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. © 2007 IEEE.
Publication Title
IEEE Transactions on Nanobioscience
Recommended Citation
Rose, J., Deaton, R., Hagiya, M., & Suyama, A. (2007). Coupled equilibrium model of hybridization error for the DNA microarray and tag-antitag systems. IEEE Transactions on Nanobioscience (1), 18-27. https://doi.org/10.1109/TNB.2007.891896
