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. 2017 Oct 18;8(10):278. doi: 10.3390/genes8100278

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© 2017 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).

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DNA bending in the regulatory complexes and in the nucleosome core particles (NCP). (a) Blue lines: the local helical bend of DNA in NCP structures of the PDB codes 5f99 [29] and 5cpk [30]; red lines: the bends for the regulatory complexes 4mzr [31], 1bl0 [32], 3tmm [33], 1zs4 [34], 4nnu [35], 1l3l [36], and 6cro [37]. The local helical axis bend was calculated by the Curves+ program [23] as the Ax-bend parameter. The x axis denotes the DNA residue numbering in 5f99. (b) The left duplex displays DNA from the structure of human TFIIB-related factor 2 and TATA box binding protein bound to U6#2 promoter DNA (PDB code 4roc [21]), where the DNA backbone acquires the A-DNA form (CANA letter AAA) at the bend. The duplex on the right depicts first 75 base pairs from DNA in NCP of the PDB code 5f99 [29]. Dinucleotides adopting the structure described by the CANA letter AAA (BB2) are highlighted in red (blue) color.

DNA bending in the regulatory complexes and in the nucleosome core particles (NCP). (a) Blue lines: the local helical bend of DNA in NCP structures of the PDB codes 5f99 [29] and 5cpk [30]; red lines: the bends for the regulatory complexes 4mzr [31], 1bl0 [32], 3tmm [33], 1zs4 [34], 4nnu [35], 1l3l [36], and 6cro [37]. The local helical axis bend was calculated by the Curves+ program [23] as the Ax-bend parameter. The x axis denotes the DNA residue numbering in 5f99. (b) The left duplex displays DNA from the structure of human TFIIB-related factor 2 and TATA box binding protein bound to U6#2 promoter DNA (PDB code 4roc [21]), where the DNA backbone acquires the A-DNA form (CANA letter AAA) at the bend. The duplex on the right depicts first 75 base pairs from DNA in NCP of the PDB code 5f99 [29]. Dinucleotides adopting the structure described by the CANA letter AAA (BB2) are highlighted in red (blue) color.