We report a general method of measuring the complexity of SELEX pools. In analogy to measurements of genome size by C0t analysis, the complexity of a SELEX pool is measured by determining the reannealing rate of its double-stranded PCR product. We applied this technique to study the selection dynamics of a recently reported SELEX to neutrophil elastase. We found that the number of sequences decreased from 107 in round 6 to ∼60 by round 15, the final round. The intermediate rounds are a mixture of a high abundance/low complexity pool with a low abundance/high complexity pool. As the SELEX progresses, the former pool expands at the expense of the latter. This technique should be useful for studying and optimizing SELEX dynamics, as well as for monitoring the progress of SELEX experiments.
