title: Coupled equilibrium model of hybridization error for the DNA microarray and tag-antitag systems.
abstract: In this work, a detailed coupled equilibrium model is presented for predicting the ensemble average probability of hybridization error per chip-hybridized input strand, providing the first ensemble average method for estimating postannealing microarray/TAT system error rates. Following a detailed presentation of the model and implementation via the software package NucleicPark, under a mismatched statistical zipper model of duplex formation, error response is simulated for both mean-energy and randomly encoded TAT systems versus temperature and input concentration. Limiting expressions and simulated model behavior indicate the occurrence of a transition in hybridization error response, from a logarithmically convex function of temperature for excess inputs (high-error behavior), to a monotonic, log-linear function of temperature for dilute inputs (low-error behavior), a novel result unpredicted by uncoupled equilibrium models. Model scaling behavior for random encodings is investigated versus system size and strand-length. Application of the model to TAT system design is also undertaken, via the in silico evolution of a high-fidelity 100-strand TAT system, with an error response improved by nine standard deviations over the performance of the mean random encoding.
authors: Institute of Information Communication Technology, Ritsumeikan Asia Pacific University, Beppu 874-8577, Japan. jarose@apu.ac.jp
authors: John A
authors: JA
authors: Rose
authors: Russell J
authors: RJ
authors: Deaton
authors: Masami
authors: M
authors: Hagiya
authors: Akira
authors: A
authors: Suyama
mesh_terms: D000465:Algorithms; D016477:Artifacts; D003198:Computer Simulation; D020224:Expressed Sequence Tags; D017403:In Situ Hybridization / Q000379:methods*; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity