### Author Topic: How to determine DNA topology form parameters  (Read 8594 times)

#### zhangzf

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• Posts: 2
##### How to determine DNA topology form parameters
« on: April 05, 2011, 11:24:36 pm »
Hi, I am analyzing a protein-DNA complex in which DNA is severely curved. The protein could constrain negative DNA supercoils in vitro and I am trying to find some clues to the structural basis of DNA supercoiling from the parameters of DNA calculated by 3dna (listed as following).
Is it possible to infer whether the supercoils come from DNA unwinding or writhing (e.g., the DNA fragment in nucleosome) from these parameters? If so, how to make it? And the DNA has an average h-twist value of 35.29 and thus a h=(360/35.29)=10.20 bp/turn. Does it means that the DNA is over-twisted, since h is less than 10.5 bp/turn?
Thanks
****************************************************************************
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3DNA (v1.5, Nov. 2002) by Xiang-Jun Lu at Wilma K. Olson's Lab.
****************************************************************************
1. The list of the parameters given below correspond to the 5' to 3' direction
of strand I and 3' to 5' direction of strand II.

2. All angular parameters, except for the phase angle of sugar pseudo-
rotation, are measured in degrees in the range of [-180, +180], and all
displacements are measured in Angstrom units.
****************************************************************************
RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)

Strand I                    Strand II          Helix
1   (0.006) B:.101_:[.DG]G-----C[.DC]:.116_:C (0.005)     |
2   (0.012) B:.102_:[.DT]T-----A[.DA]:.115_:C (0.007)     |
3   (0.012) B:.103_:[.DA]A-----T[.DT]:.114_:C (0.010)     |
4   (0.013) B:.104_:[.DA]A-----T[.DT]:.113_:C (0.011)     |
5   (0.007) B:.105_:[.DT]T-----A[.DA]:.112_:C (0.010)     |
6   (0.008) B:.106_:[.DT]T-----A[.DA]:.111_:C (0.008)     |
7   (0.008) B:.107_:[.DA]A-----T[.DT]:.110_:C (0.007)     |
8   (0.003) B:.108_:[.DC]C-----G[.DG]:.109_:C (0.008)     |
****************************************************************************
Detailed H-bond information: atom-name pair and length [ON]
1 G-----C  [3]  O6 - N4  3.04  N1 - N3  2.96  N2 - O2  2.83
2 T-----A  [2]  N3 - N1  2.64  O4 - N6  2.96
3 A-----T  [2]  N6 - O4  2.98  N1 - N3  2.70
4 A-----T  [2]  N6 - O4  3.02  N1 - N3  2.80
5 T-----A  [2]  N3 - N1  2.77  O4 - N6  3.11
6 T-----A  [2]  N3 - N1  2.76  O4 - N6  2.94
7 A-----T  [2]  N6 - O4  2.96  N1 - N3  2.85
8 C-----G  [3]  O2 - N2  2.70  N3 - N1  2.86  N4 - O6  2.93
****************************************************************************
Overlap area in Angstrom^2 between polygons defined by atoms on successive
bases. Polygons projected in the mean plane of the designed base-pair step.

Values in parentheses measure the overlap of base ring atoms only. Those
outside parentheses include exocyclic atoms on the ring. Intra- and
inter-strand overlap is designated according to the following diagram:

i2  3'      5' j2
/|      |
|       |
Strand I |       | II
|       |
|       |
|      |/
i1  5'      3' j1

