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Nucleic Acid Standards

A Standard Reference Frame for the
Description of Nucleic Acid Base-pair Geometry
Supplementary Material

3DNA: Analysis & Rebuilding of 3-Dimensional Nucleic Acid Structures

by Xiang-Jun Lu

@ Wilma K. Olson's Laboratory at Rutgers (olson@rutchem.rutgers.edu)


   
****************************************************************************

1. The list of the parameters given below are along 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

****************************************************************************

File name: pdt012.pdb

Date and time: Mon Mar  6 08:36:53 2000



Number of base-pairs: 12

Number of atoms: 486

****************************************************************************

RMS deviation of the bases (* denotes a non-Watson-Crick base pair)



        Base I        Base II

   1   (0.037) G --- C (0.018)

   2   (0.024) T --- A (0.019)

   3   (0.027) A --- T (0.032)

   4   (0.030) T --- A (0.041)

   5   (0.028) A --- T (0.029)

   6   (0.027) T --- A (0.062)

   7   (0.041) A --- T (0.041)

   8   (0.019) A --- T (0.026)

   9   (0.071) A --- T (0.032)

  10   (0.020) A --- T (0.035)

  11   (0.015) C --- G (0.032)

  12   (0.025) G --- C (0.024)

****************************************************************************

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      14.89     39.74     65.86      0.45      0.11     -0.88

