Free energy estimation of short DNA duplex hybridizations

Background: Estimation of DNA duplex hybridization free energy is widely used for predicting cross-hybridizations in DNA computing and microarray experiments. A number of software programs based on different methods and parametrizations are available for the theoretical estimation of duplex free energies. However, significant differences in free energy values are sometimes observed among estimations obtained with various methods, thus being difficult to decide what value is the accurate one. Results: We present in this study a quantitative comparison of the similarities and differences among four published DNA/DNA duplex free energy calculation methods and an extended Nearest-Neighbour Model for perfect matches based on triplet interactions. The comparison was performed on a benchmark data set with 695 pairs of short oligos that we collected and manually curated from 29 publications. Sequence lengths range from 4 to 30 nucleotides and span a large GC-content percentage range. For perf...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Dan C. Tulpan, Mirela Andronescu, Serge Leger
• Keywords: BMCBI 2010, Extended Nearest-neighbour Model, Free Energy, Nearest-Neighbour Model