step      i1-i2        i1-j2        j1-i2        j1-j2        sum
1 GT/AC  6.35( 1.96)  0.00( 0.00)  0.00( 0.00)  4.55( 2.68) 10.90( 4.64)
2 TA/TA  6.08( 1.15)  0.00( 0.00)  0.00( 0.00)  4.32( 0.15) 10.40( 1.30)
3 AA/TT  4.44( 2.23)  0.00( 0.00)  0.00( 0.00)  4.94( 0.85)  9.39( 3.08)
4 AT/AT  6.30( 2.60)  0.00( 0.00)  0.00( 0.00)  6.15( 2.46) 12.45( 5.06)
5 TT/AA  7.53( 1.30)  0.00( 0.00)  0.00( 0.00)  6.47( 4.32) 14.00( 5.62)
6 TA/TA  1.38( 0.00)  0.00( 0.00)  0.00( 0.00)  1.68( 0.00)  3.05( 0.00)
7 AC/GT  4.96( 3.39)  0.00( 0.00)  0.00( 0.00)  4.71( 1.07)  9.67( 4.46)
****************************************************************************
Origin (Ox, Oy, Oz) and mean normal vector (Nx, Ny, Nz) of each base-pair in
the coordinate system of the given structure

bp        Ox        Oy        Oz        Nx        Ny        Nz
1 G-C      12.62     21.58     20.04     -0.13     -0.82     -0.56
2 T-A      12.06     19.25     18.00     -0.13     -0.81     -0.57
3 A-T      11.05     16.20     17.25     -0.01     -0.86     -0.50
4 A-T      10.44     10.39     17.09      0.24     -0.91      0.35
5 T-A      11.26      7.86     18.38      0.15     -0.89      0.44
6 T-A      11.48      4.89     19.71      0.11     -0.78      0.62
7 A-T      11.67      1.50     20.79      0.16     -0.80      0.57
8 C-G      11.36     -1.21     22.97      0.18     -0.79      0.58
****************************************************************************
Local base-pair parameters
bp        Shear    Stretch   Stagger    Buckle  Propeller  Opening
1 G-C      -0.45     -0.09      0.09      0.54     -5.10      1.29
2 T-A      -0.05     -0.26     -0.07      6.55     -6.73      4.61
3 A-T       0.12     -0.15      0.19     24.95     -9.76      4.64
4 A-T       0.05     -0.08     -0.31    -18.35      2.76      3.14
5 T-A      -0.18     -0.10      0.09     -0.15     -4.90      6.04
6 T-A      -0.10     -0.16     -0.22     10.46     -1.22      1.56
7 A-T       0.12     -0.10      0.18      9.68    -10.37     -2.26
8 C-G       0.38     -0.18      0.02      6.90     -7.15      1.29
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave.     -0.01     -0.14     -0.00      5.07     -5.31      2.54
s.d.      0.24      0.06      0.18     12.23      4.35      2.63
****************************************************************************
Local base-pair step parameters
step       Shift     Slide      Rise      Tilt      Roll     Twist
1 GT/AC     -0.25     -0.27      3.13      0.87     -0.36     30.76
2 TA/TA      0.22      1.27      3.03      1.86      8.58     26.99
3 AA/TT     -0.06      1.39      5.67     -0.67     52.71     20.29
4 AT/AT      0.13     -0.28      2.95     -4.54      6.16     22.16
5 TT/AA     -0.29      0.44      3.22      5.15     11.21     23.56
6 TA/TA     -0.16      1.20      3.35     -1.96     -3.80     46.76
7 AC/GT      0.78     -0.48      3.37      0.51     -1.07     34.74
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave.      0.05      0.47      3.53      0.17     10.49     29.32
s.d.      0.37      0.82      0.96      3.05     19.41      9.19
****************************************************************************
Local base-pair helical parameters
step       X-disp    Y-disp   h-Rise     Incl.       Tip   h-Twist
1 GT/AC     -0.45      0.63      3.13     -0.68     -1.63     30.77
2 TA/TA      0.64     -0.02      3.28     17.79     -3.85     28.35
3 AA/TT     -5.03     -0.01      3.41     70.43      0.89     56.22
4 AT/AT     -2.55     -1.68      2.69     15.46     11.40     23.43
5 TT/AA     -2.02      1.99      2.99     25.36    -11.64     26.55
6 TA/TA      1.82      0.04      3.25     -4.77      2.47     46.94
7 AC/GT     -0.63     -1.23      3.40     -1.79     -0.86     34.76
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave.     -1.17     -0.04      3.16     17.40     -0.46     35.29
s.d.      2.26      1.20      0.26     26.03      6.94     11.97
****************************************************************************
Structure classification:

