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Varying Cation Types Differentially Stabilizes Poly(dA:dT) DNA
Author(s) -
Schultz Thomas,
Grilley Dan
Publication year - 2019
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.2019.33.1_supplement.775.8
Subject(s) - nucleosome , dna , base pair , minor groove , biophysics , naked dna , histone , chemistry , circular dichroism , context (archaeology) , biology , crystallography , biochemistry , paleontology , plasmid
The two meters of DNA in your cells is packaged by eight histone proteins into a complex called a nucleosome, which allows it to fit into a space one millionth of a meter in diameter. Storage in nucleosomes makes DNA inaccessible to the cellular machinery that is responsible for reading the information contained within the DNA and expressing the genetic code. Nucleosomes form on only approximately 70% of the DNA, and are excluded from forming on poly(dA:dT) tracts (A‐tracts). In nucleosomes, AA base steps are preferentially found at positions of high bending towards the minor groove such that a pattern of AA base steps spaced 10 base pairs apart leads to a highly stable nucleosome. Conversely, many AA base steps linked together to form an A‐tract will exclude nucleosomes. This A‐tract nucleosome exclusion is biologically important as it allows A‐tracts to act as regulatory elements and provide access to DNA binding proteins such as transcription and replication factors. In the context of a nucleosome and in naked DNA, AA base steps are known to form a narrowed minor groove. This narrowed minor groove brings the negative charges of the phosphodiester backbone into closer proximity which is normally not favored due to like‐charges repulsing. Our research is focused on the energetics of forming the narrowed minor groove that occurs in A‐tracts with a specific focus on the stabilization caused by cations. Using absorbance and circular dichroism spectroscopy, we show that the structure and stability of A‐tract DNA is dependent on the size and hydrogen bonding capacity of the cations that are in solution. This cation dependence tracks with the size of the A‐tract DNA, supporting the idea that there is cooperativity between AA base steps. To test the biological importance of these findings, we performed in vitro nucleosome reconstitutions in which generic sequence DNA and A‐tract DNA compete for limited quantities of histone proteins. Using these competitive reconstitutions, we show that A‐tracts are excluded from nucleosomes in a manner that depends on the cation in solution. Our results show that A‐tract structure, unlike generic sequence DNA, is sensitive to the type of cation that is present inside of cells, and that this sensitivity is important for understanding the packaging of DNA into nucleosomes. Support or Funding Information This research was supported by an Undergraduate Research and Creativity grant to TS. This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .