Improving specificity of DNA hybridization-based methods

Improving specificity of DNA hybridization-based methods.

Methods based on DNA reassociation in solution with the subsequent PCR amplification of certain hybrid molecules, such as coincidence cloning and subtractive hybridization, all suffer from a common imperfection: cross-hybridization between various types of paralogous repetitive DNA fragments. Although the situation can be slightly improved by the addition of repeat-specific competitor DNA into ...

Specificity of Hybridization Between DNA Sequences Based on Free Energy

We investigated the specificity of hybridization based on a minimum free energy (∆Gmin) through gel electrophoresis analysis. The analysis, using 94 pairs of sequences with length 20, showed that sequences that hybridize each other can be separated using the constraint ∆Gmin ≤ −14.0, but cannot be separated using the number of base pairs (BP ) in the range from 9 to 18. This demonstrates that t...

Sensitivity, specificity, and the hybridization isotherms of DNA chips.

Competitive hybridization, at the surface and in the bulk, lowers the sensitivity of DNA chips. Competitive surface hybridization occurs when different targets can hybridize with the same probe. Competitive bulk hybridization takes place when the targets can hybridize with free complementary chains in the solution. The effects of competitive hybridization on the thermodynamically attainable per...

Statistical Methods for Analyzing DNA-DNA Hybridization Data

Improving Sequential Feature Selection Methods’ Performance by Means of Hybridization

In this paper we propose the general scheme of defining hybrid feature selection algorithms based on standard sequential search with the aim to improve feature selection performance, especially on high-dimensional or large-sample data. We show experimentally that “hybridization” has not only the potential to dramatically reduce FS search time, but in some cases also to actually improve classifi...