Dynamic basis for one-dimensional DNA scanning by the mismatch repair complex Msh2-Msh6

Abstract

The ability of proteins to locate specific sites or structures among a vast excess of nonspecific DNA is a fundamental theme in biology. Yet the basic principles that govern these mechanisms remain poorly understood. For example, mismatch repair proteins must scan millions of base pairs to find rare biosynthetic errors, and they then must probe the surrounding region to identify the strand discrimination signals necessary to distinguish the parental and daughter strands. To determine how these proteins might function we used single-molecule optical microscopy to answer the following question: how does the mismatch repair complex Msh2-Msh6 interrogate undamaged DNA? Here we show that Msh2-Msh6 slides along DNA via one-dimensional diffusion. These findings indicate that interactions between Msh2-Msh6 and DNA are dominated by lateral movement of the protein along the helical axis and have implications for how MutS family members travel along DNA at different stages of the repair reaction.

Figure 1. Experimental Design

(A) Biotinylated λ-DNA (48,502 bp) was tethered by both ends to solid anchor points on a microfluidic sample chamber surface otherwise coated with a lipid bilayer. Msh2-Msh6 was labeled with QDs and injected into the sample chamber. (B) Panel shows images of a YOYO1-stained DNA (green) bound by Msh2-Msh6 (magenta). When the DNA is broken, both it and the bound proteins diffuse away from the sample chamber surface (Movie S1). Off-axis signals correspond to proteins that were not bound to the DNA. (C) Atomic structure illustrating the clamp-like appearance of T. aquaticus MutS in the presence and absence of DNA (Obmolova et al., 2000).

Figure 2. Visualizing Movement of Msh2-Msh6 on DNA

(A)–(F) show kymograms spanning 200 s intervals highlighting the movement of Msh2-Msh6. These examples come from experiments performed in the presence of 1 mM ADP. Kymograms were generated by excising the area that encompassed a single DNA and plotting the resulting images as a function of time. Time (s) is indicated at the top of the panels, and distance (µm) is indicated at the right of each panel. The long axis of the DNA is vertically oriented in each picture, and the starting positions of the protein complexes (magenta) bound to the DNA (green dashed line) are depicted at the left-hand side of each panel. Immobile complexes are also shown to serve as stationary reference points. Time-dependent variations in signal intensity are due to the photophysical characteristics of the QDs (see Figure 3).

Figure 3. Msh2-Msh6 Moves on DNA via 1D Diffusion

(A) Shows a kymogram illustrating the movement of a single QD-tagged Msh2-Msh6 complex over a 140 s duration. Time (s) and relative distance (µm) are indicated at the bottom and right, respectively. The inset shows the rapid blinking of the QD over a 5.9 s period; signal intensity is in arbitrary units (A.U.). (B) Panel shows the same kymogram with data generated from the tracking algorithm superimposed on the image of the moving complex (also see Movie S2). (C and D) Panels show details of the tracking and the resulting plot of MSD versus time interval, respectively. The displacement from the origin is indicated in mm (left vertical axis), and the total range spanned is indicated in bp (right vertical axis). The diffusion coefficient for this protein complex was calculated from the slope (dashed line) of the MSD plot.

Figure 4. General Characteristics of Msh2-Msh6 Diffusion

(A) The graph in (A) shows representative MSD plots for four different Msh2-Msh6 complexes. (B) A histogram of the diffusion coefficients calculated from the tracked proteins. This panel presents the cumulative information derived from 125 tracked complexes of Msh2-Msh6 in buffer containing 50 mM NaCl and either 1 mM ADP (N = 97; shown in red) or 1 mM ATP (N = 28; shown in blue). (C) Panel shows a plot of the net displacement of Msh2-Msh6 from the origin after a 120 s period. (D) Panel shows the range spanned by Msh2-Msh6 as it travels back and forth along the DNA over a 120 s period. (E) A histogram of the apparent cumulative distance traversed by Msh2-Msh6 in 120 s. (F) Panel is a histogram showing the average apparent velocities of the proteins calculated from the cumulative distance traveled divided by total time. The means and standard deviations for all plots were determined from Gaussian fits to the binned data. Movie S3 shows all 125 individual diffusion trajectories, the corresponding MSD plots, and the linear fits to each plot.

Figure 5. Molecular Collisions between Msh2-Msh6 Complexes Bound to the Same Molecule of DNA

(A) Shows an overview of the experimental design. Here Msh2-Msh6 was labeled with either magenta (λ_em = 705 nm) or green (λ_em = 565 nm) QDs, mixed together, and then injected into the same sample chamber. (B) Shows a kymogram illustrating the magenta and green Msh2-Msh6 complexes diffusing along the same molecule of DNA over a 10 min period (Movie S4). Time (s) is indicated at the top of each panel, and distance is indicated at the right. Apparent collision events are evident as magenta and green complexes approach one another and become white.

Figure 6. ATP Causes the Immobile Population of Msh2-Msh6 to Begin Diffusing and Then Dissociate from DNA

(A) Panel shows the assay used to probe the effects of ATP on the immobile population of Msh2-Msh6. The proteins are magenta, and the DNA is green. The DNA is tethered to the surface by only one end (“T”), and the free end (“F”) is only observed when flow is applied. Flow is from top to bottom in each panel, and the distance between T and F is ~13 µm. The panels were extracted from a movie, and the time stamps correspond to the specified frames (Movie S5). The upper panel shows the field after transiently pausing buffer flow (flow ON/OFF control), and the cartoon at the left depicts the behavior of the molecules in the absence of flow. The middle panel shows the same field after resuming flow. Each magenta spot in the image corresponds to at least one Msh2-Msh6 complex, and there are 274 identifiable magenta spots in this experiment and 124 DNA molecules (Movie S5). The lower panel shows the same DNA molecules after the injection of 2 mM ATP. (B) Panel shows a kymogram showing one DNA molecule and the bound Msh2-Msh6. Arrowheads highlight the dissociation of Msh2-Msh6 (Figure S7). (C) Panel summarizes the behavior of 510 total Msh2-Msh6 complexes (from three separate experiments) after the injection of ATP into the sample chamber. “Distance traveled before dissociation” corresponds to the distance that Msh2-Msh6 moved prior to falling off the DNA. Dissociation events that occurred from internal positions on the DNA are colored red (N = 149), and those that occurred at the end of the DNA molecules are colored blue (N = 88).

Figure 7. Model for DNA Scanning by Msh2-Msh6

We present a biophysical model depicting the proposed interactions between Msh2-Msh6 (magenta) and DNA substrates (cyan). Below the DNA is a hypothetical energy landscape describing its bending propensity (Vlahovicek et al., 2003), and we speculate that minima in the landscape correlate with regions that are either intrinsically bent or highly flexible. Positions corresponding to deep depressions in the landscape (e.g., lesions or nicks) will interact favorably with the diffusing protein, and the depth of the energy minima will dictate how long the protein remains at any given site. Proteins that locate deep traps can escape in a reaction driven by the exchange of ADP for ATP.