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The fidelity of the tag-antitag system II: reconciliation with the stringency picture

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3 Author(s)
Rose, J.A. ; Dept. of Comput. Sci., Tokyo Univ., Japan ; Hagiya, M. ; Suyama, A.

An equilibrium model was reported for predicting the hybridization error of a tag-antitag (TAT) system in response to a dilute input [J. Rose, et al., in DNA Computing, (Springer, 2001), 138]. One notable aspect of the model was its disagreement with the error behavior expected via a consideration of the melting temperatures (T'ms) of planned and error TAT duplexes, in isolation (the stringency picture). In this work, an equilibrium approach is applied to model TAT system error in response to a general, single-tag input. This model is implemented, using two-state and statistical zipper models of duplex formation, via Mathematica™ and NucleicPark, respectively. Under appropriate nondilute conditions (high unplanned sequence-similarity; equimolar/excess input), an error minimum is predicted between the T'ms of planned and unplanned TAT duplexes, as expected via stringency considerations, providing a reconciliation between the two models of hybridization fidelity. On the other hand, predictions for a dilute input agree closely with the model in Rose, et al., supporting the view that a Tm-based model is not fully adequate. A TAT set is then reported, evolved to support experimental validation, which exhibits excess input, signal-to-noise ratios that uniformly span the dynamic range of current fluorescence measurement equipment.

Published in:

Evolutionary Computation, 2003. CEC '03. The 2003 Congress on  (Volume:4 )

Date of Conference:

8-12 Dec. 2003