Probing Hybridization parameters from microarray experiments: nearest neighbor model and beyond

TL;DR

This study uses optimized microarray experiments to analyze DNA hybridization thermodynamics, testing the additivity principle of the nearest-neighbor model and exploring mismatch behaviors to improve hybridization accuracy.

Contribution

It provides new experimental insights into DNA mismatch penalties and tests the limits of the nearest-neighbor model in a high-throughput setting.

Findings

Mismatch penalties correlate with melting experiments.

Additivity breaks down for mismatches closer than 5 nt.

Certain GA mismatches exhibit outlier thermodynamic behavior.

Abstract

In this article it is shown how optimized and dedicated microarray experiments can be used to study the thermodynamics of DNA hybridization for a large number of different conformations in a highly parallel fashion. In particular, free energy penalties for mismatches are obtained in two independent ways and are shown to be correlated with values from melting experiments in solution reported in the literature. The additivity principle, which is at the basis of the nearest-neighbor model, and according to which the penalty for two isolated mismatches is equal to the sum of the independent penalties, is thoroughly tested. Additivity is shown to break down for a mismatch distance below 5 nt. The behavior of mismatches in the vicinity of the helix edges, and the behavior of tandem mismatches are also investigated. Finally, some thermodynamic outlying sequences are observed and highlighted. These sequences contain combinations of GA mismatches. The analysis of the microarray data reported in this article provides new insights on the DNA hybridization parameters and can help to increase the accuracy of hybridization-based technologies.