Table 1.
Average values and dispersion of base pair step parameters* in DNA crystal complexes
| Step | N | Twist, deg | Tilt, deg | Roll, deg | Shift, Å | Slide, Å | Rise, Å | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CG | 88 | 36.1 | (5.5) | 0 | (4.2) | 5.4 | (5.2) | 0 | (0.87) | 0.41 | (0.56) | 3.39 | (0.27) |
| CA | 110 | 37.3 | (6.5) | 0.5 | (3.7) | 4.7 | (5.1) | 0.09 | (0.55) | 0.53 | (0.89) | 3.33 | (0.26) |
| TA | 134 | 37.8 | (5.5) | 0 | (2.7) | 3.3 | (6.6) | 0 | (0.52) | 0.05 | (0.71) | 3.42 | (0.24) |
| AG | 106 | 31.9 | (4.5) | −1.7 | (3.3) | 4.5 | (3.4) | 0.09 | (0.69) | −0.25 | (0.41) | 3.34 | (0.23) |
| GG | 97 | 32.9 | (5.2) | −0.1 | (3.7) | 3.6 | (4.5) | 0.05 | (0.76) | −0.22 | (0.64) | 3.42 | (0.24) |
| AA | 129 | 35.1 | (3.9) | −1.4 | (3.3) | 0.7 | (5.4) | −0.03 | (0.57) | −0.08 | (0.45) | 3.27 | (0.22) |
| GA | 117 | 36.3 | (4.4) | −1.5 | (3.8) | 1.9 | (5.3) | −0.28 | (0.46) | 0.09 | (0.70) | 3.37 | (0.26) |
| AT | 140 | 29.3 | (4.5) | 0 | (2.5) | 1.1 | (4.9) | 0 | (0.57) | −0.59 | (0.31) | 3.31 | (0.21) |
| AC | 137 | 31.5 | (4.2) | −0.1 | (3.1) | 0.7 | (3.9) | 0.13 | (0.59) | −0.58 | (0.41) | 3.36 | (0.23) |
| GC | 86 | 33.6 | (4.7) | 0 | (3.9) | 0.3 | (4.6) | 0 | (0.61) | −0.38 | (0.56) | 3.40 | (0.24) |
| MN† | |||||||||||||
| P⋅DNA‡ | 1,840 | 34.2 | (5.5) | 0 | (3.6) | 2.7 | (5.2) | 0 | (0.64) | −0.09 | (0.69) | 3.36 | (0.25) |
| P′⋅DNA§ | 2,114 | 33.2 | (6.6) | 0 | (4.0) | 4.0 | (9.3) | 0 | (0.65) | −0.05 | (0.77) | 3.41 | (0.47) |
| B–DNA§ | 724 | 35.4 | (6.3) | 0 | (3.4) | 1.4 | (5.1) | 0 | (0.51) | 0.35 | (0.78) | 3.32 | (0.19) |
Dimer steps taken from B–DNA and protein–DNA files in the Nucleic Acid Database (1). See http://rutchem.rutgers.edu/∼olson/pdna.html for a complete listing with citations.
Parameters computed with Compdna (2). Dispersion noted in parentheses.
Average MN parameters for a generic MpN dimer step are based on equal weighting of average parameters of the 16 common dimers, i.e., AA and TT, AG and CT, etc., have identical averages except for different signs of Tilt and Shift (16). The number of MN entries thus exceeds the sum of the 10 unique dimers, and self-complementary steps, e.g., CG, are counted twice in the sample. The dispersion of MN steps is computed from weighted mean–square and mean values, ΔθMN = (〈θMN2〉 − 〈θMN〉2)1/2.
Averages 〈θ〉 and rms deviations Δθ exclude terminal dimer units, which may adopt alternate conformations or be affected by crystal packing, and steps with single-stranded nicks and mismatches. Protein-bound DNA samples also omit “melted” residues, where displacements of complementary base pairs (16) deviate from their averages by >3Δθ before culling. To separate intrinsic from protein-induced conformational deformations and to obtain quasi-Gaussian distributions, we excluded outlying states of extreme bending, twisting, and/or stretching in a stepwise fashion until there were no base step parameters outside the 3Δθ limit.
Unrestricted samples that include dimer steps outside the 3Δθ limit with secondary clusters of data points at some steps, i.e., CA in B–DNA (2). The unculled B–DNA data set presented here differs insignificantly from the B–DNA sample with no states outside the 3Δθ limit.