Abstract
A formula is derived to estimate the expected frequency of potential secondary structure of a given stem length and loop size in a random sequence of nucleotides of known length and composition. An example is provided using the SV40 sequence which shows significant non-randomness in stem length but whose significance is reduced by more than six orders of magnitude by taking nearest neighbor frequencies into account.
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Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Müller U. R., Fitch W. M. Evolutionary selection for perfect hairpin structures in viral DNAs. Nature. 1982 Aug 5;298(5874):582–585. doi: 10.1038/298582a0. [DOI] [PubMed] [Google Scholar]
- Reddy V. B., Thimmappaya B., Dhar R., Subramanian K. N., Zain B. S., Pan J., Ghosh P. K., Celma M. L., Weissman S. M. The genome of simian virus 40. Science. 1978 May 5;200(4341):494–502. doi: 10.1126/science.205947. [DOI] [PubMed] [Google Scholar]
- Van Heuverswyn H., Fiers W. Nucleotide sequence of the Hind-C fragment of simian virus 40 DNA. Comparison of the 5'-untranslated region of wild-type virus and of some deletion Mutants. Eur J Biochem. 1979 Oct;100(1):51–60. doi: 10.1111/j.1432-1033.1979.tb02032.x. [DOI] [PubMed] [Google Scholar]