8/31/2023 0 Comments Dna complement calculator![]() ![]() The accuracy of computing free energies for DNA duplexes is an important aspect for all prediction methods, considering their direct application for selecting, for example, microarray probes that perfectly hybridize with their complements within a pre-specified hybridization interval, while avoiding self-hybridization for each probe. A large collection of thermodynamic nearest-neighbour parameters were acquired by interpolation of results obtained from various experimental processes like NMR and optical melting studies. The Thermodynamic Nearest-Neighbour (TNN) Model is a state-of-the-art approach that is used to estimate the stability of a single or a pair of DNA (or RNA) molecules based on pairwise base interactions and structural conformations. Nevertheless, the accuracy of DNA duplex stability predictions largely varies with sequence length, base composition and experimental conditions. Predicting the stability of a DNA duplex from base sequences is a well studied problem nowadays. The extended Nearest-Neighbour Model based on triplet interactions presented in this work is capable of performing accurate estimations of free energies for perfect match duplexes under both standard and non-standard experimental conditions and may serve as a baseline for further developments in this area of research. Conclusionsīased on our preliminary results, we conclude that no statistically significant differences exist among free energy approximations obtained with 4 publicly available and widely used programs, when benchmarked against a collection of 695 pairs of short oligos collected and curated by the authors of this work based on 29 publications. The proposed model was trained on experimental data with temperature, sodium and sequence concentration characteristics that span a wide range of values, thus conferring the model a higher power of generalization when used for free energy estimations of DNA duplexes under non-standard experimental conditions. For perfect matches, we propose an extension of the Nearest-Neighbour Model that matches or exceeds the performance of the existing ones, both in terms of correlations and root mean squared errors. Sequence lengths range from 4 to 30 nucleotides and span a large GC-content percentage range. The comparison was performed on a benchmark data set with 695 pairs of short oligos that we collected and manually curated from 29 publications. 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. 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. A number of software programs based on different methods and parametrizations are available for the theoretical estimation of duplex free energies. Estimation of DNA duplex hybridization free energy is widely used for predicting cross-hybridizations in DNA computing and microarray experiments. ![]()
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