title: Compression of the DNA substrate by a viral packaging motor is supported by removal of intercalating dye during translocation.
abstract: Viral genome packaging into capsids is powered by high-force-generating motor proteins. In the presence of all packaging components, ATP-powered translocation in vitro expels all detectable tightly bound YOYO-1 dye from packaged short dsDNA substrates and removes all aminoacridine dye from packaged genomic DNA in vivo. In contrast, in the absence of packaging, the purified T4 packaging ATPase alone can only remove up to ∼1/3 of DNA-bound intercalating YOYO-1 dye molecules in the presence of ATP or ATP-γ-S. In sufficient concentration, intercalating dyes arrest packaging, but rare terminase mutations confer resistance. These distant mutations are highly interdependent in acquiring function and resistance and likely mark motor contact points with the translocating DNA. In stalled Y-DNAs, FRET has shown a decrease in distance from the phage T4 terminase C terminus to portal consistent with a linear motor, and in the Y-stem DNA compression between closely positioned dye pairs. Taken together with prior FRET studies of conformational changes in stalled Y-DNAs, removal of intercalating compounds by the packaging motor demonstrates conformational change in DNA during normal translocation at low packaging resistance and supports a proposed linear "DNA crunching" or torsional compression motor mechanism involving a transient grip-and-release structural change in B form DNA.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
authors.forename: Aparna Banerjee
authors.initials: AB
authors.lastname: Dixit
authors.forename: Krishanu
authors.initials: K
authors.lastname: Ray
authors.forename: Lindsay W
authors.initials: LW
authors.lastname: Black
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D017122:Bacteriophage T4 / Q000235:genetics / Q000378:metabolism; D001583:Benzoxazoles; D001665:Binding Sites; D042003:DNA Packaging / Q000502:physiology*; D004279:DNA, Viral / Q000737:chemistry / Q000378:metabolism*; D004706:Endodeoxyribonucleases / Q000235:genetics / Q000378:metabolism; D031541:Fluorescence Resonance Energy Transfer; D005456:Fluorescent Dyes; D005814:Genes, Viral; D007364:Intercalating Agents; D008958:Models, Molecular; D020409:Molecular Motor Proteins / Q000378:metabolism; D016297:Mutagenesis, Site-Directed; D009154:Mutation; D009690:Nucleic Acid Conformation; D011806:Quinolinium Compounds; D013379:Substrate Specificity; D019065:Virus Assembly / Q000502:physiology*
chemical_list: D001583:Benzoxazoles; D004279:DNA, Viral; D005456:Fluorescent Dyes; D007364:Intercalating Agents; D020409:Molecular Motor Proteins; D011806:Quinolinium Compounds; C075296:1,1'-((4,4,7,7-tetramethyl)-4,7-diazaundecamethylene)bis-4-(3-methyl-2,3-dihydro(benzo-1,3-oxazole)-2-methylidene)quinolinium; D000255:Adenosine Triphosphate; D004706:Endodeoxyribonucleases; C104812:terminase, phage T4