This is a right-handed nucleic acid structure
****************************************************************************
lambda: virtual angle between C1'-YN1 or C1'-RN9 glycosidic bonds and the
base-pair C1'-C1' line

C1'-C1': distance between C1' atoms for each base-pair
RN9-YN1: distance between RN9-YN1 atoms for each base-pair
RC8-YC6: distance between RC8-YC6 atoms for each base-pair

bp     lambda(I) lambda(II)  C1'-C1'   RN9-YN1   RC8-YC6
1 G-C      53.9      57.6      10.7       9.0       9.9
2 T-A      56.4      57.4      10.2       8.6       9.7
3 A-T      57.8      56.4      10.1       8.5       9.6
4 A-T      56.8      56.9      10.4       8.7       9.8
5 T-A      56.1      59.7      10.3       8.8       9.9
6 T-A      55.1      55.1      10.5       8.8       9.8
7 A-T      54.1      53.1      10.7       8.9       9.8
8 C-G      55.7      54.1      10.6       8.9       9.8
****************************************************************************
Classification of each dinucleotide step in a right-handed nucleic acid
structure: A-like; B-like; TA-like; intermediate of A and B, or other cases

step       Xp      Yp      Zp     XpH     YpH     ZpH    Form
1 GT/AC   -3.34    9.13   -0.26   -3.78    9.12   -0.37     B
2 TA/TA   -3.96    8.37   -1.67   -3.36    8.49    0.82     B
3 AA/TT   -2.69    8.83   -0.20   -7.13    3.48    8.11
4 AT/AT   -3.51    9.24   -0.46   -6.12    9.03    2.03     B
5 TT/AA   -3.56    9.17   -0.77   -5.55    8.66    3.10     B
6 TA/TA   -2.33    8.54   -0.27   -0.62    8.50   -0.92     B
7 AC/GT   -3.00    9.15   -0.14   -3.60    9.15   -0.41     B
****************************************************************************
Minor and major groove widths: direct P-P distances and refined P-P distances
which take into account the directions of the sugar-phosphate backbones

(Subtract 5.8 Angstrom from the values to take account of the vdw radii
of the phosphate groups, and for comparison with FreeHelix and Curves.)

Ref: M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of
Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343.

Minor Groove        Major Groove
P-P     Refined     P-P     Refined
1 GT/AC       ---       ---       ---       ---
2 TA/TA       ---       ---       ---       ---
3 AA/TT      21.4       ---      18.1       ---
4 AT/AT      20.0      18.2      19.2      17.8
5 TT/AA      16.7       ---      17.2       ---
6 TA/TA       ---       ---       ---       ---
7 AC/GT       ---       ---       ---       ---
****************************************************************************
Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 3.05(1.38)
****************************************************************************
Main chain and chi torsion angles:

Note: alpha:   O3'(i-1)-P-O5'-C5'
beta:    P-O5'-C5'-C4'
gamma:   O5'-C5'-C4'-C3'
delta:   C5'-C4'-C3'-O3'
epsilon: C4'-C3'-O3'-P(i+1)
zeta:    C3'-O3'-P(i+1)-O5'(i+1)

chi for pyrimidines(Y): O4'-C1'-N1-C2
chi for purines(R): O4'-C1'-N9-C4

Strand I
base    alpha    beta   gamma   delta  epsilon   zeta    chi
1 G     ---     ---     64.2   139.7   173.0   -98.2  -101.4
2 T    -79.7  -178.8    65.7   141.6   -92.2  -110.8  -108.0
3 A     44.1  -118.3  -163.7    78.9  -152.3   -77.1  -108.4
4 A    -55.3  -166.5    51.7   145.7  -179.4   -91.4   -92.9
5 T    -74.6   166.0    59.8    89.2  -163.3   -88.2  -126.8
6 T    -58.3   169.8    45.2   144.4  -123.1   169.8   -85.9
7 A    -58.4   136.5    49.9   136.4  -165.5   -94.8  -105.6
8 C    -54.2   163.2    33.4    87.3    ---     ---   -129.2

