Editing Nucleosome (section)

=====Histone - DNA interactions=====
The nucleosome contains over 120 direct protein-DNA interactions and several hundred water-mediated ones.<ref name="pmid12079350">{{cite journal | vauthors = Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ | title = Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution | journal = Journal of Molecular Biology | volume = 319 | issue = 5 | pages = 1097–1113 | date = June 2002 | pmid = 12079350 | doi = 10.1016/S0022-2836(02)00386-8 }}</ref> Direct protein - DNA interactions are not spread evenly about the octamer surface but rather located at discrete sites. These are due to the formation of two types of DNA binding sites within the octamer; the α1α1 site, which uses the α1 helix from two adjacent histones, and the L1L2 site formed by the L1 and L2 loops. Salt links and [[hydrogen bonding]] between both side-chain basic and hydroxyl groups and main-chain amides with the DNA backbone phosphates form the bulk of interactions with the DNA. This is important, given that the ubiquitous distribution of nucleosomes along genomes requires it to be a non-sequence-specific DNA-binding factor. Although nucleosomes tend to prefer some DNA sequences over others,<ref>{{cite journal | vauthors = Segal E, Fondufe-Mittendorf Y, Chen L, Thåström A, Field Y, Moore IK, Wang JP, Widom J | display-authors = 6 | title = A genomic code for nucleosome positioning | journal = Nature | volume = 442 | issue = 7104 | pages = 772–778 | date = August 2006 | pmid = 16862119 | pmc = 2623244 | doi = 10.1038/nature04979 | bibcode = 2006Natur.442..772S }}</ref> they are capable of binding practically to any sequence, which is thought to be due to the flexibility in the formation of these water-mediated interactions. In addition, non-polar interactions are made between protein side-chains and the deoxyribose groups, and an arginine side-chain intercalates into the DNA minor groove at all 14 sites where it faces the octamer surface.
The distribution and strength of DNA-binding sites about the octamer surface distorts the DNA within the nucleosome core. The DNA is non-uniformly bent and also contains twist defects. The twist of free B-form DNA in solution is 10.5 bp per turn.  However, the overall twist of nucleosomal DNA is only 10.2 bp per turn, varying from a value of 9.4 to 10.9 bp per turn.