Table 1

Occurrence of the ten dinucleotide steps for each sequence in each of the six nucleosomal DNA sequences

Occurrence

Step

Sequence number

Total

1

2

3

4

5

6


AA/TT

32

(22.1)

25

(17.4)

27

(18.8)

28

(19.3)

28

(19.3)

25

(18.1)

805

(19.1)


AG/CT

18

(12.4)

18

(12.5)

16

(11.1)

18

(12.4)

16

(11.0)

18

(12.3)

478

(11.4)


GA/TC

22

(15.2)

16

(11.1)

18

(12.5)

18

(12.4)

18

(12.4)

16

(11.0)

520

(12.4)


GG/CC

12

(8.3)

12

(8.3)

14

(9.7)

12

(8.3)

14

(9.7)

14

(9.6)

396

(9.4)


AC/GT

14

(9.7)

14

(9.7)

12

(8.3)

12

(8.3)

12

(8.3)

14

(9.6)

356

(8.5)


AT/AT

11

(7.6)

15

(10.4)

15

(10.4)

15

(10.3)

15

(10.3)

15

(10.3)

431

(10.3)


GC/GC

6

(4.1)

8

(5.6)

8

(5.6)

8

(5.5)

8

(5.5)

8

(5.5)

230

(5.5)


CA/TG

18

(12.4)

28

(19.4)

26

(18.1)

28

(19.3)

26

(17.9)

28

(19.2)

758

(18.0)


CG/CG

6

(4.1)

0

(0.0)

2

(1.4)

0

(0.0)

2

(1.4)

0

(0.0)

50

(1.2)


TA/TA

6

(4.1)

8

(5.6)

6

(4.2)

6

(4.1)

6

(4.1)

6

(4.1)

180

(4.3)


Overall

145

144

144

145

145

146

4204


The last column lists the total size of the dataset for the entire dataset of twenty-nine crystal structures. Thus if Ni is the occurrence for a step in sequence i, then the number in the last column is calculated as N1+N2+2*N3+3*N4+20*N5+2*N6. The numbers in parentheses denote the population as percentages, of the total size for the respective sequence, and each column adds up to 100.

Of the total of 4204 steps, 4198 steps incorporate Watson-Crick basepairs. The remaining 6 steps are part of three TCA/TGA trinucleotides and each incorporates a non-Watson-Crick C:G basepair. All the 58 terminal steps are AT/AT, and incorporate Watson-Crick basepairs. Only the 4140 non-terminal steps incorporating Watson-Crick basepairs have been considered for all the analysis described in this work.

Marathe and Bansal BMC Structural Biology 2011 11:1   doi:10.1186/1472-6807-11-1

Open Data