Strand II
base    alpha    beta   gamma   delta  epsilon   zeta    chi
1 C    -59.3   159.3    52.0    84.9    ---     ---   -132.6
2 A    -56.2   173.3    43.7   124.7  -175.6  -101.0   -97.6
3 T    -62.4  -174.8    57.6   121.1  -170.5   -93.4  -106.8
4 T    -71.4   175.2    46.9    81.2  -145.2   -85.3  -116.6
5 A    -72.2   164.0    51.5    92.3  -176.6   -79.6  -119.8
6 A    -66.2  -160.2    53.5   141.7  -166.8   -89.6   -96.4
7 T    -72.1  -164.1    56.1   132.0   170.1  -100.3  -108.7
8 G     ---     ---   -156.5   152.2   175.2   -98.8  -115.2
****************************************************************************
Sugar conformational parameters:

Note: v0: C4'-O4'-C1'-C2'
v1: O4'-C1'-C2'-C3'
v2: C1'-C2'-C3'-C4'
v3: C2'-C3'-C4'-O4'
v4: C3'-C4'-O4'-C1'

tm: amplitude of pseudorotation of the sugar ring
P:  phase angle of pseudorotation of the sugar ring

Strand I
base       v0      v1      v2      v3      v4      tm       P    Puckering
1 G    -16.2    29.8   -31.7    23.4    -4.7    32.2   169.6    C2'-endo
2 T    -38.2    46.7   -37.8    17.5    12.5    45.9   145.5    C2'-endo
3 A    -13.9   -12.8    32.7   -41.9    35.3    41.4    37.8    C4'-exo
4 A     -4.7    23.7   -32.8    30.5   -16.5    33.4   190.4    C3'-exo
5 T    -43.9    22.5     5.7   -31.3    46.7    47.3    83.0    O4'-endo
6 T    -36.5    47.9   -40.3    21.1     9.4    46.7   149.6    C2'-endo
7 A    -16.9    27.4   -27.6    18.8    -1.4    28.7   164.2    C2'-endo
8 C    -26.1     2.7    19.9   -35.3    38.6    38.8    59.2    C4'-exo

Strand II
base       v0      v1      v2      v3      v4      tm       P    Puckering
1 C    -30.9     7.3    17.6   -36.3    42.2    41.8    65.1    C4'-exo
2 A    -24.4    28.0   -21.0     7.6    10.5    27.7   139.5    C1'-exo
3 T    -20.2    21.0   -14.8     3.6    10.4    21.5   133.5    C1'-exo
4 T    -25.9    -0.4    24.3   -39.9    41.4    42.4    55.0    C4'-exo
5 A    -34.2    15.6     7.3   -27.3    38.7    38.3    79.0    O4'-endo
6 A     -7.7    22.5   -28.3    24.2   -10.6    28.3   183.0    C3'-exo
7 T    -24.9    32.7   -28.4    14.9     6.2    32.5   150.8    C2'-endo
8 G    -10.0    30.0   -37.3    32.5   -14.4    37.4   183.5    C3'-exo
****************************************************************************
Same strand P--P and C1'--C1' virtual bond distances

Strand I                    Strand II
base      P--P     C1'--C1'       base      P--P     C1'--C1'
1 G/T       ---       4.9         1 C/A       6.8       4.3
2 T/A       6.7       4.9         2 A/T       6.7       4.9
3 A/A       7.0       6.4         3 T/T       5.5       6.5
4 A/T       6.9       4.5         4 T/A       6.4       5.1
5 T/T       6.3       5.2         5 A/A       6.7       4.4
6 T/A       6.7       5.1         6 A/T       6.7       5.3
7 A/C       6.8       4.5         7 T/G       ---       5.2
****************************************************************************
Helix radius (radial displacement of P, O4', and C1' atoms in local helix
frame of each dimer)

