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In the parameter space of the model parameters, we seek for the nearest parameters vectors of belonging to the learning initial database.
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Thermodynamic models have been used to compare solution hybridization free energy (nearest neighbor) parameters to surface-solution hybridization free energy parameters [34], [35], [36].
Nearest neighbor parameters for Δ H° were found through the same process, and Δ S° parameters were calculated from Δ S° = (Δ H° – Δ G°)/ TM.
Thermodynamic evaluation of duplex stability using nearest neighbor parameters is more accurate than those based on evaluation of GC content.
The resulting nearest neighbor parameters are listed in Table 3.
This led to a penalty in nearest neighbor parameters for homocytidine loops.
The extinction coefficient (at 260 nm) was calculated using the HyTher server, which uses nearest neighbors parameters.
The database of RNA sequences from which GU nearest neighbor parameters were derived is relatively small, however, compared to that for Watson Crick nearest neighbors.
Optical melting curves were measured for 29 RNA duplexes with GU pairs to improve nearest neighbor parameters for predicting stabilities of helixes.
These patterns may explain the poor fit of nearest neighbor parameters for the 5′GU/3′UG motif when duplexes containing the 5′G GUGG3′C UGG motif are included in the fit.
Another difference between GT and GU is that the 5′G GTGG3′C TGG motif fits the nearest neighbor parameters for the 5′GT/3′TG motif better than their respective uracil-substituted RNA motifs.
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