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Table 1 Occurrence of the ten unique dinucleotide steps in the four datasets (numbers in parentheses indicate percentage occurrence).

From: Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs

 

Occurence

 

RNA

Free

Complex

HTH

Dinucleotide Sequence*

 

All

A-like (Z p > 1.3 Ã…)

B-like (Z p ≤ 0.8 Å)

All

Excl. TEH†

All

Excl. TC ‡

AA/TT

15 (5.4)

45 (11.1)

NA

45 (21.5)

211 (17.2)

126 (16.2)

259 (16.6)

208 (15.0)

AG/CT

29 (10.5)

17 (4.2)

3 (1.5)

14 (6.7)

151 (12.3)

92 (11.8)

138 (8.9)

120 (8.7)

GA/TC

19 (6.9)

42 (10.3)

2 (1.0)

40 (19.1)

142 (11.6)

71 (9.1)

164 (10.5)

151 (10.9)

GG/CC

36 (13.0)

97 (23.9)

90 (45.9)

7 (3.3)

120 (9.8)

84 (10.8)

134 (8.6)

118 (8.5)

AC/GT

36 (13.0)

23 (5.7)

13 (6.6)

10 (4.8)

134 (10.9)

98 (12.6)

188 (12.1)

173 (12.5)

AT/AT

9 (3.3)

28 (6.9)

4 (2.0)

24 (11.5)

102 (8.3)

54 (6.9)

155 (9.9)

143 (10.3)

GC/GC

44 (15.9)

39 (9.6)

25 (12.8)

13 (6.2)

63 (5.1)

48 (6.2)

83 (5.3)

71 (5.1)

CA/TG (BI)

43 (15.6)

17 (4.2)

13 (6.6)

4 (1.9)

93 (7.6)

71 (9.1)

152 (9.7)

139 (10.0)

CA/TG (BII)

NA

12 (3.0)

NA

12 (5.7)

60 (4.9)

57 (7.3)

63 (4.0)

60 (4.3)

CG/CG

37 (13.4)

73 (18.0)

43 (21.9)

30 (14.4)

50 (4.1)

32 (4.1)

82 (5.3)

75 (5.4)

TA/TA

8 (3.0)

13 (3.2)

3 (1.5)

10 (4.8)

101 (8.2)

45 (5.8)

141 (9.0)

126 (9.1)

TOTAL

276

406

196

209

1227

778

1559

1384

  1. †TEH – TBP, Endonuclease and Hyperthermophile chromosomal protein SAC7D containing structures (excluded)
  2. ‡TC – TBP and CAP containing structures (excluded)
  3. * RNA oligomers contain Uracil (U) instead of Thymine (T). d(U)-containing steps are not included for the DNA datasets. The CA/TG step was classified as having BII conformation, if either the Cytosine or the Thymine base or both were observed to have the backbone torsion angle values ε - ζ > 0.