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Questions and answers => General discussions (Q&As) => Topic started by: Jane on March 25, 2013, 01:49:52 pm

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Title: zero or negative helical rise?
Post by: Jane on March 25, 2013, 01:49:52 pm

Hi, Xiangjun!

I am a little confused about zero or even negative helical rise for some base-pair step parameter output, for example DNA in PDBID 1XVK. Do you have any comment or reference on this ? Thanks a lot!

Best,
Jane

Title: Re: zero or negative helical rise?
Post by: xiangjun on March 25, 2013, 04:20:39 pm

The issue you noticed with negative rise in 1xvk etc is due to the extensive non-canonical base pairs. Under such circumstance, as in more commonly seen in RNA structures, the meaning of base-pair step and helical parameters may not make (much) intuitive sense. Yet, these parameters are required to rigorously characterize the structure. Note that the base-pair parameters (Shear, Stretch, Stagger, Buckle, Propeller and Opening) still have their normal interpretation.

I'd recommend you use DSSR (http://forum.x3dna.org/rna-structures/dssr-software-for-defining-the-(secondary)-structures-of-rna/), which shows clearly the two Hoogsteen pairs, among other things, as show below. Check also files dssr-torsions.dat, dssr-pairs.pdb etc.

HTH,

Xiang-Jun

****************************************************************************
    DSSR: Software for Defining the (Secondary) Structures of RNA
      by Xiang-Jun Lu (xiangjun@x3dna.org), beta-r08-on-20130323

   The program is currently under active development. As always, we
   greatly appreciate your feedback! Please report all DSSR-related
   issues on the 3DNA Forum (http://forum.x3dna.org/), and I strive
   to promptly respond to any questions posted there.
****************************************************************************
Date and time: Mon Mar 25 16:15:39 2013
File name: 1xvk.pdb1
    no. of DNA/RNA chains: 1 [A=16]
    no. of nucleotides:    16
    no. of waters:         112
    no. of metals:         2 [Mg=2]
****************************************************************************
List of 8 base pair(s)
   1 1:A.DG1          2:A.DC8          [G+C]              00-n/a    cHW cM+W
       74.1(syn) C2'-endo lambda=47.5; -100.4(anti) C2'-endo lambda=61.6
       d(C1'-C1')=8.31 d(N1-N9)=6.64 d(C6-C8)=6.16 tor(N1-C1'-C1'-N9)=-0.1
       H-bonds[2]: "N7*N3[2.69]; O6(carbonyl)-N4(amino)[2.85]"
       bp_pars: [0.46    -3.41   -0.35   3.71    -5.92   67.37]
   2 1:A.DC2          2:A.DG7          [C-G] WC           19-XIX    cWW cW-W
       -103.9(anti) C4'-exo  lambda=55.5; -105.3(anti) C1'-exo  lambda=52.5
       d(C1'-C1')=10.53 d(N1-N9)=8.80 d(C6-C8)=9.65 tor(N1-C1'-C1'-N9)=0.0
       H-bonds[3]: "O2(carbonyl)-N2(amino)[2.76]; N3-N1(imino)[2.89]; N4(amino)-O6(carbonyl)[2.74]"
       bp_pars: [0.27    -0.18   0.35    -22.28  3.73    -2.75]
   3 1:A.DG3          2:A.DC6          [G-C] WC           19-XIX    cWW cW-W
       -108.4(anti) C1'-exo  lambda=54.1; -107.8(anti) C4'-exo  lambda=54.2
       d(C1'-C1')=10.47 d(N1-N9)=8.77 d(C6-C8)=9.65 tor(N1-C1'-C1'-N9)=-2.6
       H-bonds[3]: "O6(carbonyl)-N4(amino)[2.87]; N1(imino)-N3[2.88]; N2(amino)-O2(carbonyl)[2.81]"
       bp_pars: [-0.38   -0.18   0.41    22.84   2.54    -2.67]
   4 1:A.DT4          2:A.DA5          [T+A] Hoogsteen    23-XXIII  cWH cW+M
       -95.4(anti) C2'-endo lambda=59.7; 68.3(syn) C1'-exo  lambda=53.5
       d(C1'-C1')=8.37 d(N1-N9)=6.77 d(C6-C8)=6.17 tor(N1-C1'-C1'-N9)=0.5
       H-bonds[2]: "N3(imino)-N7[2.86]; O4(carbonyl)-N6(amino)[2.80]"
       bp_pars: [-0.69   3.57    0.31    -3.48   7.41    -70.55]
   5 1:A.DA5          2:A.DT4          [A+T] Hoogsteen    23-XXIII  cHW cM+W
       68.3(syn) C1'-exo  lambda=53.5; -95.4(anti) C2'-endo lambda=59.7
       d(C1'-C1')=8.37 d(N1-N9)=6.77 d(C6-C8)=6.17 tor(N1-C1'-C1'-N9)=0.5
       H-bonds[2]: "N7-N3(imino)[2.86]; N6(amino)-O4(carbonyl)[2.80]"
       bp_pars: [0.69    -3.57   -0.31   3.48    -7.41   70.54]
   6 1:A.DC6          2:A.DG3          [C-G] WC           19-XIX    cWW cW-W
       -107.8(anti) C4'-exo  lambda=54.2; -108.3(anti) C1'-exo  lambda=54.1
       d(C1'-C1')=10.47 d(N1-N9)=8.77 d(C6-C8)=9.65 tor(N1-C1'-C1'-N9)=-2.6
       H-bonds[3]: "O2(carbonyl)-N2(amino)[2.81]; N3-N1(imino)[2.88]; N4(amino)-O6(carbonyl)[2.87]"
       bp_pars: [0.38    -0.18   0.41    -22.84  2.54    -2.67]
   7 1:A.DG7          2:A.DC2          [G-C] WC           19-XIX    cWW cW-W
       -105.3(anti) C1'-exo  lambda=52.5; -103.9(anti) C4'-exo  lambda=55.5
       d(C1'-C1')=10.53 d(N1-N9)=8.80 d(C6-C8)=9.65 tor(N1-C1'-C1'-N9)=0.0
       H-bonds[3]: "O6(carbonyl)-N4(amino)[2.74]; N1(imino)-N3[2.89]; N2(amino)-O2(carbonyl)[2.76]"
       bp_pars: [-0.27   -0.18   0.35    22.28   3.73    -2.75]
   8 1:A.DC8          2:A.DG1          [C+G]              00-n/a    cWH cW+M
       -100.4(anti) C2'-endo lambda=61.5; 74.1(syn) C2'-endo lambda=47.6
       d(C1'-C1')=8.31 d(N1-N9)=6.64 d(C6-C8)=6.16 tor(N1-C1'-C1'-N9)=-0.1
       H-bonds[2]: "N3*N7[2.69]; N4(amino)-O6(carbonyl)[2.86]"
       bp_pars: [-0.46   3.41    0.35    -3.71   5.93    -67.37]
****************************************************************************
List of 1 helix
  helix=1[2] bps=8
   1 1:A.DG1          2:A.DC8          [G+C]              00-n/a    cHW cM+W
   2 1:A.DC2          2:A.DG7          [C-G] WC           19-XIX    cWW cW-W
   3 1:A.DG3          2:A.DC6          [G-C] WC           19-XIX    cWW cW-W
   4 1:A.DT4          2:A.DA5          [T+A] Hoogsteen    23-XXIII  cWH cW+M
   5 1:A.DA5          2:A.DT4          [A+T] Hoogsteen    23-XXIII  cHW cM+W
   6 1:A.DC6          2:A.DG3          [C-G] WC           19-XIX    cWW cW-W
   7 1:A.DG7          2:A.DC2          [G-C] WC           19-XIX    cWW cW-W
   8 1:A.DC8          2:A.DG1          [C+G]              00-n/a    cWH cW+M
****************************************************************************
List of 2 stems
  stem=1[#1] bps=2
   1 1:A.DC2          2:A.DG7          [C-G] WC           19-XIX    cWW cW-W
   2 1:A.DG3          2:A.DC6          [G-C] WC           19-XIX    cWW cW-W

