Detection of oligonucleotide-ligand complexes by ESI-MS (DOLCE-MS) as a component of high throughput screening

With the advent of combinatorial chemistry and high throughput screening, a major bottleneck in the pharmaceutical industry has changed from quickly f inding active compounds to limiting them to a manageable number for proper follow-up. With hundreds to thousands of active compounds identified by a m ultitude of biological screens, there need to be rapid and unambiguous meth ods for eliminating false positive, toxic, or otherwise difficult compounds from further scrutiny. We have used electrospray ionization mass spectrome try as a rapid screening method to identify compounds from viral screens th at yield a positive assay response by interaction with DNA rather than inhi biting the target enzyme. Both the sample preparation and data acquisition have been automated, allowing the screening of all hits from relevant biolo gical screens (up to 1,000/week). The assay was validated using several kno wn DNA intercalators and minor groove binders. These "standards" and many b ut not all of our "active compounds" were shown to form noncovalent complex es with a variety of different DNA:DNA and DNA:RNA duplexes.