The Fidelity of the Tag-Antitag System

In the universal DNA chip method, target RNAs are mapped onto a set of DNA tags. Parallel hybridization of these tags with an indexed, complementary antitag array then provides an estimate of the relative RNA concentrations in the original solution. Although both error estimation and error reduction are important to process application, a physical model of hybridization delity for the TAT system has yet to be proposed. In this work, an equilibrium chemistry model of TAT hybridation is used to estimate the error probability per hybridized tag ( ). The temperature dependence of is then discussed in detail, and compared with the predictions of the stringency picture. In combination with a modi ed statistical zipper model of duplex formation, implemented by the Mjolnir software package, is applied to investigate the error behavior of small to moderate sized TAT sets. In the rst simulation, the delities of (1) 105 random encodings, (2) a recently reported Hamming encoding, and (3) an -based...

• Type: Conference
• Year: 2001
• Where: DNA
• Authors: John A. Rose, Russell J. Deaton, Masami Hagiya, Akira Suyama
• Keywords: Bioinformatics, DNA 2001, Random Tat Encodings, TAT Hybridation, TAT Sets