zero or negative helical rise?

[Jane]

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

[xiangjun]

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, 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
.((..((..))..)).

[Jane]

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

[xiangjun]

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".

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