Helical parametrs for 2′,5′-Linked RNA or DNA

[drozdzu]

Dear Sir,

I would like to ask whether is it possible (or will be) using x3DNA program to calculate helical parameters for DNA or RNA structures with
2' - 5' linklage ?
eg:
http://pubs.acs.org/doi/abs/10.1021/ja810068e

Sincerely

Paul

[xiangjun]

Could you try 3DNA on the structure you linked to ("Solution Structure and Thermodynamics of 2′,5′ RNA Intercalation"), and report back any problem you have?

Xiang-Jun

PS: In posting a question, it'd be very helpful to attach a structure file, or provide a PDB id.

[drozdzu]

Dear Sir,

I am sorry for not specify the pdb code.
Structure has 2KD4 code.

Output file after processing structure 2KD4 using x3dna can be found in the attachment.
I am sending also file with x3dna information from terminal.

Sincerely
Paul

[xiangjun]

Thanks for pointing out the PDB id (2kd4) of the structure you are interested in, and attaching the corresponding 3DNA output files. As always, such information is useful by making our discussions concrete.

Browsing through the output file (2kd4.out) and looking at the structure with Jmol, it appears to me 3DNA has no problem to analyze this structure.

First, the twist angles associate with intercalated steps are smaller, while those for the flanking steps are larger, than normal A-DNA twist values.

Local base-pair step parameters
    step       Shift     Slide      Rise      Tilt      Roll     Twist
   1 GC/GC      1.21      0.19      3.77      5.32    -16.06      9.14
   2 CC/GG      0.42     -1.82      4.09    -13.22      0.06     37.79
   3 CG/CG     -0.08     -1.17      6.68     -7.87    -11.95     20.28
   4 GC/GC      0.07     -0.19      3.40      0.22     -0.57     49.80
   5 CG/CG     -0.14     -1.18      6.62      3.50     -6.88     21.72
   6 GG/CC      0.16     -1.82      3.69     14.10     12.69     39.30
   7 GC/GC     -1.33      0.15      3.44     -6.43    -13.80      6.98

Second, the output for the sugar torsion angles are also as expected (see below for the output for strand I). Because of the 2'--5' backbone linkage, angles alpha [O3'(i-1)-P-O5'-C5'], epsilon [C4'-C3'-O3'-P(i+1)] and zeta [C3'-O3'-P(i+1)-O5'(i+1)] are not defined in the conventional sense.

Strand I
  base    alpha    beta   gamma   delta  epsilon   zeta    chi
   1 G     ---     ---   -135.8   105.5    ---     ---     18.3
   2 C     ---    145.3    62.2    86.8    ---     ---   -126.7
   3 C     ---    176.8   -35.2   134.4    ---     ---   -103.9
   4 G     ---    115.9    64.8    61.7    ---     ---   -137.3
   5 C     ---    163.8    48.4   113.5    ---     ---   -114.8
   6 G     ---    178.6    50.6    83.4    ---     ---   -120.9
   7 G     ---   -149.2    33.4   139.0    ---     ---    -83.2
   8 C     ---    154.9    20.2   120.1    ---     ---   -132.2

Note the following output from find_pair:

Code: [Select]

^^vv opposite bp direction: 1(8) 1(1)-2(2)
^^vv opposite bp direction: 1(8) 7(7)-8(8)
I have attached the stacking diagram of the first step, where one can see clearly the two base pairs have opposite orientation. The same is true for the last step. Such base flapping occurs around B-Z junctions, as in 2acj. I do not know how reliable this part of the structure is, or its relevance.

You may also want to analyze this structure (or related ones) using Curves+. I noticed that Horowitz et al. used Curves to analyze 2kd4 in their JACS publication.

HTH,

Xiang-Jun