Structural basis of Topotecan-DNA recognition probed by flow linear dichroism, circular dichroism, and Raman spectroscopy

Camptothecin (CPT) and its clinically important antitumor derivative topotecan (Tpt) were traditionally described as unique antitumor compounds exhibiting no affinity toward DNA alone or DNA topoisomerase I (top1) alone but interacting with both the enzyme and the DNA within the so-called ternary cleavable complexes. We present here the first experimental data on the molecular structure,and geometry of Tpt-DNA complexes in solution. Tpt interacts with DNA within the DNA minor groove and demonstrates the preferential binding to GC-rich DNA. The flow linear dichroism (FLD) spectra show that the Tpt binds DNA only in lactone form and its chromophore forms the angle nearly 55 degrees with the DNA long axis. Induced circular dichroism (CD) data independently confirm conclusions about Tpt preferable orientation drawn from the FLD experiments. The Raman spectroscopy data confirm the FLD and CD results and further demonstrate direct interactions of Tpt lactone ring with dG. The capability of Tpt to bind DNA in the minor groove of GC-rich DNA regions must be taken into account when considering molecular, structure of ternary cleavable complexes of CPTs, DNA, and top1 in solution.