Intercalation, helix conformation

The effects of intercalators (see also p. 262) are illustrated here using the example of the daunomycin-DNA complex, in which two daunomycin molecules (red) are inserted in the double helix (blue). The antibiotic s ring system inserts itself between G/C base pairs (bottom), while the sugar moiety occupies the minor groove in the DNA (above). This leads to a localized change of the DNA conformation that prevents replication and transcription. 

The Double Helix Chances Conformation Pnon Intercalation... 

Other modifications include a formamide residue (191), a ring fragmentation product of thymine, which exists as either a cis or a trans conformer. Both isomers are rotated out of the helix, and the bases on either side of (191) occupy the space vacated by it. A pyrene abasic site base pair in DNA duplexes adopts the usual B-form duplex, with the pyrene residue within the duplex stacking on adjacent nucleobases. The abasic site folds back over the opposite strand to shelter the hydrophobic base from exposure to water.The photoresponsive azobenzene analogues (133, R- and 5-forms) have been incorporated into DNA for NMR analysis. Both isomers intercalate between neighbouring base pairs, and the 5-isomer exhibits more disturbance in its duplex structure which is refiected in lower Tms compared to the R-isomer. ... 

A solution structure of a duplex containing an adenosine N -amino adduct of the trans (lOR)-tetrahydrobenzo [a] pyrene shows that the hydrocarbon is intercalated into the duplex on the 5 -side of the modified base. From 2D exchange data, it can be observed that the modified base inter-converts between the usual anti-conformation into the less populated syn-conformation. The lOS isomer, however, adopts a syn conformation as the major conformer. The solution structure of a 5-cis-tamoxifen-N -guanine adduct in the middle of an 11-mer duplex has been solved. The lesion is accommodated in a widened minor groove without disruption of the neighbouring base pairs, though the helix axis is bent by 30° away from the minor groove adduct site. 

---