    2 T-A      17.47     40.07     63.45      0.45      0.16     -0.88

    3 A-T      19.89     38.63     60.01      0.29     -0.60     -0.74

    4 T-A      21.97     36.70     57.32      0.12     -0.81     -0.57

    5 A-T      21.20     34.99     54.39     -0.05     -0.88     -0.47

    6 T-A      20.10     32.20     52.31     -0.52     -0.80     -0.29

    7 A-T      18.24     30.36     49.41     -0.74     -0.62     -0.27

    8 A-T      15.31     29.33     47.89     -0.90     -0.38     -0.22

    9 A-T      10.98     29.51     45.58     -0.89      0.26     -0.36

   10 A-T       7.33     29.04     44.76     -0.88      0.26     -0.41

   11 C-G       4.44     30.61     43.45     -0.86      0.24     -0.45

   12 G-C       1.51     30.61     41.49     -0.80      0.28     -0.53

****************************************************************************

Local base-pair parameters

     bp        Shear    Stretch   Stagger    Buckle  Propeller  Opening

    1 G-C      -0.15     -0.14     -0.01    -10.15    -16.01     -2.03

    2 T-A       0.01     -0.10      0.27     -9.07     -4.07      4.58

    3 A-T       0.25     -0.01     -0.03    -31.04     13.82      7.53

    4 T-A      -0.01      0.04     -0.00    -27.24     -6.21      4.48

    5 A-T       0.24      0.06     -0.57     -1.69     -5.25      6.22

    6 T-A      -0.28     -0.05     -0.60      6.33     -2.96      2.80

    7 A-T       0.10     -0.12      0.04     21.95     -9.01      1.45

    8 A-T      -0.17      0.05      0.31     32.13    -15.56      8.20

    9 A-T       0.03     -0.10      0.04      4.50     -1.30      6.12

   10 A-T       0.25     -0.04      0.11      4.53    -10.03     -3.09

   11 C-G       0.17     -0.25      0.19     -0.47    -11.17     -1.29

   12 G-C       0.36     -0.37     -0.15     -0.95     -3.40     -2.56

          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

      ave.      0.07     -0.09     -0.03     -0.93     -5.93      2.70

      s.d.      0.20      0.13      0.29     17.78      7.86      4.11

****************************************************************************

Local base-pair step parameters

    step       Shift     Slide      Rise      Tilt      Roll     Twist

   1 GT/AC      0.59     -1.03      3.34      1.44     -2.74     36.07

   2 TA/TA      0.34     -0.79      4.36     -0.92     46.84     21.48

   3 AT/AT     -1.39     -0.56      3.61      2.73     18.14     18.20

   4 TA/TA      0.08      1.83      2.96      2.14     12.15     22.48

   5 AT/AT     -0.14      0.73      3.57      0.39     29.53      4.49

   6 TA/TA     -0.38      2.02      3.33     -2.73     16.24     21.99

   7 AA/TT      0.67      0.70      3.32      3.34     16.01     22.15

   8 AA/TT      0.68      0.69      4.81      2.10     38.46     19.59

   9 AA/TT     -1.50      0.46      3.43     -2.23      1.61     36.30

  10 AC/GT      0.05     -0.73      3.46     -1.37      2.05     32.94

  11 CG/CG      0.58      0.72      3.41      4.63      4.65     39.61

          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

      ave.     -0.04      0.37      3.60      0.87     16.63     25.03

      s.d.      0.78      1.04      0.53      2.41     15.93     10.29

****************************************************************************

Local base-pair helical parameters

    step       X-disp    Y-disp     Rise     Incl.       Tip     Twist

   1 GT/AC     -1.26     -0.74      3.43     -4.42     -2.32     36.20

   2 TA/TA     -4.94     -0.47      1.16     66.71      1.30     51.29

   3 AT/AT     -6.40      3.90      2.03     45.08     -6.78     25.78

   4 TA/TA      0.52      0.44      3.46     28.57     -5.03     25.60

   5 AT/AT     -6.64      0.37      1.26     81.55     -1.07     29.87

   6 TA/TA     -0.68     -0.03      3.90     36.68      6.17     27.41

   7 AA/TT     -2.88     -0.51      3.16     36.01     -7.51     27.47

   8 AA/TT     -5.40     -0.59      2.87     63.94     -3.49     43.05

   9 AA/TT      0.49      2.07      3.53      2.58      3.57     36.40

  10 AC/GT     -1.65     -0.33      3.40      3.60      2.41     33.03

  11 CG/CG      0.49     -0.29      3.51      6.80     -6.78     40.13

          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

      ave.     -2.58      0.35      2.88     33.37     -1.77     34.20

      s.d.      2.82      1.42      0.96     29.18      4.65      8.19

****************************************************************************

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      52.7      55.1      10.7       9.0       9.8

   2 T-A      59.6      60.2      10.2       8.8       9.9

   3 A-T      60.4      62.7      10.0       8.5       9.6

   4 T-A      58.2      58.3      10.3       8.7       9.7

   5 A-T      60.4      55.9      10.6       9.0      10.1

   6 T-A      55.4      59.3      10.5       8.9       9.9

   7 A-T      58.0      56.7      10.3       8.7       9.7

   8 A-T      59.8      66.2       9.9       8.5       9.6

   9 A-T      58.7      58.6      10.4       8.8       9.9

  10 A-T      55.6      52.4      10.8       9.0      10.0

  11 C-G      54.1      53.9      10.6       8.9       9.8

  12 G-C      55.6      51.7      10.6       8.8       9.7

****************************************************************************

Classification of each dinucleotide step in a right-handed DNA structure

   A-like; B-like; TA-like; N: intermediate or other form



    step       Xp      Yp      Zp     XpH     YpH     ZpH    Form

   1 GT/AC   -2.94    8.66    1.03   -4.15    8.72    0.42     N

   2 TA/TA   -3.35    8.80    1.38   -7.81    2.55    8.53  *TA*

   3 AT/AT   -2.88    9.14    0.25   -8.87    6.39    6.48  *TA*

   4 TA/TA   -1.76    9.14   -0.78   -1.17    8.45    3.58     B

   5 AT/AT   -2.63    9.43   -1.44   -9.04    2.86    9.10  *TA*

   6 TA/TA   -1.77    9.07   -1.06   -2.30    7.98    4.41  *TA*

   7 AA/TT   -2.73    8.93   -0.73   -5.79    7.68    4.65  *TA*

   8 AA/TT   -3.72    8.90   -0.41   -8.80    4.50    7.70  *TA*

   9 AA/TT   -3.38    8.84   -0.29   -2.86    8.85    0.05     B

  10 AC/GT   -3.04    9.14    0.01   -4.62    9.12    0.55     B

  11 CG/CG   -2.88    8.89   -0.36   -2.34    8.87    0.62     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



                  Minor Groove        Major Groove

                 P-P     Refined     P-P     Refined

   1 GT/AC       ---       ---       ---       ---

   2 TA/TA       ---       ---       ---       ---

   3 AT/AT      21.8       ---      18.8       ---

   4 TA/TA      23.8      19.6      20.0      18.4

   5 AT/AT      24.7      20.2      20.3      19.5

   6 TA/TA      24.0      19.7      18.9      17.8

   7 AA/TT      22.3      18.8      19.4      18.5

   8 AA/TT      19.2      17.0      16.7      15.8

   9 AA/TT      15.0       ---      17.1       ---

  10 AC/GT       ---       ---       ---       ---

  11 CG/CG       ---       ---       ---       ---

****************************************************************************

Structure classification: 