  stem=2[#1] bps=2
   1 1:A.DC6          2:A.DG3          [C-G] WC           19-XIX    cWW cW-W
   2 1:A.DG7          2:A.DC2          [G-C] WC           19-XIX    cWW cW-W
****************************************************************************
List of 1 coaxial stack(s)
   1 Helix#1 contains 2 stems: [#1, #2]
****************************************************************************
List of 1 internal loop(s)
   1 symmetric internal loop: 8 nts; [2x2]; linked by [#1, #2]
       1:A.DG3+1:A.DT4+1:A.DA5+1:A.DC6+2:A.DG3+2:A.DT4+2:A.DA5+2:A.DC6 [GTACGTAC]
****************************************************************************
>chain-A #1 DNA* with 16 nts
GCGTACGCGCGTACGC
.((..((..))..)).

Title: Re: zero or negative helical rise?
Post by: Jane on March 28, 2013, 03:04:19 pm

Hi, Xiangjun!

Thanks for the reply! Do you mean DSSR will give better results for helical/step parameters for DNA/RNA near the non-canonical bps? Have DSSR resolved the zero/negative helical rise issue?

Thanks!

Jane

Title: Re: zero or negative helical rise?
Post by: xiangjun on March 28, 2013, 03:36:17 pm

DSSR does not calculate helical/step parameters (at least not yet), as shown clearly in the enclosed file for 1xvk in my previous reply. See also my reply to "large deviations in output values (http://forum.x3dna.org/general-discussions/large-deviations-in-output-values/)".

In 3DNA distribution, there is also a program called 'cehs' (as in SCHNAaP) which uses RC8--YC6 as the bp long axis, and mean bp normal as the z-axis. In dinucleotide steps with non-canonical bps, 'cehs' normally provides a more 'sensible' rise/twist values. Please have a try on 1xvk and report back how it goes.

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University