Document Type
Article
Publication Date
1-1-2021
Publication Title
Association for Women in Mathematics Series
Abstract
R-loops are nucleic acid structures consisting of a DNA:RNA hybrid and a DNA single strand. They form naturally during transcription when the nascent RNA hybridizes to the template DNA, forcing the coding DNA strand to wrap around the RNA:DNA duplex. Although formation of R-loops can have deleterious effects on genome integrity, there is evidence of their role as potential regulators of gene expression and DNA repair. Here we initiate an abstract model based on formal grammars to describe RNA:DNA interactions and the formation of R-loops. Separately we use a sliding window approach that accounts for properties of the DNA nucleotide sequence, such as C-richness and CG-skew, to identify segments favoring R-loops. We evaluate these properties on two DNA plasmids that are known to form R-loops and compare results with a recent energetics model from the Chédin Lab. Our abstract approach for R-loops is an initial step toward a more sophisticated framework which can take into account the effect of DNA topology on R-loop formation.
Volume
22
First Page
35
Last Page
54
DOI
10.1007/978-3-030-57129-0_3
ISSN
23645733
Rights
© TheAssociation for Women in Mathematics and the Author(s) 2021
Recommended Citation
Jonoska, Natas̆a; Obatake, Nida; Poznanović, Svetlana; Price, Candice; Riehl, Manda; and Vazquez, Mariel, "Modeling RNA:DNA Hybrids with Formal Grammars" (2021). Mathematics and Statistics: Faculty Publications, Smith College, Northampton, MA.
https://scholarworks.smith.edu/mth_facpubs/116
Comments
Archived as published.