DNA compaction by the bacteriophage protein Cox studied on the single DNA molecule level using nanofluidic channels

• Published in: Nucleic acids research Vol. 44; no. 15; pp. 7219 - 7227
• Main Authors: Frykholm, Karolin, Berntsson, Ronnie Per-Arne, Claesson, Magnus, de Battice, Laura, Odegrip, Richard, Stenmark, Pål, Westerlund, Fredrik
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 06.09.2016
• Subjects: Bacteriophage P2 - chemistry; binding; crystal-structure; Crystallography, X-Ray; DNA, Viral - chemistry; DNA, Viral - metabolism; DNA, Viral - ultrastructure; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; DNA-Binding Proteins - ultrastructure; escherichia-coli; Gene regulation, Chromatin and Epigenetics; Microscopy, Atomic Force; Microscopy, Fluorescence; Mutant Proteins - chemistry; Mutant Proteins - genetics; Mutant Proteins - metabolism; Mutation; nanochannels; Nanotechnology - instrumentation; Nanotechnology - methods; oligomerization; physical-properties; repressor; Single Molecule Imaging - instrumentation; Single Molecule Imaging - methods; sites; Viral Proteins - chemistry; Viral Proteins - genetics; Viral Proteins - metabolism; Viral Proteins - ultrastructure
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkw352

The Cox protein from bacteriophage P2 forms oligomeric filaments and it has been proposed that DNA can be wound up around these filaments, similar to how histones condense DNA. We here use fluorescence microscopy to study single DNA-Cox complexes in nanofluidic channels and compare how the Cox homologs from phages P2 and WΦ affect DNA. By measuring the extension of nanoconfined DNA in absence and presence of Cox we show that the protein compacts DNA and that the binding is highly cooperative, in agreement with the model of a Cox filament around which DNA is wrapped. Furthermore, comparing microscopy images for the wild-type P2 Cox protein and two mutants allows us to discriminate between compaction due to filament formation and compaction by monomeric Cox. P2 and WΦ Cox have similar effects on the physical properties of DNA and the subtle, but significant, differences in DNA binding are due to differences in binding affinity rather than binding mode. The presented work highlights the use of single DNA molecule studies to confirm structural predictions from X-ray crystallography. It also shows how a small protein by oligomerization can have great impact on the organization of DNA and thereby fulfill multiple regulatory functions.