Estimating the sequence complexity of a random oligonucleotide population by using in vitro thermal melting and Cot analyses

Randomly generated oligonucleotide populations have a high potential to serve as pools for selecting non-cross-hybridizing sequences, which are useful for nanoscale self-assembly and biological and biomedical applications, as well as for DNA computing applications. In this study a nonlinear kinetic model was developed for the complexity estimation of large unknown polynucleotide populations and was experimentally verified. The model was implemented to estimate the sequence complexity of the random 20 base-pair population after in vitro renaturation experiments. The kinetic behaviors of the random 20mers were also evaluated with in vitro thermal melting experiments. This study represents a step in realizing the potential of random oligonucleotides for DNA computing and nanoscale self-assembly applications for biology and medicine.