Base Stacking analysis

[xzhang32]

Hi Xiang-Jun and other 3DNA users,

I am wondering does 3DNA support base stacking analysis. To be more specific, say I have a pdb file, can I analyze two defined bases to see whether they are stacking to each other or not? If yes, could you please tell me how. This tool might help me a lot on my trajectory analysis for a RNA simulation.

Thanks.

Ju

[xiangjun]

Hi Ju,

Thanks for your interest in 3DNA. Regarding base-stacking analysis, 'analyze' in 3DNA does the job: for double helical structures, the program projects base atoms onto the "mean" base-pair plane and then calculates the overlap area, if the two base-pairs in a dinucleotide step are not too far away. It does a similar job for single-stranded structures, on neighboring nucleotides as defined in the input file.

Note that in its current setting, the 'analyze' program does not perform an exhaustive stacking analysis of all possible nucleotide bases in three-dimensional space. For that purpose, you may try FR3D from the Leontis laboratory.

I am also quite interested in extending 3DNA's functionality for RNA structure analysis, and I greatly appreciate user's feedback.

Xiang-Jun

[starcpw]

Hi Xiang-Jun,

Could you explain more about the algorithm of base stacking area analysis?

1. What is the mean base-pair plane?
2. How to project the “exocyclic atoms”?
3. As you mentioned “not too far away”, is there a threshold for stacking determination in your algorithm? And what is it?
4. How do you think the relation between stacking areas and stacking energy? Do you know any software out there for direct stacking energy estimations?

Best regards,
starcpw

[xiangjun]

Hi starcpw,

1. What is the mean base-pair plane?

It is just the average of the two related normal vectors. See the file tech_details.pdf distributed with 3DNA for details.

2. How to project the “exocyclic atoms”?

In the same way as base ring atoms. Take a look at the file stacking.pdb after running 'analyze' on a DNA structure, e.g., 355d. In the file, simply ignore the z-coordinate of the base rings atoms, or the extended layer including exocyclic atoms, you get the 'projection' of the atoms onto the mean base pair plane. Again, see tech_details.pdf for details.

Also note the following section on 'Standard stacking diagrams', quoted from the 2003 3DNA NAR paper, which should help clarify some of your confusions:

The middle frame used in calculating base pair step parameters (Slide, Roll, etc.) is used in 3DNA to reset each dinucleotide in a ‘standard’ orientation (34), which can be transformed into a high quality ‘standardized’ base stacking diagram (Fig. 6). Such diagrams allow for visual inspection of the stacking and hydrogen bonding interactions at the dimer level. A similar image in Figure 3 reveals the twist angle discrepancy in shear‐deformed (base‐mismatched) dinucleotide steps. 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. For example, the overlap areas between base rings on the left strands of the dimer steps shown in Figure 6 are 0.63 Å2 (C3···G2), 0 Å2 (G4···C3) and 1.11 Å2 (A5···G4). To account for the stacking interactions (overlap areas) of exocyclic atoms over base rings, e.g. the overlap of the amino N4 atom of residue C3 with the five‐membered pyrrole ring of base G2 in Figure 6, 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. The overlap areas of the bases on the left strand of Figure 6 increase, respectively, to 2.95, 2.66 and 3.94 Å2 when these and other exocyclic atoms are included in the calculations. The sum of the intra‐ and interstrand stacking overlaps is provided for each dinucleotide step in the 3DNA output.

3. As you mentioned “not too far away”, is there a threshold for stacking determination in your algorithm? And what is it?

The distance cutoff is 4.5 Å. If the shortest distance of any two-pair between the two sets of atoms is larger than the cutoff, then the stacking area is set to 0.

4. How do you think the relation between stacking areas and stacking energy? Do you know any software out there for direct stacking energy estimations?

Note that 3DNA is an analysis tool, based purely on geometry, and it does not perform any energy calculations. The overlap area as calculated from 3DNA is an intuitive measure of base stacking interactions, and can be 'seen' from the standard stacking diagram. See the above quotation from the original 3DNA paper, and Figure 6.

See also the following two blog posts:

• "Analysis of molecular dynamics simulations trajectories" and comments there in.
• "Quantification of base-stacking interactions using overlap area"

As for software for direct stacking energy estimations, AMBER may be helpful. Check also related publications from Jiri Sponer.

HTH,

Xiang-Jun