Table 1.
Competitive reconstitution results and the sequences of repeating 20-bp units that were used in this study
| *Sequence name | †Sequence (20 bp) | ‡Fold out-competition |
|---|---|---|
| 601 sequence | 950 ± 380 | |
| 1. p-10 AAn3GC | 5′ AAGCTGCCGGAAGCTGCCGG 3′ | 2.65 ± 0.17 |
| 3′ TTCGACGGCCTTCGACGGCC 5′ | ||
| 2. p-10 GTAC (GTAC) | 5′ GTACGGGCGGGTACGGGCGG 3′ | 1.15 ± 0.08 |
| 3′ CATGCCCGCCCATGCCCGCC 5′ | ||
| 3. p-10 ATAG (CTAT) | 5′ ATAGGGCAGCATAGGGCAGC 3′ | 0.65 ± 0.16 |
| 3′ TATCCCGTCGTATCCCGTCG 5′ | ||
| 4. p-10 ATAT (ATAT) | 5′ ATATGGCAGCATATGGCAGC 3′ | 0.77 ± 0.32 |
| 3′ TATACCGTCGTATACCGTCG 5′ | ||
| 5. p-10 TTAT (ATAA) | 5′ TTATGGCAGCTTATGGCAGC 3′ | 0.83 ± 0.21 |
| 3′ AATACCGTCGAATACCGTCG 5′ | ||
| 6. p-10 AT | 5′ ATCGGCAGCCATCGGCAGCC 3′ | 0.37 ± 0.04 |
| 3′ TAGCCGTCGGTAGCCGTCGG 5′ | ||
| 7. p-10 TAn3AA | 5′ TACGGAATCCTACGGAATCC 3′ | 326 ± 22 |
| 3′ ATGCCTTAGGATGCCTTAGG 5′ | ||
| 8. p-10 CTAC (GTAG) | 5′ CTACGGCAGCCTACGGCAGC 3′ | 447 ± 63 |
| 3′ GATGCCGTCGGATGCCGTCG 5′ | ||
| 9. p-10 TTAC (GTAA) | 5′ TTACGGCAGCTTACGGCAGC 3′ | 415 ± 116 |
| 3′ AATGCCGTCGAATGCCGTCG 5′ | ||
| 10. p-10 TTAA (TTAA) | 5′ TTAAGGCAGCTTAAGGCAGC 3′ | 64 ± 11 |
| 3′ AATTCCGTCGAATTCCGTCG 5′ | ||
| 11. p-10 CTAA (TTAG) | 5′ CTAAGGCAGCCTAAGGCAGC 3′ | 132 ± 79 |
| 3′ GATTCCGTCGGATTCCGTCG 5′ | ||
| 12. p-10 ATAC (GTAT) | 5′ ATACCGGCAGATACCGGCAG 3′ | 104 ± 79 |
| 3′ TATGGCCGTCTATGGCCGTC 5′ | ||
| 13. p-10 CTAG (CTAG) | 5′ CTAGGCAGCCCTAGGCAGCC 3′ | 494 ± 148 |
| 3′ GATCCGTCGGGATCCGTCGG 5′ | ||
| 14. p-10 CTACN6 (mix) | 5′ CTACNNNNNNCTACNNNNNN 3′ | 355 ± 45 |
| 3′ GATGXXXXXXGATGXXXXXX 5′ | ||
| 15. p-10 TAN8 (mix) | 5′ TANNNNNNNNTANNNNNNNN 3′ | 42 ± 14 |
| 3′ ATXXXXXXXXATXXXXXXXX 5′ | ||
| 16. p-10 TA/AT | 5′ TACGGCAGCCATCGGCAGCC 3′ | 0.66 ± 0.08 |
| 3′ ATGCCGTCGGTAGCCGTCGG 5′ | ||
| 17. p-10 TA/GG | 5′ TACGGCAGCCGGCGGCAGCC 3′ | 1.08 ± 0.36 |
| 3′ ATGCCGTCGGCCGCCGTCGG 5′ | ||
| 18. p-10 TA/AA | 5′ TACGGCAGCCAACGGCAGCC 3′ | 118 ± 16 |
| 3′ ATGCCGTCGGTTGCCGTCGG 5′ |
*n3 indicates the presence of three specified nucleotides.
(mix) indicates a mixture of randomly chosen nucleotides.
Nucleotides in parenthesis represent the complementary nucleotides on the other strand.
†N and X stand for randomly chosen nucleotides in one strand, and its complement, respectively.
Bold di- and tri-nucleotides represent the periodic sequence motif of interest.
‡Fold that the 200-bp synthetic DNAs out-compete nucleosomal DNA. Standard deviations shown are calculated from three independent measurements (n = 3), except for the 601 sequence (n = 6).