Width of the minor groove in the free d(GTATGGCCATAC)2 dodecanucleotide, in the complex with two trabectedin molecules, and in the (chromomycin A3)2–d(TTGGCCAA)2complex Width of the minor groove is measured as the shortest interphosphate distances across the groove (P-P distance – 5.8 Å). The P-P distance in regular B-DNA is 5.9 Å. Measurement of O1′–O1′ distances provides similar relative differences. Mean values for trabectedin (×2) were obtained from the 4 ns of the MD simulations; S.D. is shown in parentheses. Chromomycin A3 values are measured and averaged for the TGGCCA sequence in the two X-ray crystal structures present in PDB entry 1VAQ. Positionally equivalent phosphates in both complexes are shown in bold.
| P5-P24 | P6-P23 | P7-P22 | P8-P21 | P9-P20 | P10-P19 | P11-P18 | P12-P17 | P5-P16 | P6-P15 | P7-P14 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Å | |||||||||||
| Free | 7.1 (1.5) | 8.1 (1.4) | 7.1 (1.7) | 5.6 (1.7) | 5.5 (1.3) | 6.5 (1.6) | 7.6 (1.5) | 6.8 (1.5) | |||
| Trabectedin (×2) | 6.5 (1.5) | 7.8 (0.8) | 9.4 (0.4) | 8.7 (0.6) | 8.7 (0.6) | 10.1 (0.5) | 9.7 (1.5) | 8.3 (1.6) | |||
| Chromomycin A3 | 9.9 | 9.2 | 9.1 |