Abstract
An examination of 51 mRNA sequences in GENBANK has revealed that calculated mRNA folding free energies are more negative than expected. Free energy minimization calculations of native mRNA sequences are more negative than randomized mRNA sequences with the same base composition and length. Randomization only of the coding region of genes also yields folding free energies of less negative magnitude than the original native mRNA sequence. Examination of the predicted basepairing within the coding sequence finds an unequal distribution between the three possible frames. The wobble-to-1 frame, which is ”in-frame”, is preferred significantly compared to randomized sets of mRNA sequences. This suggests that evolution may bias or adjust the local selection of codons to favor the global formation of more mRNA structures. This would result in greater negative folding free energies as seen in the 51 mRNAs examined.
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© 2000 Springer Science+Business Media Dordrecht
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Seffens, W., Digby, D. (2000). Gene Sequences are Locally Optimized for Global mRNA Folding. In: Floudas, C.A., Pardalos, P.M. (eds) Optimization in Computational Chemistry and Molecular Biology. Nonconvex Optimization and Its Applications, vol 40. Springer, Boston, MA. https://doi.org/10.1007/978-1-4757-3218-4_8
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DOI: https://doi.org/10.1007/978-1-4757-3218-4_8
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