1. DnaB Drives DNA Branch Migration and Dislodges Proteins While Encircling Two DNA Strands 
Daniel L. Kaplan, Mike O'Donnell 
Molecular Cell 
Volume 10, Issue 3, Pages (September 2002)
DOI: /S (02)

2. Figure 1
DnaB Displaces Protein from DNA While Encircling One Strand or Two Strands
(A and B) Synthetic duplex substrates contain a 5′ ssDNA tail that serves as an assembly site for the ring-shaped DnaB hexamer. DNAs are labeled with 32P (asterisk). DnaB was incubated with substrate containing: (A) fork (5′ and 3′ ssDNA tails) or (B) only a 5′ ssDNA tail. Positions of substrate and product are indicated to the right of each native gel.
(C) Quantitation of results of (A) (squares) and (B) (circles).
(D) DnaB displaces 32P-EBNA1PK from 5′-tailed duplex DNA. The scheme illustrates that 32P-EBNA1PK displaced from the synthetic substrate by DnaB is trapped by a plasmid which contains 24 EBNA1 sites.
(E) Quantitation of the results in (D) and similar experiments. The oligonucleotides used to construct these substrates are detailed in Supplemental Table S1 at
Molecular Cell  , DOI: ( /S (02) )

3. Figure 2 Encounter of DnaB with Holliday Junctions
DnaB is incubated with ATP and synthetic Holliday junctions containing either (A) a 5′ tail, (B) a fork (5′ and 3′ tails), (C) a 3′ tail, or (D) no ssDNA tail. DnaB is incubated with a 5′-tailed Holliday junction and (E) AMP-PNP or (F) various nucleotide cofactors (8 min). The diagrams and arrows to the right and left of each gel indicate the position of each product in the gel as determined by analysis of standards in each gel.
Molecular Cell  , DOI: ( /S (02) )

4. Figure 3 DnaB Catalyzes Branch Migration of a Holliday Junction
(A) The scheme illustrates the proposed path of product formation. First, DnaB, while encircling two strands, catalyzes branch migration to provide duplexes 1-4 and 2-3 (Reaction I). These products contain forked ends and can be unwound by DnaB in subsequent steps, as shown in Reactions II and III. Reannealing of strands with complementary sequences can also occur (not shown).
(B) DnaB action on a 5′-tailed Holliday junction with reversed polarity of the 3-4 duplex. The open circle represents a 5′-5′ DNA connection, the closed circle represents a 3′-3′ connection.
(C) DnaB action on a 5′-tailed Holliday junction with reversed polarity of the 3-4 and 2-3 duplexes. The 2-3 duplex is GC rich.
(D) DnaB action on a 5′-tailed Holliday junction with strand 2 labeled with 32P.
(E) DnaB action on a 5′-tailed Holliday junction with strand 2 labeled with 32P. The 3-4 and 2-3 duplexes have reversed polarity. The 2-3 duplex is GC rich.
Molecular Cell  , DOI: ( /S (02) )

5. Figure 4
Hexameric T7 gp4B Also Catalyzes Branch Migration, but UvrD Does Not
(A) Analysis of T7 gp4B helicase on a 5′-tailed Holliday junction with reversed polarity of the 2-3 and 3-4 duplexes. The 2-3 duplex is GC rich.
(B) Analysis of UvrD helicase with a 3′-tailed Holliday junction with reversed polarity of the 2-3 duplex.
Molecular Cell  , DOI: ( /S (02) )

6. Figure 5
DnaB Encircles Both Strands 1 and 4 during Branch Migration, as Determined by Biotin/Streptavidin Blocks
(A) Analysis of DnaB on a 5′-tailed Holliday junction (strand 2 labeled) with the biotin/streptavidin positioned on strand 4 or strand 1. Results of product analysis on a native gel are quantified in the plot (squares, no biotin; triangles, biotin on strand 1; circles, biotin on strand 4).
(B) DnaB action on a 5′-tailed Holliday junction, with strand 1 labeled and the biotin/streptavidin positioned on strand 3 or strand 2 (squares, no biotin; triangles, biotin on strand 3, circles, biotin on strand 2).
Molecular Cell  , DOI: ( /S (02) )

7. Figure 6
DnaB Tracks on Only One Strand, Even Though it Encircles Two Strands
DnaB action was analyzed on synthetic Holliday junctions with different modifications.
(A) Reaction rate of DnaB with 5′-tailed Holliday junctions containing a 2-3 duplex reverse polarity (left diagram, triangles in graph), a 3-4 duplex reverse polarity (middle diagram, circles in graph), a 1-2 duplex reverse polarity (right diagram, diamonds in graph), or no reverse polarity (squares, no diagram shown).
(B) Reaction rate of DnaB with 5′-tailed Holliday junctions containing a shortened 1-2 duplex (left panel, triangles in graph) or a shortened 3-4 duplex (right panel, squares in graph).
(C) Reaction rate of DnaB with 5′-tailed Holliday junctions containing no hexaethylene glycol 1-phosphate (squares in graph), or hexaethylene glycol 1-phosphate within strand 2 (left panel, circles in graph) or strand 1 (right panel, triangles in graph). The zigzag line represents replacement of nine nucleotides with three hexaethylene glycol 1-phosphate groups.
Molecular Cell  , DOI: ( /S (02) )

8. Figure 7 DnaB Action in Branch Migration and Protein Displacement
(A) Mechanism of DnaB branch migration of a 5′-tailed Holliday junction with heterologous duplex arms. Step i: DnaB loads onto and encircles strand 1. Step ii: DnaB slips onto the 1-4 duplex with both strands positioned in the central channel. Step iii: DnaB binds mainly to strand 1 and translocates along this strand in the 5′ to 3′ direction with enough force to simultaneously unwind the 1-2 and 3-4 duplexes. Step iv: once branch migration is complete, DnaB dissociates.
(B) DnaB clears protein upstream from a leading strand nick (left panel) or a lagging strand lesion (right panel). Left panel: when DnaB encounters a nick in the leading strand, it may encircle both parental strands and translocate upstream. DnaB then displaces DNA-bound proteins, which may enable DNA repair proteins to initiate repair. Right panel: DnaB may bind to the lagging strand downstream from a polymerase stalled at a lesion. DnaB will translocate upstream and displace the DNA polymerase, thereby enabling proteins to repair the lesion.
(C) DnaB-catalyzed branch migration near a replication fork. Left panel: in gap repair, the strand bearing the DNA lesion is paired with a sister strand via recombination (left branch of pathway) or fork regression (right branch of pathway). In the recombinative pathway, DnaB may bind to the leading strand and drive branch migration of the Holliday junction away from the replication fork, thereby allowing DNA repair. In fork regression, DnaB may bind to the lagging strand and drive DNA branch migration, thereby moving the DNA lesion away from the replication fork to allow repair. Right panel: in daughter-strand gap repair, DnaB may bind to the leading strand and drive branch migration of the Holliday junction away from the replication fork.
Molecular Cell  , DOI: ( /S (02) )