question on +/- signs of local bp parameters

[Jane]

Hi!

I am confused with the meaning of the +/- values of the local base pair parameters, like opening, shear, ect. I noticed in a Bform DNA duplex, a AT(looking from the primary strand) pair usually have a + opening while a TA pair usually has a -opening angles. Is +/- supposed to differentiate this kind of situation? I checked the two pair in pymol and can not tell any differences between the opening the + and - opening angles(both open to the major groove side.) Thanks!

[xiangjun]

Thanks for using 3DNA and posting your questions on the Forum.

For B-DNA structures, some base-pair parameters (e.g., shear, opening) are normally quite small, so the difference between +/- values are not that obvious. For some extreme cases, however, the meaning in +/- is immediately obvious. For example, the famous U-G & G-U wobble pairs are distinguished by +/- shear -- see my post "Difference in shear of neighboring base pairs affects twist angle".

As for opening, if you could provide some concrete examples, I will help you work them through to see the difference.

HTH,

Xiang-Jun
 

[Jane]

Thanks for your reply!

One specific case for opening is 1XVR(PDBID), in which the middle two AT and TA Hoogsteen base pair have similarly large openings and opposite signs. I am wondering what the opposite signs(+/-) actually imply in terms of structure. I could hardly tell the differences in opening by visualization through pymol. Thanks!

Cheers,
Jane

[xiangjun]

Thanks for providing an example that helps to illustrate the 'asymmetry' of the A-T vs T-A Hoogsteen pair when put in a structural context. The difference in opening can be understood in the same way as shear in G-U vs U-G wobble pair. See the figure below where the A and T on one strand are aligned on their base reference frames; note the different orientations of T and A.

In 3DNA, the Hoogsteen pair is of the M+N type; thus if the bases are swapped to N+M, all bp parameters change signs.

Code: [Select]

    3 T+A      -0.52      3.62      0.46     -6.35     10.24    -67.69
    4 A+T       0.60     -3.57     -0.56      6.51    -11.43     67.59
3DNA is unique in rigorously quantifying such differences using the six rigid-body bp parameters.

HTH,

Xiang-Jun

[Jane]

Hi, Xiangjun!

Thank you so much for your reply!

I am still a little confused about what the local coordinates on the purine base looks like when it adopts syn conformation. Could you please add on local coordinates (x1,y1,z1 and x2,y2,z2) to the bases in the example to show the differences between T+A and A+T? Thanks a lot!

Best,
Jane

[Jane]

Sorry I have one more question to follow up:
 
based on my understanding, does the +/- sign for local base pair parameters only show the orientation differences but not the relative angle? i.e. the absolute value of opening angle/buckle/... could represent the relative angle between the two bases in a pair regardless of spatial orientations of the two? Thanks a lot!

[xiangjun]

Hi Jane,

I do not quite get what you mean for your follow up question.

Regarding the local reference frame, please have a look of the 2003 3DNA paper, especially Figure 2 (below):


and Figure 1 of the base reference frame paper:


Specifically, the x-axis points from the minor-groove side to the major groove side. For the aligned A and T bases, it's horizontal, pointing to the right. It's a good exercise for you to work out where the x-axes for DT-104 and DA-105 point to. Then you should be able to figure out why one opening is positive, and another is negative.

Note that in 3DNA, the reference frame is defined purely based on the base atoms, not taking consideration of the syn/anti chi torsion angle. See my post "The chi (χ) torsion angle characterizes base/sugar relative orientation".

Xiang-Jun

[Jane]

Hi, Xiangjun!

I think my question has been pretty much covered; thank you so much!

Best,
Jane