Table 2.
Nucleosomal sequences characterized according to the TRX scale
| sequences | %s | 140 dinucleotide steps |
72 dinucleotide steps |
ΔΔG | RA | RA | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| POW10 | ξs | ξf | POW10 | ξs | ξf | |||||
| 601 | 46 | 0.0065 | 2.2 | 2.6 | 0.0064 | 2.4 | 2.8 | −2.9 | 1 | |
| 618 | 51 | 0.0054 | 1.9 | 2.0 | 0.0086 | 1.7 | 1.9 | −2.3 | ||
| f2 | 58 | 0.0094 | 2.9 | 2.1 | 0.0102 | 2.5 | 2.3 | 2.47 | ||
| f3 | 55 | 0.0065 | 2.4 | 2.3 | 0.0102 | 2.5 | 2.3 | 1.60 | ||
| h2 | 47 | 0.0035 | 2.0 | 2.3 | 0.0029 | 2.4 | 2.1 | 0.11 | ||
| h3 | 58 | 0.0021 | 2.7 | 2.0 | 0.0001 | 4.1 | 1.5 | 0.15 | ||
| g1 | 45 | 0.0076 | 1.8 | 2.5 | 0.0082 | 2.0 | 2.6 | 1 | ||
| g2 | 39 | 0.0025 | 1.8 | 3.2 | 0.0007 | 2.1 | 4.4 | 0.16 | ||
| g3 | 40 | 0.0031 | 1.6 | 2.7 | 0.0027 | 1.5 | 2.8 | 0.15 | ||
| g4 | 36 | 0.0054 | 1.5 | 2.7 | 0.0047 | 1.4 | 2.8 | 0.14 | ||
| g5 | 37 | 0.0020 | 1.4 | 3.1 | 0.0005 | 1.1 | 3.7 | 0.12 | ||
The 147 bp sequences (Supplementary Table S4), their nomenclature and the relative affinities (RA) are from Dr Segal’s web site http://genie.weizmann.ac.il/pubs/nucleosomes06/index.html. The relative affinities are referenced to either 601 (values in columns 9 and 10) or g1 (values in last column) sequences. The central regions of f2 and f3 are identical. The ΔΔG (kcal/mol) values are referenced to that measured for the 5S sequence (55). The percentage of stiff complementary dinucleotides (%s) is given for each sequence. FT analyses were performed considering the TRX scores as a signal along either the 140 innermost or the 72 central dinucleotide steps of the DNA sequences. POW10 is the integrated power of the FT peak at 0.1 ± 0.01 frequency (periodicity of 10 ± 1 bp). The characteristic lengths were calculated for the stiff (ξs) and flexible (ξf) blocks defined by their TRX scores (Table 1).