At the molecular level CPTs act by selectively inhibiting the religation step of hTopI catalysis by specifically binding the protein-DNA cleavage intermediate in a well-defined manner that highly depends on the presence of DNA [13�C15]. This leads to the accumulation of covalent cleavage intermediates in the genomic DNA, which by collision with DNA tracking processes such as the replication machinery causes DNA fragmentation and ultimately cell death [10]. Consequently, the cytotoxic effect of CPTs correlates directly with the intra-cellular activity level of hTopI and depends on active replication [10,16,17]. This explains the anti-cancer effect of the drugs, since most cancer cells are characterized both by an increased hTopI activity and increased replication rate relative to healthy cells.

Another factor determining the effectiveness of cancer treatment with CPTs may be the susceptibility of hTopI towards the drugs. Consistently, point-mutations in the gene expressing TopI that affect drug interaction to the cleavage complexes are well known causes of cellular resistance towards CPTs [10,18,19].Real-time measurement of the strand rotation step of hTopI catalysis has been achieved previously by the clever manipulation of single DNA molecules using magnetic tweezers [20,21]. However, to our knowledge a real-time sensor for measuring the DNA cleavage-religation steps of the catalysis, which presents the clinically most relevant activities of hTopI (CPT shifts the cleavage-religation equilibrium), has not been reported previously.

In the current manuscript we demonstrate optical real-time measurement of these activities of hTopI using a two oligonucleotide-composed hairpin shaped DNA sensor with a quencher-fluorophore pair. Upon reaction with hTopI the quencher and fluorophore becomes separated allowing detection of the light emitted from the fluorophore. This sensor design enabled quantitative measurement of hTopI DNA cleavage-ligation activity using a qPCR machine, which is standard in most research- and many clinical laboratories. Moreover, the sensor was demonstrated to be specific towards hTopI activity even when present in crude biological samples and was suitable for measuring the inhibition of hTopI by CPTs. Hence, in longer terms the presented sensor may provide Batimastat a relatively fast and easy mean for predicting the drug response of individual patients as well as it may prove valuable for fast high-throughput drug screening programs.

2.?Experimental Section2.1. Yeast Strains and Construction of hTopI Expression PlasmidsThe yeast Saccharomyces cerevisiae top1-null strain RS190 was a kind gift from R. Sternglanz (State University of New York, Stony Brook, NY, USA). Plasmid pHT143, for expression of recombinant full-length hTopI, was described previously [22].2.2. Expression and Purification of hTopI and Preparation of Cell ExtractsThe plasmid pHT143 was transformed into the S.