Strand I                      Strand II
step         P        O4'       C1'        P        O4'        C1'
1 GT/AC      10.3       7.1       6.7       9.5       6.0       5.5
2 TA/TA       8.9       6.1       5.2       9.5       6.2       5.5
3 AA/TT       7.5       8.4       7.9       8.3       8.5       8.1
4 AT/AT       9.7       6.9       6.2      12.2       9.3       8.5
5 TT/AA      12.1       9.2       8.4       8.5       6.0       5.2
6 TA/TA       8.6       5.8       5.4       8.4       5.4       5.2
7 AC/GT       9.0       5.6       5.1      10.6       7.7       7.3
****************************************************************************
Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz)
for each dinucleotide step

bp        Px        Py        Pz        Hx        Hy        Hz
1 GT/AC     12.94     20.61     18.63     -0.10     -0.81     -0.57
2 TA/TA     11.12     17.96     17.25     -0.24     -0.92     -0.30
3 AA/TT     12.02     13.05     21.41     -0.83     -0.51      0.22
4 AT/AT      8.86      9.60     19.91     -0.04     -0.98      0.18
5 TT/AA     11.85      7.51     21.52     -0.33     -0.83      0.45
6 TA/TA     13.12      3.09     19.63      0.20     -0.75      0.64
7 AC/GT     11.36     -0.66     20.85      0.15     -0.79      0.60

#### xiangjun

• with-posts
• Posts: 1643
##### Re: How to determine DNA topology form parameters
« Reply #1 on: April 06, 2011, 09:57:18 pm »
Quote from: "zhangzf"
Hi, I am analyzing a protein-DNA complex in which DNA is severely curved. The protein could constrain negative DNA supercoils in vitro and I am trying to find some clues to the structural basis of DNA supercoiling from the parameters of DNA calculated by 3dna (listed as following).

Is it possible to infer whether the supercoils come from DNA unwinding or writhing (e.g., the DNA fragment in nucleosome) from these parameters? If so, how to make it?
Thanks for using 3DNA. Your question "How to determine DNA topology form parameters" seems to be beyond the scope of 3DNA (at least in its current versions). In my understanding, DNA topology is at a "higher" level than can be directly accounted for by the base-pair and dinucleotide structural parameters calculated by 3DNA.

Quote from: "zhangzf"
And the DNA has an average h-twist value of 35.29 and thus a h=(360/35.29)=10.20 bp/turn. Does it means that the DNA is over-twisted, since h is less than 10.5 bp/turn?
I would be very cautious in trying to draw any firm conclusion from such a subtle difference in helical twist. For one thing, the widely cited empirical value of 10.5 bp/turn is based on (presumably) B-form DNA in solution. The DNA in your protein-DNA complex is only 8-bp long and is severely curved.

Since you [red:3v097b1n]highlighted in red of twist and h-twist[/red:3v097b1n] in the enclosed 3DNA output file, I think the following two threads in the forum may help clarify confusions 3DNA users often have with the two and other related parameters:
In connection with DNA supercoiling, there is yet another twist in the twist parameter: please see "Two perspectives on the twist of DNA." by Britton, Olson & Tobias (J Chem Phys. 2009 Dec 28;131(24):245101).

HTH,

Xiang-Jun

[hr:3v097b1n][/hr:3v097b1n]PS: To the extent 3DNA may be useful to you, please consider to update your copy to 3DNA v2.0 -- it is simply a better version than v1.5!

#### zhangzf

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##### Re: How to determine DNA topology form parameters
« Reply #2 on: April 07, 2011, 01:36:02 am »