This is a right-handed DNA

****************************************************************************

Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs

Helix:    -0.330   0.059  -0.942

Point1:   17.070  33.763  63.928

Point2:    8.913  35.226  40.643

Deviation from regular linear helix: 1.27(2.30)

****************************************************************************

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     ---     ---     74.3    81.2  -139.4   -68.4  -179.4

   2 T    -81.2   176.2    67.0    85.1  -135.7   -67.2  -156.6

   3 A    -77.4  -168.0    53.9   120.5  -163.2   -92.2  -125.7

   4 T    -81.0  -178.8    43.9    85.5  -157.9   -94.0  -124.9

   5 A    -56.9   162.0    48.7    95.9  -147.7   -70.4  -104.1

   6 T    -70.5   176.5    40.8    86.6  -169.4  -101.4   -97.5

   7 A    -60.7   162.4    53.8   106.0  -157.0   -80.4  -104.9

   8 A    -71.1   166.9    55.1    92.8  -133.1   -76.1  -114.4

   9 A    -66.1   168.2    64.9   140.2  -119.8  -174.7  -100.4

  10 A    -73.9   143.4    53.2   131.5  -172.5   -96.5  -115.5

  11 C    -64.8   168.7    61.2   114.6  -164.0   -83.7  -127.6

  12 G    -91.1   169.6    72.8   135.0    ---     ---   -103.8



Strand II

  base    alpha    beta   gamma   delta  epsilon   zeta    chi

   1 C   -101.8   127.8    82.0    76.1    ---     ---   -151.0

   2 A    -67.5   172.1    60.0   146.8  -120.7  -131.4  -103.2

   3 T    -68.4   173.4    52.8    89.5  -152.4   -84.0  -121.3

   4 A    -69.5   151.8    60.0    88.6  -147.2   -62.6  -111.8

   5 T    -69.9   172.7    54.6    87.3  -159.7  -101.1  -108.1

   6 A    -68.2   162.7    52.1    88.2  -155.4   -78.3  -110.7

   7 T    -77.7   170.3    46.8    91.1  -157.0   -92.3  -115.3

   8 T    -81.7   178.1    63.5   105.5  -161.8   -82.8  -119.7

   9 T    -66.7   169.3    47.5   107.6  -161.9   -89.6  -113.2

  10 T    -80.2  -178.9    70.0   130.2  -163.0   -95.7  -117.1

  11 G    -76.6   136.9    48.5   129.1   177.9   -89.9  -114.3

  12 C     ---     ---     54.3   126.2   -98.8   172.5  -101.4

****************************************************************************

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      1.8   -24.6    38.7   -39.4    22.7    40.4    16.7    C3'-endo

