Editing DNA-binding protein (section)

==Non-specific DNA-protein interactions==
Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein interactions. Within chromosomes, DNA is held in complexes with structural proteins. These proteins organize the DNA into a compact structure called [[chromatin]]. In [[eukaryote]]s, this structure involves DNA binding to a complex of small basic proteins called [[histone]]s. In [[prokaryote]]s, multiple types of proteins are involved.<ref>{{cite journal |vauthors=Sandman K, Pereira S, Reeve J |title=Diversity of prokaryotic chromosomal proteins and the origin of the nucleosome |journal=Cell Mol Life Sci |volume=54 |issue=12 |pages=1350–64 |year=1998 |pmid=9893710 |doi=10.1007/s000180050259|s2cid=21101836 |pmc=11147202 }}</ref><ref>{{cite journal |author=Dame RT |title=The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin |journal=Mol. Microbiol. |volume=56 |issue=4 |pages=858–70 |year=2005 |pmid=15853876 |doi=10.1111/j.1365-2958.2005.04598.x|doi-access= }}</ref> The histones form a disk-shaped complex called a [[nucleosome]], which contains two complete turns of double-stranded DNA wrapped around its surface. These non-specific interactions are formed through basic residues in the histones making [[ionic bond]]s to the acidic sugar-phosphate backbone of the DNA, and are therefore largely independent of the base sequence.<ref>{{cite journal |vauthors=Luger K, Mäder A, Richmond R, Sargent D, Richmond T |title=Crystal structure of the nucleosome core particle at 2.8 A resolution |journal=Nature |volume=389 |issue=6648 |pages=251–60 |year=1997 |pmid=9305837 |doi= 10.1038/38444|bibcode=1997Natur.389..251L |s2cid=4328827 }}</ref> [[Chemical]] modifications of these basic [[amino acid]] residues include [[methylation]], [[phosphorylation]] and [[acetylation]].<ref>{{cite journal |vauthors=Jenuwein T, Allis C |title=Translating the histone code |journal=Science |volume=293 |issue=5532 |pages=1074–80 |year=2001 |pmid=11498575 |doi=10.1126/science.1063127|citeseerx=10.1.1.453.900 |s2cid=1883924 }}</ref> These chemical changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to [[transcription factor]]s and changing the rate of transcription.<ref>{{cite book |author=Ito T |title=Protein Complexes that Modify Chromatin |chapter=Nucleosome Assembly and Remodeling |journal=Curr Top Microbiol Immunol |volume=274 |pages=1–22 |pmid=12596902 |year=2003 |doi=10.1007/978-3-642-55747-7_1|series=Current Topics in Microbiology and Immunology |isbn=978-3-642-62909-9 }}</ref> Other non-specific DNA-binding proteins in chromatin include the high-mobility group (HMG) proteins, which bind to bent or distorted DNA.<ref>{{cite journal |author=Thomas J |title=HMG1 and 2: architectural DNA-binding proteins |journal=Biochem Soc Trans |volume=29 |issue=Pt 4 |pages=395–401 |year=2001 |pmid=11497996 |doi=10.1042/BST0290395}}</ref> Biophysical studies show that these architectural HMG proteins bind, bend and loop DNA to perform its biological functions.<ref>{{Cite journal |doi = 10.1093/nar/gku635|pmid = 25063301|pmc = 4132745|title = DNA bridging and looping by HMO1 provides a mechanism for stabilizing nucleosome-free chromatin|journal = Nucleic Acids Research|volume = 42|issue = 14|pages = 8996–9004|year = 2014|last1 = Murugesapillai|first1 = Divakaran|last2 = McCauley|first2 = Micah J.|last3 = Huo|first3 = Ran|last4 = Nelson Holte|first4 = Molly H.|last5 = Stepanyants|first5 = Armen|last6 = Maher|first6 = L. James|last7 = Israeloff|first7 = Nathan E.|last8 = Williams|first8 = Mark C.}}</ref><ref>{{Cite journal | doi=10.1007/s12551-016-0236-4| pmid=28303166|title = Single-molecule studies of high-mobility group B architectural DNA bending proteins| journal=Biophysical Reviews| volume=9| issue=1| pages=17–40|year = 2017|last1 = Murugesapillai|first1 = Divakaran| last2=McCauley| first2=Micah J.| last3=Maher| first3=L. James| last4=Williams| first4=Mark C.| pmc=5331113}}</ref> These proteins are important in bending arrays of nucleosomes and arranging them into the larger structures that form chromosomes.<ref>{{cite journal |vauthors=Grosschedl R, Giese K, Pagel J |title=HMG domain proteins: architectural elements in the assembly of nucleoprotein structures |journal=Trends Genet |volume=10 |issue=3 |pages=94–100 |year=1994 |pmid=8178371 |doi=10.1016/0168-9525(94)90232-1}}</ref> Recently FK506 binding protein 25 (FBP25) was also shown to non-specifically bind to DNA which helps in DNA repair.<ref>{{Cite journal |last1=Prakash |first1=Ajit |last2=Shin |first2=Joon |last3=Rajan |first3=Sreekanth |last4=Yoon |first4=Ho Sup |date=2016-04-07 |title=Structural basis of nucleic acid recognition by FK506-binding protein 25 (FKBP25), a nuclear immunophilin |url=https://doi.org/10.1093/nar/gkw001 |journal=Nucleic Acids Research |volume=44 |issue=6 |pages=2909–2925 |doi=10.1093/nar/gkw001 |pmid=26762975 |pmc=4824100 |issn=0305-1048}}</ref>