PMID: 8587101Dec 1, 1995Paper

Reciprocal relationship between stem-loop potential and substitution density in retroviral quasispecies under positive Darwinian selection

Journal of Molecular Evolution
D R Forsdyke

Abstract

Nucleic acids have the potential to form intrastrand stem-loops if complementary bases are suitably located. Computer analyses of poliovirus and retroviral RNAs have revealed a reciprocal relationship between "statistically significant" stem-loop potential and "sequence variability." The statistically significant stem-loop potential of a nucleic acid segment has been defined as a function of the difference between the folding energy of the natural segment (FONS) and the mean folding energy of a set of randomized (shuffled) versions of the natural segment (FORS-M). Since FONS is dependent on both base composition and base order, whereas FORS-M is solely dependent on base composition (a genomic characteristic), it follows that statistically significant stem-loop potential (FORS-D) is a function of base order (a local characteristic). In retroviral genomes, as in all DNA genomes studied, positive FORS-D values are widely distributed. Thus there have been pressures on base order both to encode specific functions and to encode stem-loops. As in the case of DNA genomes under positive Darwinian selection pressure, in HIV-1 specific function appears to dominate in rapidly evolving regions. Here high sequence variability, expressed as s...Continue Reading

Citations

Apr 23, 2003·Molecular and Biochemical Parasitology·H Y Xue, D R Forsdyke
Oct 16, 2002·Trends in Parasitology·Donald R Forsdyke
May 16, 2000·Journal of Bacteriology·B E Wright
Aug 30, 2013·Journal of Virology·Fabio Zanini, Richard A Neher
Apr 14, 2011·Evolutionary Bioinformatics Online·Atish KathpalSwati Patankar
Aug 19, 2007·Journal of Theoretical Biology·Donald R Forsdyke
Nov 28, 2013·PloS One·Damian LabudaScott M Williams
May 23, 2013·PLoS Computational Biology·Haipeng Li, Thomas Wiehe
Dec 18, 2013·PloS One·Sebastian Bossert, Peter Pfaffelhuber
Mar 4, 2014·PLoS Genetics·Saber QanbariHenner Simianer
Jan 30, 2013·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Jacob E CrawfordBrian P Lazzaro
Oct 4, 2014·American Journal of Human Genetics·Joseph Lachance, Sarah A Tishkoff
Apr 23, 2013·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Elena Claudia CoipanKatsuhisa Takumi
Dec 1, 1996·DNA and Cell Biology·S P HeximerD R Forsdyke
May 15, 2021·Genome Biology and Evolution·Christine MordsteinGrzegorz Kudla

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