   2 T     -2.8   -19.3    34.0   -36.9    24.3    37.0    23.1    C3'-endo

   3 A    -25.5    24.1   -14.9     0.6    15.2    25.6   125.6    C1'-exo 

   4 T    -25.0     3.1    18.7   -34.8    37.1    37.4    60.1    C4'-exo 

   5 A     -2.2   -12.2    21.7   -24.3    16.1    23.8    24.5    C3'-endo

   6 T    -18.9    -2.4    21.5   -34.2    32.5    34.5    51.5    C4'-exo 

   7 A      5.0   -14.1    17.8   -15.7     6.5    17.8     3.1    C3'-endo

   8 A     -5.3   -12.2    24.7   -29.1    21.1    28.4    29.6    C3'-endo

   9 A    -32.5    40.4   -33.6    16.1    10.0    40.0   147.1    C2'-endo

  10 A    -23.8    28.4   -22.9    10.3     8.3    28.1   144.5    C2'-endo

  11 C    -36.1    29.6   -14.3    -5.9    25.8    34.7   114.3    C1'-exo 

  12 G    -34.1    39.7   -30.9    12.3    13.4    39.3   141.8    C1'-exo 



Strand II

 base       v0      v1      v2      v3      v4      tm       P    Puckering

   1 C    -30.0     4.0    21.7   -41.7    43.8    44.5    60.7    C4'-exo 

   2 A    -32.1    42.3   -37.9    20.7     6.5    42.6   152.8    C2'-endo

   3 T    -19.2    -2.0    21.0   -33.4    32.5    34.2    52.1    C4'-exo 

   4 A      3.3   -23.5    34.8   -34.2    18.9    35.8    13.8    C3'-endo

   5 T    -23.4     1.0    20.6   -35.4    36.3    37.4    56.6    C4'-exo 

   6 A    -13.9    -7.3    25.2   -34.5    29.0    34.0    42.1    C4'-exo 

   7 T    -32.2    11.3    11.4   -31.2    39.3    38.8    72.9    O4'-endo

   8 T    -35.6    23.2    -4.0   -16.4    31.8    35.0    96.6    O4'-endo

   9 T    -38.6    27.2    -7.5   -14.7    32.7    37.5   101.5    O4'-endo

  10 T    -37.6    39.1   -28.4     7.4    18.2    40.2   135.0    C1'-exo 

  11 G    -23.9    27.6   -21.4     8.7     9.2    27.3   141.7    C1'-exo 

  12 C    -46.8    45.5   -27.6     2.3    26.5    46.8   126.1    C1'-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       ---       5.7         1 C/A       6.8       5.0

   2 T/A       5.6       6.4         2 A/T       5.8       5.7

   3 A/T       6.2       5.6         3 T/A       6.1       5.3

   4 T/A       5.5       5.3         4 A/T       5.9       5.1

   5 A/T       5.9       5.6         5 T/A       5.9       5.4

   6 T/A       5.8       5.2         6 A/T       5.8       5.3

   7 A/A       6.3       5.0         7 T/T       6.3       5.2

   8 A/A       5.6       5.8         8 T/T       6.1       5.7

   9 A/A       6.8       5.3         9 T/T       6.8       4.7

  10 A/C       6.9       4.8        10 T/G       7.0       5.0

  11 C/G       6.6       5.0        11 G/C       ---       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       8.5       6.7       5.9      10.8       7.8       7.1

   2 TA/TA       8.2       8.3       8.0       8.3       8.6       8.0

   3 AT/AT      15.4      13.4      12.5       7.9       9.1       9.0

   4 TA/TA       9.5       7.0       5.9       7.6       5.7       4.4

   5 AT/AT       9.9      10.1       9.6       9.0       9.7       9.3

   6 TA/TA       7.3       6.1       4.9       9.3       6.8       5.8

   7 AA/TT       8.0       7.5       6.8      11.3       8.5       7.6

   8 AA/TT       9.2       9.1       8.6      10.7       9.5       8.8

   9 AA/TT      11.0       8.3       7.6       7.7       4.5       3.9

  10 AC/GT       9.9       7.0       6.4      10.6       7.6       7.1

  11 CG/CG       9.1       6.1       5.3       9.3       6.7       5.9

****************************************************************************

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     16.12     38.54     64.41      0.53      0.13     -0.84

   2 TA/TA     17.54     35.14     62.69     -0.63     -0.01     -0.78

   3 AT/AT     19.36     31.35     61.98     -0.43     -0.33     -0.84

   4 TA/TA     22.20     35.60     55.84     -0.25     -0.56     -0.79

   5 AT/AT     14.63     34.39     55.46     -0.27      0.33     -0.90

   6 TA/TA     18.63     31.65     50.97     -0.45     -0.41     -0.79

   7 AA/TT     15.95     32.55     48.40     -0.60     -0.25     -0.76

   8 AA/TT     13.98     34.25     45.54     -0.16     -0.21     -0.96

   9 AA/TT      8.65     30.28     46.86     -0.90      0.19     -0.38

  10 AC/GT      6.55     29.83     42.63     -0.89      0.18     -0.41

  11 CG/CG      2.68     30.58     42.91     -0.83      0.11     -0.55