Dependence of nucleosome mechanical stability on DNA mismatches
Thuy TM Ngo,
Bailey Liu,
Feng Wang,
Aakash Basu,
Carl Wu,
Taekjip Ha
Affiliations
Thuy TM Ngo
Department of Physics, Center for Physics in Living Cells University of Illinois Urbana-Champaign, Urbana, United States; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, United States; Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, United States; Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States; Division of Oncological Sciences, Oregon Health and Science University, Portland, United States
Department of Biophysics, Johns Hopkins University, Baltimore, United States
Feng Wang
Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, United States
Aakash Basu
Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, United States; Department of Biosciences, Durham University, Durham, United Kingdom
Department of Biology, Johns Hopkins University, Baltimore, United States; Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, United States
Department of Physics, Center for Physics in Living Cells University of Illinois Urbana-Champaign, Urbana, United States; Department of Biophysics, Johns Hopkins University, Baltimore, United States; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, United States; Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, United States; Department of Pediatrics, Harvard Medical School, Boston, United States; Howard Hughes Medical Institute, Boston, United States
The organization of nucleosomes into chromatin and their accessibility are shaped by local DNA mechanics. Conversely, nucleosome positions shape genetic variations, which may originate from mismatches during replication and chemical modification of DNA. To investigate how DNA mismatches affect the mechanical stability and the exposure of nucleosomal DNA, we used an optical trap combined with single-molecule FRET and a single-molecule FRET cyclization assay. We found that a single base-pair C-C mismatch enhances DNA bendability and nucleosome mechanical stability for the 601-nucleosome positioning sequence. An increase in force required for DNA unwrapping from the histone core is observed for single base-pair C-C mismatches placed at three tested positions: at the inner turn, at the outer turn, or at the junction of the inner and outer turn of the nucleosome. The results support a model where nucleosomal DNA accessibility is reduced by mismatches, potentially explaining the preferred accumulation of single-nucleotide substitutions in the nucleosome core and serving as the source of genetic variation during evolution and cancer progression. Mechanical stability of an intact nucleosome, that is mismatch-free, is also dependent on the species as we find that yeast nucleosomes are mechanically less stable and more symmetrical in the outer turn unwrapping compared to Xenopus nucleosomes.
