 3DNA NAR paper:

The stacking interactions are quantified in 3DNA by the shared overlap area, in A², 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.

Sorry, 3DNA cannot be helpful in this case. You may try programs that calculate "Solvent Accessible Surface Area".

Xiang-Jun

[rala.atulk]

Hi Xiang-Jun,

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

Regards,
Atul