Table 1. The 12 letters of the CANA DNA structural alphabet based on the NtC step-conformer classes and their presence in the 58 069 analyzed steps.
A brief annotation and other characteristics of all 44 NtC classes are given in Supplementary Table S1.
| Protein–DNA | Naked DNA | |||||
|---|---|---|---|---|---|---|
| The main features of the CANA letters | CANA letter | No. | % | No. | % | NtC classes merged into the CANA letter |
| A-form conformers | AAA | 1942 | 3.8 | 1063 | 14.6 | AA00 + AA01 + AA02 + AA03 + AA04 |
| Conformers bridging A-form to B-form | A-B | 2393 | 4.7 | 368 | 5 | AB01 + AB02 + AB03 |
| Conformers bridging B-form to A-form | B-A | 3530 | 7 | 616 | 8.4 | BA01–BA10, BA13–BA17 |
| The most frequent ‘canonical’ B-form | BBB | 17513 | 34.5 | 1561 | 21.4 | BB00 |
| Less populated BI conformer | 2B1 | 3076 | 6.1 | 486 | 6.7 | BB01 |
| Less populated BI conformers with switched α1/γ1 values | 3B1 | 2696 | 5.3 | 52 | 0.7 | BB02 + BB03 |
| Conformers bridging BI-form to BII-form | B12 | 3286 | 6.5 | 213 | 2.9 | BB04 + BB05 |
| BII conformers | BB2 | 2521 | 5 | 603 | 8.3 | BB07 + BB08 |
| Various minor B conformers | miB | 2610 | 5.1 | 192 | 2.6 | BB10–BB16 |
| Conformers with bases in syn orientation, may occur in quadruplexes and other nonduplexes | SQX | 214 | 0.4 | 248 | 3.4 | AB1S + BBS1 + BB1S + BB2S + NS1S + NS02 + NS03 + NS04 + NS05 |
| Z-forms | ZZZ | 154 | 0.3 | 175 | 2.4 | ZZ1S + ZZ2S + ZZS1 + ZZS2 |
| All assigned steps | 39935 | 78.7 | 5577 | 76.4 | ||
| Non-assigned steps | NAN | 10839 | 21.3 | 1718 | 23.6 | |
| All steps | 50774 | 100.0 | 7295 | 100.0 | ||